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Conserved domains on  [gi|528520254|ref|XP_002660968|]
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uncharacterized protein si:ch73-173p19.1 [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
548-859 6.53e-16

Leucine-rich repeat (LRR) protein [Transcription];


:

Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 81.13  E-value: 6.53e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 548 LSFLNSPLITDAGLSVLSNLSKLQHLNLSSCskltdsclQHITGLRSLTFLALDQTKVSDAGLLLylqSGSSALCQLSLN 627
Cdd:COG4886   76 LLSLLLLSLLLLGLTDLGDLTNLTELDLSGN--------EELSNLTNLESLDLSGNQLTDLPEEL---ANLTNLKELDLS 144
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 628 QTAITEstlrvLPASV---PQLRMLSIKHTKVSDVSA-LAELKNLQTLHLDGTGVQE--NSLQCLashPSLSALSLAG-- 699
Cdd:COG4886  145 NNQLTD-----LPEPLgnlTNLKSLDLSNNQLTDLPEeLGNLTNLKELDLSNNQITDlpEPLGNL---TNLEELDLSGnq 216
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 700 ---IPVAdgnhtleiIAGL-RLTQLTLpgrhsvtdsglsflsrqtllleldltDYTQLTDhgITQLSSMTRLKKLSLSNT 775
Cdd:COG4886  217 ltdLPEP--------LANLtNLETLDL--------------------------SNNQLTD--LPELGNLTNLEELDLSNN 260
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 776 QVSDsgLQGLIRLKELQELCLDRTAVTSRGVAALITHLPHLQVMGLASTQVGDTVIRRGLVHCPQLLKLNLSRTRITDQG 855
Cdd:COG4886  261 QLTD--LPPLANLTNLKTLDLSNNQLTDLKLKELELLLGLNSLLLLLLLLNLLELLILLLLLTTLLLLLLLLKGLLVTLT 338

                 ....
gi 528520254 856 LKFL 859
Cdd:COG4886  339 TLAL 342
UBX cd01767
Ubiquitin regulatory domain X (UBX) structurally similar to a beta-grasp ubiquitin-like fold; ...
189-257 1.37e-14

Ubiquitin regulatory domain X (UBX) structurally similar to a beta-grasp ubiquitin-like fold; The UBXD family of proteins contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. Members in this family function as cofactors of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. Based on domain composition, UBXD proteins can be divided into two main groups, with and without ubiquitin-associated (UBA) domain.


:

Pssm-ID: 340466 [Multi-domain]  Cd Length: 74  Bit Score: 69.21  E-value: 1.37e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 189 LMIRLPSGESMRERFPADTPLSQVVEYIAS-RHPSLPAFSLLQGFPRKRFGETELTCSLRSLGLTPNAAL 257
Cdd:cd01767    2 IQIRLPDGSRIQRRFSKSDTLQDLYDFVESnLGDSPSSFSLVTSFPRRVLTDEDSDKTLEELGLTPNAVL 71
UBA_like_SF super family cl21463
UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains ...
6-43 1.67e-05

UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. UBA domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only bind the UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains. CUE domain containing proteins are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. This superfamily also includes many UBA-like domains found in AMP-activated protein kinase (AMPK) related kinases, the NXF family of mRNA nuclear export factors, elongation factor Ts (EF-Ts), nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. Although many UBA-like domains may have a conserved TG but not GF/Y-loop, they still show a high level of structural and sequence similarity with three-helical ubiquitin binding domains.


The actual alignment was detected with superfamily member cd14333:

Pssm-ID: 473871  Cd Length: 38  Bit Score: 42.53  E-value: 1.67e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 528520254   6 TIGGFISTLTEMGFSHDQIQAAMQAGFFSVTEAAEWLL 43
Cdd:cd14333    1 TVDSLLACLASMGFDLDDCQEAIQAGKLTVESAIEWLL 38
tolA super family cl35847
cell envelope integrity inner membrane protein TolA; Provisional
108-163 4.75e-04

cell envelope integrity inner membrane protein TolA; Provisional


The actual alignment was detected with superfamily member PRK09510:

Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 43.64  E-value: 4.75e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 528520254 108 RIKQDKSNFH--EQQRQKVAQEARAERRQKKQERELVLKRIAEDR-RSQQEKAQTEATA 163
Cdd:PRK09510  66 RQQQQQKSAKraEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERlAAQEQKKQAEEAA 124
 
Name Accession Description Interval E-value
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
548-859 6.53e-16

Leucine-rich repeat (LRR) protein [Transcription];


Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 81.13  E-value: 6.53e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 548 LSFLNSPLITDAGLSVLSNLSKLQHLNLSSCskltdsclQHITGLRSLTFLALDQTKVSDAGLLLylqSGSSALCQLSLN 627
Cdd:COG4886   76 LLSLLLLSLLLLGLTDLGDLTNLTELDLSGN--------EELSNLTNLESLDLSGNQLTDLPEEL---ANLTNLKELDLS 144
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 628 QTAITEstlrvLPASV---PQLRMLSIKHTKVSDVSA-LAELKNLQTLHLDGTGVQE--NSLQCLashPSLSALSLAG-- 699
Cdd:COG4886  145 NNQLTD-----LPEPLgnlTNLKSLDLSNNQLTDLPEeLGNLTNLKELDLSNNQITDlpEPLGNL---TNLEELDLSGnq 216
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 700 ---IPVAdgnhtleiIAGL-RLTQLTLpgrhsvtdsglsflsrqtllleldltDYTQLTDhgITQLSSMTRLKKLSLSNT 775
Cdd:COG4886  217 ltdLPEP--------LANLtNLETLDL--------------------------SNNQLTD--LPELGNLTNLEELDLSNN 260
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 776 QVSDsgLQGLIRLKELQELCLDRTAVTSRGVAALITHLPHLQVMGLASTQVGDTVIRRGLVHCPQLLKLNLSRTRITDQG 855
Cdd:COG4886  261 QLTD--LPPLANLTNLKTLDLSNNQLTDLKLKELELLLGLNSLLLLLLLLNLLELLILLLLLTTLLLLLLLLKGLLVTLT 338

                 ....
gi 528520254 856 LKFL 859
Cdd:COG4886  339 TLAL 342
UBX cd01767
Ubiquitin regulatory domain X (UBX) structurally similar to a beta-grasp ubiquitin-like fold; ...
189-257 1.37e-14

Ubiquitin regulatory domain X (UBX) structurally similar to a beta-grasp ubiquitin-like fold; The UBXD family of proteins contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. Members in this family function as cofactors of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. Based on domain composition, UBXD proteins can be divided into two main groups, with and without ubiquitin-associated (UBA) domain.


Pssm-ID: 340466 [Multi-domain]  Cd Length: 74  Bit Score: 69.21  E-value: 1.37e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 189 LMIRLPSGESMRERFPADTPLSQVVEYIAS-RHPSLPAFSLLQGFPRKRFGETELTCSLRSLGLTPNAAL 257
Cdd:cd01767    2 IQIRLPDGSRIQRRFSKSDTLQDLYDFVESnLGDSPSSFSLVTSFPRRVLTDEDSDKTLEELGLTPNAVL 71
UBX pfam00789
UBX domain; This domain is present in ubiquitin-regulatory proteins and is a general ...
187-257 2.11e-13

UBX domain; This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module.


Pssm-ID: 395637 [Multi-domain]  Cd Length: 80  Bit Score: 66.16  E-value: 2.11e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528520254  187 CILMIRLPSGESMRERFPADTPLSQVVEYIAS-RHPSLPAFSLLQGFPRKRFGETELTCSLRSLGLTPNAAL 257
Cdd:pfam00789   5 TRLQIRLPDGSRLVRRFNSSDKLQTVYDFVDSnRYDDLEPFSLNTPFPRRPLTDLDYSKTLKEAGLLPNSTL 76
AMN1 cd09293
Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in ...
750-888 2.80e-13

Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model.


Pssm-ID: 187754 [Multi-domain]  Cd Length: 226  Bit Score: 70.05  E-value: 2.80e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 750 YTQLTDHGITQLSSM--TRLKKLSLSNTQVSDSGLQGLIRLKELQELCLD-RTAVTSRGVAALITHLPHLQVMGL-ASTQ 825
Cdd:cd09293   11 LGQITQSNISQLLRIlhSGLEWLELYMCPISDPPLDQLSNCNKLKKLILPgSKLIDDEGLIALAQSCPNLQVLDLrACEN 90
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 826 VGDTVIRRGLVHCPQLLKLNLSRTR----ITDQGLKFL---CRMqLSQVNLDGTGVTLVGIANLISACPH 888
Cdd:cd09293   91 ITDSGIVALATNCPKLQTINLGRHRnghlITDVSLSALgknCTF-LQTVGFAGCDVTDKGVWELASGCSK 159
UBX smart00166
Domain present in ubiquitin-regulatory proteins; Present in FAF1 and Shp1p.
187-257 1.38e-10

Domain present in ubiquitin-regulatory proteins; Present in FAF1 and Shp1p.


Pssm-ID: 197552 [Multi-domain]  Cd Length: 77  Bit Score: 58.08  E-value: 1.38e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528520254   187 CILMIRLPSGESMRERFPADTPLSQVVEYI--ASRHPSLPaFSLLQGFPRKRFGETELTCSLRSLGLTPNAAL 257
Cdd:smart00166   2 CRLQIRLPDGSRLVRRFPSSDTLRTVYEFVsaALGDGNDP-FTLNSPFPRRTFTKDDYSKKLLELALLPSSTL 73
UBA_unchar_Eumetazoa cd14333
UBA domain found in some hypothetical proteins from Eumetazoa; The family includes some ...
6-43 1.67e-05

UBA domain found in some hypothetical proteins from Eumetazoa; The family includes some uncharacterized Eumetazoan proteins. Although their biological function remain unclear, they all contain a very conserved ubiquitin-associated (UBA) domain which is a commonly occurring sequence motif found in proteins involved in ubiquitin-mediated proteolysis.


Pssm-ID: 270518  Cd Length: 38  Bit Score: 42.53  E-value: 1.67e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 528520254   6 TIGGFISTLTEMGFSHDQIQAAMQAGFFSVTEAAEWLL 43
Cdd:cd14333    1 TVDSLLACLASMGFDLDDCQEAIQAGKLTVESAIEWLL 38
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
108-163 4.75e-04

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 43.64  E-value: 4.75e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 528520254 108 RIKQDKSNFH--EQQRQKVAQEARAERRQKKQERELVLKRIAEDR-RSQQEKAQTEATA 163
Cdd:PRK09510  66 RQQQQQKSAKraEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERlAAQEQKKQAEEAA 124
Nop25 pfam09805
Nucleolar protein 12 (25kDa); Members of this family of proteins are part of the yeast nuclear ...
116-166 7.12e-04

Nucleolar protein 12 (25kDa); Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export.


Pssm-ID: 430839 [Multi-domain]  Cd Length: 134  Bit Score: 40.71  E-value: 7.12e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528520254  116 FH--EQQRQKVAQEA---------RAERRQKKQERELVLKRIAEDRRSQQEKAQTEATADTS 166
Cdd:pfam09805  26 FHkrKLQRRKKAQEQaekkareerIEERKELREERKKELEKHVEEVNELLKEAEADDEEEEE 87
LRR_4 pfam12799
Leucine Rich repeats (2 copies); Leucine rich repeats are short sequence motifs present in a ...
644-675 7.27e-04

Leucine Rich repeats (2 copies); Leucine rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains.


Pssm-ID: 463713 [Multi-domain]  Cd Length: 44  Bit Score: 38.00  E-value: 7.27e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 528520254  644 PQLRMLSIKHTKVSDVSALAELKNLQTLHLDG 675
Cdd:pfam12799   1 PNLEVLDLSNNQITDIPPLAKLPNLETLDLSG 32
YqiK COG2268
Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];
118-163 9.91e-04

Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];


Pssm-ID: 441869 [Multi-domain]  Cd Length: 439  Bit Score: 42.55  E-value: 9.91e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 528520254 118 EQQRQKVAQEARAERRQKKQERElVLKRIAEDRRSQQEKAQTEATA 163
Cdd:COG2268  287 EREREIELQEKEAEREEAELEAD-VRKPAEAEKQAAEAEAEAEAEA 331
UBA smart00165
Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 ...
11-43 1.58e-03

Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.


Pssm-ID: 197551 [Multi-domain]  Cd Length: 37  Bit Score: 36.70  E-value: 1.58e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 528520254    11 ISTLTEMGFSHDQIQAAMQAGFFSVTEAAEWLL 43
Cdd:smart00165   5 IDQLLEMGFSREEALKALRAANGNVERAAEYLL 37
sucrsPsyn_pln TIGR02468
sucrose phosphate synthase/possible sucrose phosphate phosphatase, plant; Members of this ...
133-204 2.77e-03

sucrose phosphate synthase/possible sucrose phosphate phosphatase, plant; Members of this family are sucrose-phosphate synthases of plants. This enzyme is known to exist in multigene families in several species of both monocots and dicots. The N-terminal domain is the glucosyltransferase domain. Members of this family also have a variable linker region and a C-terminal domain that resembles sucrose phosphate phosphatase (SPP) (EC 3.1.3.24) (see TIGR01485), the next and final enzyme of sucrose biosynthesis. The SPP-like domain likely serves a binding and not a catalytic function, as the reported SPP is always encoded by a distinct protein.


Pssm-ID: 274147 [Multi-domain]  Cd Length: 1050  Bit Score: 41.69  E-value: 2.77e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528520254   133 RQKKQ-ERELVlKRIAEdRRSQQEKAQTEATADTSPSSAQGQRLGGRVETSVDnhcilmirlPSGESMRERFP 204
Cdd:TIGR02468   89 RKKKQlEWEEA-QRLAK-RRLERERGRREATADMSEDLSEGEKGDVAGDISVA---------GGEPSTKGRLP 150
UBA pfam00627
UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes ...
11-42 3.45e-03

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.


Pssm-ID: 395502 [Multi-domain]  Cd Length: 37  Bit Score: 35.88  E-value: 3.45e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 528520254   11 ISTLTEMGFSHDQIQAAMQAGFFSVTEAAEWL 42
Cdd:pfam00627   6 IQRLVEMGFDREQVREALRATGNNVERAAEYL 37
 
Name Accession Description Interval E-value
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
548-859 6.53e-16

Leucine-rich repeat (LRR) protein [Transcription];


Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 81.13  E-value: 6.53e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 548 LSFLNSPLITDAGLSVLSNLSKLQHLNLSSCskltdsclQHITGLRSLTFLALDQTKVSDAGLLLylqSGSSALCQLSLN 627
Cdd:COG4886   76 LLSLLLLSLLLLGLTDLGDLTNLTELDLSGN--------EELSNLTNLESLDLSGNQLTDLPEEL---ANLTNLKELDLS 144
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 628 QTAITEstlrvLPASV---PQLRMLSIKHTKVSDVSA-LAELKNLQTLHLDGTGVQE--NSLQCLashPSLSALSLAG-- 699
Cdd:COG4886  145 NNQLTD-----LPEPLgnlTNLKSLDLSNNQLTDLPEeLGNLTNLKELDLSNNQITDlpEPLGNL---TNLEELDLSGnq 216
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 700 ---IPVAdgnhtleiIAGL-RLTQLTLpgrhsvtdsglsflsrqtllleldltDYTQLTDhgITQLSSMTRLKKLSLSNT 775
Cdd:COG4886  217 ltdLPEP--------LANLtNLETLDL--------------------------SNNQLTD--LPELGNLTNLEELDLSNN 260
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 776 QVSDsgLQGLIRLKELQELCLDRTAVTSRGVAALITHLPHLQVMGLASTQVGDTVIRRGLVHCPQLLKLNLSRTRITDQG 855
Cdd:COG4886  261 QLTD--LPPLANLTNLKTLDLSNNQLTDLKLKELELLLGLNSLLLLLLLLNLLELLILLLLLTTLLLLLLLLKGLLVTLT 338

                 ....
gi 528520254 856 LKFL 859
Cdd:COG4886  339 TLAL 342
UBX cd01767
Ubiquitin regulatory domain X (UBX) structurally similar to a beta-grasp ubiquitin-like fold; ...
189-257 1.37e-14

Ubiquitin regulatory domain X (UBX) structurally similar to a beta-grasp ubiquitin-like fold; The UBXD family of proteins contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. Members in this family function as cofactors of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. Based on domain composition, UBXD proteins can be divided into two main groups, with and without ubiquitin-associated (UBA) domain.


Pssm-ID: 340466 [Multi-domain]  Cd Length: 74  Bit Score: 69.21  E-value: 1.37e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 189 LMIRLPSGESMRERFPADTPLSQVVEYIAS-RHPSLPAFSLLQGFPRKRFGETELTCSLRSLGLTPNAAL 257
Cdd:cd01767    2 IQIRLPDGSRIQRRFSKSDTLQDLYDFVESnLGDSPSSFSLVTSFPRRVLTDEDSDKTLEELGLTPNAVL 71
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
534-776 9.56e-14

Leucine-rich repeat (LRR) protein [Transcription];


Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 74.20  E-value: 9.56e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 534 ELLRQLRAFTCLKHLSFLNSPlITDAGlSVLSNLSKLQHLNLSSCsKLTDscLQH-ITGLRSLTFLALDQTKVSDAGLLL 612
Cdd:COG4886  150 DLPEPLGNLTNLKSLDLSNNQ-LTDLP-EELGNLTNLKELDLSNN-QITD--LPEpLGNLTNLEELDLSGNQLTDLPEPL 224
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 613 ylqSGSSALCQLSLNQTAITEstlrvLP--ASVPQLRMLSIKHTKVSDVSALAELKNLQTLHLDGTGVQENSLQCLashP 690
Cdd:COG4886  225 ---ANLTNLETLDLSNNQLTD-----LPelGNLTNLEELDLSNNQLTDLPPLANLTNLKTLDLSNNQLTDLKLKEL---E 293
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 691 SLSALSLAGIPVADGNHTLEIIAGLRLTQLTLPGRHSVTDSGLSFLSRQTLLLELDLTDYTQLTDHGITQLSSMTRLKKL 770
Cdd:COG4886  294 LLLGLNSLLLLLLLLNLLELLILLLLLTTLLLLLLLLKGLLVTLTTLALSLSLLALLTLLLLLNLLSLLLTLLLTLGLLG 373

                 ....*.
gi 528520254 771 SLSNTQ 776
Cdd:COG4886  374 LLEATL 379
UBX pfam00789
UBX domain; This domain is present in ubiquitin-regulatory proteins and is a general ...
187-257 2.11e-13

UBX domain; This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module.


Pssm-ID: 395637 [Multi-domain]  Cd Length: 80  Bit Score: 66.16  E-value: 2.11e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528520254  187 CILMIRLPSGESMRERFPADTPLSQVVEYIAS-RHPSLPAFSLLQGFPRKRFGETELTCSLRSLGLTPNAAL 257
Cdd:pfam00789   5 TRLQIRLPDGSRLVRRFNSSDKLQTVYDFVDSnRYDDLEPFSLNTPFPRRPLTDLDYSKTLKEAGLLPNSTL 76
AMN1 cd09293
Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in ...
750-888 2.80e-13

Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model.


Pssm-ID: 187754 [Multi-domain]  Cd Length: 226  Bit Score: 70.05  E-value: 2.80e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 750 YTQLTDHGITQLSSM--TRLKKLSLSNTQVSDSGLQGLIRLKELQELCLD-RTAVTSRGVAALITHLPHLQVMGL-ASTQ 825
Cdd:cd09293   11 LGQITQSNISQLLRIlhSGLEWLELYMCPISDPPLDQLSNCNKLKKLILPgSKLIDDEGLIALAQSCPNLQVLDLrACEN 90
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 826 VGDTVIRRGLVHCPQLLKLNLSRTR----ITDQGLKFL---CRMqLSQVNLDGTGVTLVGIANLISACPH 888
Cdd:cd09293   91 ITDSGIVALATNCPKLQTINLGRHRnghlITDVSLSALgknCTF-LQTVGFAGCDVTDKGVWELASGCSK 159
UBX_UBXN4 cd16117
Ubiquitin regulatory domain X (UBX) found in UBX domain protein 4 (UBXN4) and similar proteins; ...
187-257 4.37e-13

Ubiquitin regulatory domain X (UBX) found in UBX domain protein 4 (UBXN4) and similar proteins; UBXN4, also termed ERAD (endoplasmic-reticulum-associated protein degradation) substrate erasing protein (erasin), or UBX domain-containing protein 2 (UBXD2), or UBXDC1, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN4 is an endoplasmic reticulum (ER) localized protein that interacts with p97 (also known as VCP or Cdc48) via its UBX domain. Erasin exists in a complex with other p97/VCP-associated factors involved in endoplasmic-reticulum-associated protein degradation (ERAD). p97 is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The overexpression of UBXN4 increases degradation of a classical ERAD substrate and UBXN4 levels are increased in ER stressed cells. Anti-UBXN4 staining is increased in neuropathological lesions in brains of patients with Alzheimer's disease.


Pssm-ID: 340534 [Multi-domain]  Cd Length: 77  Bit Score: 65.04  E-value: 4.37e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528520254 187 CILMIRLPSGESMRERFPADTPLSQVVEYIASR-HPSLPAFSLLQGFPRKRFGETELTCSLRSLGLTPNAAL 257
Cdd:cd16117    2 ARIQFRLPDGSSFTNQFPSDAPLEEARQFVAQTvGPAYGPFSLATTFPRREFTDDDYQKTLLELELAPSAAL 73
UBX_UBXN1 cd01772
Ubiquitin regulatory domain X (UBX) found in UBX domain protein 1 (UBXN1) and similar proteins; ...
185-257 5.18e-12

Ubiquitin regulatory domain X (UBX) found in UBX domain protein 1 (UBXN1) and similar proteins; UBXN1, also termed SAPK substrate protein 1 (SAKS1), UBA/UBX 33.3 kDa protein (Y33K), or UBXD10, is a widely expressed protein containing an N-terminal ubiquitin-associated (UBA) domain, a coiled-coil region, and a C-terminal ubiquitin-like (Ubl or UBX) domain that has a beta-grasp ubiquitin-like fold without the C-terminal double glycine motif. UBXN1 has been identified as a substrate for stress-activated protein kinases (SAPKs). It binds polyubiquitin and valosin-containing protein (VCP), suggesting a role as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. In addition, UBXN1 specifically binds to Homer2b. It may also interact with ubiquitin (Ub) and be involved in the Ub-proteasome proteolytic pathways. UBXN1 can also associate with autoubiquitinated BRCA1 tumor suppressor and inhibit its enzymatic function through its UBA domains.


Pssm-ID: 340470 [Multi-domain]  Cd Length: 81  Bit Score: 62.33  E-value: 5.18e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 528520254 185 NHCILMIRLPSGESMRERFPADTPLSQVVEYI-ASRHPSLPAFSLLQGFPRKRFGETELTCSLRSLGLTPNAAL 257
Cdd:cd01772    5 DECRLQVRLTNGSTLTQTFGAKEQLAAVRLYVeLNRTDGDGPFSLMTTFPRKVFTEEDMEKPLKELGLVPSAVL 78
RNA1 COG5238
Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Translation, ...
597-892 5.91e-12

Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Translation, ribosomal structure and biogenesis];


Pssm-ID: 444072 [Multi-domain]  Cd Length: 434  Bit Score: 68.66  E-value: 5.91e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 597 FLALDQTKVSDAGLLLYL-QSGSSALCQLSLNQTAITESTLRVLPASVPQLRMLSIKHTKVSdvsalaelKNLQTLHLDG 675
Cdd:COG5238  118 DLRRIMAKTLEDSLILYLaLPRRINLIQVLKDPLGGNAVHLLGLAARLGLLAAISMAKALQN--------NSVETVYLGC 189
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 676 TGVQENSLQCLASH----PSLSALSLAGIPVadGNHTLEIIAGL-----RLTQLTLPGRHsVTDSGLSFLSRQTLLLELD 746
Cdd:COG5238  190 NQIGDEGIEELAEAltqnTTVTTLWLKRNPI--GDEGAEILAEAlkgnkSLTTLDLSNNQ-IGDEGVIALAEALKNNTTV 266
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 747 LTDY---TQLTDHG----ITQLSSMTRLKKLSLSNTQVSDSGL----QGLIRLKELQELCLDRTAVTSRGVAALITHL-- 813
Cdd:COG5238  267 ETLYlsgNQIGAEGaialAKALQGNTTLTSLDLSVNRIGDEGAialaEGLQGNKTLHTLNLAYNGIGAQGAIALAKALqe 346
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 814 -PHLQVMGLASTQVGDT---VIRRGLVHCPQLLKLNLSRTRITDQGLKFLCRM----QLSQVNLDGTGVTLVGIANLISA 885
Cdd:COG5238  347 nTTLHSLDLSDNQIGDEgaiALAKYLEGNTTLRELNLGKNNIGKQGAEALIDAlqtnRLHTLILDGNLIGAEAQQRLEQL 426

                 ....*..
gi 528520254 886 CPHLSSV 892
Cdd:COG5238  427 LERIKSV 433
UBX smart00166
Domain present in ubiquitin-regulatory proteins; Present in FAF1 and Shp1p.
187-257 1.38e-10

Domain present in ubiquitin-regulatory proteins; Present in FAF1 and Shp1p.


Pssm-ID: 197552 [Multi-domain]  Cd Length: 77  Bit Score: 58.08  E-value: 1.38e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528520254   187 CILMIRLPSGESMRERFPADTPLSQVVEYI--ASRHPSLPaFSLLQGFPRKRFGETELTCSLRSLGLTPNAAL 257
Cdd:smart00166   2 CRLQIRLPDGSRLVRRFPSSDTLRTVYEFVsaALGDGNDP-FTLNSPFPRRTFTKDDYSKKLLELALLPSSTL 73
AMN1 cd09293
Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in ...
644-856 4.46e-10

Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model.


Pssm-ID: 187754 [Multi-domain]  Cd Length: 226  Bit Score: 60.80  E-value: 4.46e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 644 PQLRMLS-IKHTKVSDVSALAEL--KNLQTLHLdgtgvqensLQCLASHPSLSALSlagipvadgnhtleiiAGLRLTQL 720
Cdd:cd09293    3 PLLFILHkLGQITQSNISQLLRIlhSGLEWLEL---------YMCPISDPPLDQLS----------------NCNKLKKL 57
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 721 TLPGRHSVTDSGLSFLSrqtllleldltdytqltdhgitqlSSMTRLKKLSLSN-TQVSDSGLQGLIR-LKELQELCLDR 798
Cdd:cd09293   58 ILPGSKLIDDEGLIALA------------------------QSCPNLQVLDLRAcENITDSGIVALATnCPKLQTINLGR 113
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 528520254 799 T----AVTSRGVAALITHLPHLQVMGLASTQVGD-TVIRRGLVHCPQLLKLNLSR-TRITDQGL 856
Cdd:cd09293  114 HrnghLITDVSLSALGKNCTFLQTVGFAGCDVTDkGVWELASGCSKSLERLSLNNcRNLTDQSI 177
LRR_RI cd00116
Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 ...
649-891 5.00e-10

Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).


Pssm-ID: 238064 [Multi-domain]  Cd Length: 319  Bit Score: 61.99  E-value: 5.00e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 649 LSIKHTKVSDVSA---LAELKNLQTLHLDGTGVQENSLQCLAS----HPSLSALSLAGipvadgNHTLEIIAGLRLTQLT 721
Cdd:cd00116    3 LSLKGELLKTERAtelLPKLLCLQVLRLEGNTLGEEAAKALASalrpQPSLKELCLSL------NETGRIPRGLQSLLQG 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 722 LPgrhsvTDSGLSFLSRQTllleldltdyTQLTDHGITQLSSMTR---LKKLSLSNTQVSDSGLQGLIR-LKELQ----E 793
Cdd:cd00116   77 LT-----KGCGLQELDLSD----------NALGPDGCGVLESLLRsssLQELKLNNNGLGDRGLRLLAKgLKDLPpaleK 141
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 794 LCLDRTAVTSRGVAALITHLPH---LQVMGLASTQVGDTVIR---RGLVHCPQLLKLNLSRTRITDQGLKFLC-----RM 862
Cdd:cd00116  142 LVLGRNRLEGASCEALAKALRAnrdLKELNLANNGIGDAGIRalaEGLKANCNLEVLDLNNNGLTDEGASALAetlasLK 221
                        250       260
                 ....*....|....*....|....*....
gi 528520254 863 QLSQVNLDGTGVTLVGIANLISACPHLSS 891
Cdd:cd00116  222 SLEVLNLGDNNLTDAGAAALASALLSPNI 250
UBX_UBXN3A cd01771
Ubiquitin regulatory domain X (UBX) found in FAS associated factor 1 (FAF1, also known as ...
187-253 1.12e-07

Ubiquitin regulatory domain X (UBX) found in FAS associated factor 1 (FAF1, also known as UBXN3A) and similar proteins; UBX domain-containing protein 3A (UBXN3A),also termed UBX domain-containing protein 12 (UBXD12), or FAF1, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem ubiquitin-like (Ubl) domains, which shows high structural similarity with UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. This family corresponds to UBX domain.


Pssm-ID: 340469  Cd Length: 80  Bit Score: 49.92  E-value: 1.12e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528520254 187 CILMIRLPSGESMRERFPADTPLSQVVEYIASRHPSLPAFSLLQGFPRKRFGETELTCSLRSLGLTP 253
Cdd:cd01771    5 SKLRFRLPGGEFLTRRFLASEPLQVLLNFVASKGYPPDEYKLLTTFPRRDLTQLDPSKTLEELKLFP 71
AMN1 cd09293
Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in ...
523-701 1.40e-07

Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model.


Pssm-ID: 187754 [Multi-domain]  Cd Length: 226  Bit Score: 53.10  E-value: 1.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 523 FVLNCYPYTTNELLRQLRA--FTCLKHLSFLNSPLItDAGLSVLSNLSKLQHLNLSSCSKLTDSCL----QHITGLRSLT 596
Cdd:cd09293    6 FILHKLGQITQSNISQLLRilHSGLEWLELYMCPIS-DPPLDQLSNCNKLKKLILPGSKLIDDEGLialaQSCPNLQVLD 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 597 FLALDQtkVSDAGlLLYLQSGSSALCQLSL----NQTAITESTLRVLPASVPQLRMLSIKHTKVSDVS--ALAEL--KNL 668
Cdd:cd09293   85 LRACEN--ITDSG-IVALATNCPKLQTINLgrhrNGHLITDVSLSALGKNCTFLQTVGFAGCDVTDKGvwELASGcsKSL 161
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 528520254 669 QTLHLDG----TGVQENSLQCLASHPSLSALSLAGIP 701
Cdd:cd09293  162 ERLSLNNcrnlTDQSIPAILASNYFPNLSVLEFRGCP 198
LRR_RI cd00116
Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 ...
587-869 1.30e-06

Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).


Pssm-ID: 238064 [Multi-domain]  Cd Length: 319  Bit Score: 51.20  E-value: 1.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 587 QHITGLRSLTFLALDQTKVSDAGLLLY---LQSGSSAL-CQLSLNQTAITESTLRVLPasvpqlrmlsikhtkvsdvSAL 662
Cdd:cd00116   17 ELLPKLLCLQVLRLEGNTLGEEAAKALasaLRPQPSLKeLCLSLNETGRIPRGLQSLL-------------------QGL 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 663 AELKNLQTLHLdgtgvQENSLQCLASHPSLSALSLAGIPVADGNHTLEIIAGLRLTQLTLPGR-HSVTDSGLSflsrqtl 741
Cdd:cd00116   78 TKGCGLQELDL-----SDNALGPDGCGVLESLLRSSSLQELKLNNNGLGDRGLRLLAKGLKDLpPALEKLVLG------- 145
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 742 lleldltdYTQLTDHGITQLS----SMTRLKKLSLSNTQVSDSGL----QGLIRLKELQELCLDRTAVTSRGVAAL---I 810
Cdd:cd00116  146 --------RNRLEGASCEALAkalrANRDLKELNLANNGIGDAGIralaEGLKANCNLEVLDLNNNGLTDEGASALaetL 217
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528520254 811 THLPHLQVMGLASTQVGDTVIRR---GLVHC-PQLLKLNLSRTRITDQGLKFLCRMQLSQVNL 869
Cdd:cd00116  218 ASLKSLEVLNLGDNNLTDAGAAAlasALLSPnISLLTLSLSCNDITDDGAKDLAEVLAEKESL 280
PPP1R42 cd21340
protein phosphatase 1 regulatory subunit 42; Protein phosphatase 1 regulatory subunit 42 ...
564-703 4.19e-06

protein phosphatase 1 regulatory subunit 42; Protein phosphatase 1 regulatory subunit 42 (PPP1R42), also known as leucine-rich repeat-containing protein 67 (lrrc67) or testis leucine-rich repeat (TLRR) protein, plays a role in centrosome separation. PPP1R42 has been shown to interact with the well-conserved signaling protein phosphatase-1 (PP1) and thereby increasing PP1's activity, which counters centrosome separation. Inhibition of PPP1R42 expression increases the number of centrosomes per cell while its depletion reduces the activity of PP1 leading to activation of NEK2, the kinase responsible for phosphorylation of centrosomal linker proteins promoting centrosome separation.


Pssm-ID: 411060 [Multi-domain]  Cd Length: 220  Bit Score: 48.63  E-value: 4.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 564 LSNLSKLQHL-----------NLSSCSKLT-----DSCLQHITGLRSLTFLaldQTkvsdagllLYLQsgssalcqlslN 627
Cdd:cd21340   42 LEFLTNLTHLylqnnqiekieNLENLVNLKklylgGNRISVVEGLENLTNL---EE--------LHIE-----------N 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 628 QTAITESTLRVLPASV----PQLRMLSIKHTKVSDVSALAELKNLQTLHLDGTGVQ--ENSLQCLASHPSLSALSLAGIP 701
Cdd:cd21340  100 QRLPPGEKLTFDPRSLaalsNSLRVLNISGNNIDSLEPLAPLRNLEQLDASNNQISdlEELLDLLSSWPSLRELDLTGNP 179

                 ..
gi 528520254 702 VA 703
Cdd:cd21340  180 VC 181
UBX_UBXN7 cd01773
Ubiquitin regulatory domain X (UBX) found in UBX domain protein 7 (UBXN7) and similar proteins; ...
187-261 7.97e-06

Ubiquitin regulatory domain X (UBX) found in UBX domain protein 7 (UBXN7) and similar proteins; UBXN7, also termed UBX domain-containing protein 7 (UBXD7), belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN7 functions as a ubiquitin-binding adaptor that mediates the interaction between the AAA+ ATPase p97 (also known as VCP or Cdc48) and the transcription factor HIF1-alpha. It binds only to the active, NEDD8- or Rub1-modified form of cullins. In addition to having a UBX domain, UBXD7 contains a ubiquitin-associated (UBA), ubiquitin-associating (UAS), and ubiquitin-interacting motif (UIM) domains. Either UBA or UIM could serve as a docking site for neddylated-cullins. UBA domain is required for binding ubiquitylated-protein substrates, while the UIM motif is responsible for the binding to cullin RING ligases (CRLs), and the UBX domain is essential for p97 binding.


Pssm-ID: 340471  Cd Length: 76  Bit Score: 44.54  E-value: 7.97e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528520254 187 CILMIRLPSGESMRERFPADTPLSQVVEYIASRHPSLPAFSLLQGFPRKRFGETELTCSLRSLGLTPNAALCIQT 261
Cdd:cd01773    2 SKLMLRFPDGKREQLSLPASAKLKALVKYVSSKGYPNERYELVTNFPRRKLSHLDYDITLKEAGLCPQETIFVQE 76
UBA_unchar_Eumetazoa cd14333
UBA domain found in some hypothetical proteins from Eumetazoa; The family includes some ...
6-43 1.67e-05

UBA domain found in some hypothetical proteins from Eumetazoa; The family includes some uncharacterized Eumetazoan proteins. Although their biological function remain unclear, they all contain a very conserved ubiquitin-associated (UBA) domain which is a commonly occurring sequence motif found in proteins involved in ubiquitin-mediated proteolysis.


Pssm-ID: 270518  Cd Length: 38  Bit Score: 42.53  E-value: 1.67e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 528520254   6 TIGGFISTLTEMGFSHDQIQAAMQAGFFSVTEAAEWLL 43
Cdd:cd14333    1 TVDSLLACLASMGFDLDDCQEAIQAGKLTVESAIEWLL 38
UBX_UBXN11 cd17077
Ubiquitin regulatory domain X (UBX) found in UBX domain protein 11 (UBXN11) and similar ...
187-260 3.01e-05

Ubiquitin regulatory domain X (UBX) found in UBX domain protein 11 (UBXN11) and similar proteins; UBXN11, also termed colorectal tumor-associated antigen COA-1, or socius, or UBX domain-containing protein 5 (UBXD5), belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN11 may function as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. UBXN11 also acts as a novel interacting partner of Rnd proteins (Rnd1, Rnd2, and Rnd3/RhoE), new members of Rho family of small GTPases. It directly binds to Rnd GTPases through its C-terminal region, and further participates in disassembly of actin stress fibers. UBXN11 also binds directly to Galpha12 and Galpha13 through its N-terminal region. As a novel activator of the Galpha12 family, UBXN11 promotes the Galpha12-induced RhoA activation.


Pssm-ID: 340597  Cd Length: 76  Bit Score: 42.98  E-value: 3.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 187 CILMIRLPSGE-----SMRerfPADTpLSQVVEYIAS-RHPSLPAFSLLQGFPRKRFgeTELTCSLRSLGLTPNAALCIQ 260
Cdd:cd17077    3 TTLRIKSENGEqtyilKMR---FSDT-IGDLRRYLDKhRSKDAASYEIVTTFPNKVY--DDDSATLEELGLVPNATLHLR 76
LRR_RI cd00116
Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 ...
543-821 1.84e-04

Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).


Pssm-ID: 238064 [Multi-domain]  Cd Length: 319  Bit Score: 44.65  E-value: 1.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 543 TCLKHLSFL-NSPLITDAGLSVLSNLSKLQHLNLSSCSKLTDSC--LQHITGLRSLTFLALDQTKVSDAGLLLY---LQS 616
Cdd:cd00116   55 ELCLSLNETgRIPRGLQSLLQGLTKGCGLQELDLSDNALGPDGCgvLESLLRSSSLQELKLNNNGLGDRGLRLLakgLKD 134
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 617 GSSALCQLSLNQTAIT----ESTLRVLPAsVPQLRMLSIKHTKVSD------VSALAELKNLQTLHLdgtgvQENSLQCL 686
Cdd:cd00116  135 LPPALEKLVLGRNRLEgascEALAKALRA-NRDLKELNLANNGIGDagiralAEGLKANCNLEVLDL-----NNNGLTDE 208
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 687 AShpslSALSlagipvadgnHTLEIIAGLRLTQLtlpGRHSVTDSGLSFLSRQTllleldltdytqltdhgitqLSSMTR 766
Cdd:cd00116  209 GA----SALA----------ETLASLKSLEVLNL---GDNNLTDAGAAALASAL--------------------LSPNIS 251
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528520254 767 LKKLSLSNTQVSDSGLQGLIRL----KELQELCLDRTAVTSRG--VAALITHLPHLQVMGL 821
Cdd:cd00116  252 LLTLSLSCNDITDDGAKDLAEVlaekESLLELDLRGNKFGEEGaqLLAESLLEPGNELESL 312
RNA1 COG5238
Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Translation, ...
587-841 1.94e-04

Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Translation, ribosomal structure and biogenesis];


Pssm-ID: 444072 [Multi-domain]  Cd Length: 434  Bit Score: 44.78  E-value: 1.94e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 587 QHITGLRSLTFLALDQTKVSDAGLLlylqsgssalcqlslnqtAITEstlrvlpasvpqlrmlsikhtkvsdvsALAELK 666
Cdd:COG5238  230 EALKGNKSLTTLDLSNNQIGDEGVI------------------ALAE---------------------------ALKNNT 264
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 667 NLQTLHLDGTGVQENSLQCLASH----PSLSALSLAGIPVADgnhtleiiAGLRLTQLTLPGRHSVTDSGLSflsrqtll 742
Cdd:COG5238  265 TVETLYLSGNQIGAEGAIALAKAlqgnTTLTSLDLSVNRIGD--------EGAIALAEGLQGNKTLHTLNLA-------- 328
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 743 leldltdYTQLTDHG----ITQLSSMTRLKKLSLSNTQVSDSGLQGLIRL----KELQELCLDRTAVTSRGVAALITHLP 814
Cdd:COG5238  329 -------YNGIGAQGaialAKALQENTTLHSLDLSDNQIGDEGAIALAKYlegnTTLRELNLGKNNIGKQGAEALIDALQ 401
                        250       260
                 ....*....|....*....|....*....
gi 528520254 815 HLQV--MGLASTQVGDTVIRRGLVHCPQL 841
Cdd:COG5238  402 TNRLhtLILDGNLIGAEAQQRLEQLLERI 430
UBA_atUPL1_2_like cd14327
UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 ...
11-43 3.28e-04

UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 (atUPL2) and similar proteins; The family includes two highly similar 405-kDa HECT E3 ubiquitin-protein ligases (UPLs), UPL1 and UPL2, from Arabidopsis thaliana. The HECT E3 UPL family plays a prominent role in the ubiquitination of plant proteins. The biological functions of UPL1 and UPL2 remain unclear. Both of them contain a ubiquitin-associated (UBA) domain and a C-terminal HECT domain. UBA domain may be involved in ubiquitin metabolism. HECT domain is necessary and sufficient for their E3 catalytic activity, but requires ATP, E1 and an E2 of the Arabidopsis UBC8 family to ubiquitinate proteins.


Pssm-ID: 270512 [Multi-domain]  Cd Length: 38  Bit Score: 38.82  E-value: 3.28e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 528520254  11 ISTLTEMGFSHDQIQAA-MQAGFFSVTEAAEWLL 43
Cdd:cd14327    3 VAQLVEMGFSRERAEEAlRAVGTNSVELAMEWLF 36
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
108-163 4.75e-04

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 43.64  E-value: 4.75e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 528520254 108 RIKQDKSNFH--EQQRQKVAQEARAERRQKKQERELVLKRIAEDR-RSQQEKAQTEATA 163
Cdd:PRK09510  66 RQQQQQKSAKraEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERlAAQEQKKQAEEAA 124
Nop25 pfam09805
Nucleolar protein 12 (25kDa); Members of this family of proteins are part of the yeast nuclear ...
116-166 7.12e-04

Nucleolar protein 12 (25kDa); Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export.


Pssm-ID: 430839 [Multi-domain]  Cd Length: 134  Bit Score: 40.71  E-value: 7.12e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528520254  116 FH--EQQRQKVAQEA---------RAERRQKKQERELVLKRIAEDRRSQQEKAQTEATADTS 166
Cdd:pfam09805  26 FHkrKLQRRKKAQEQaekkareerIEERKELREERKKELEKHVEEVNELLKEAEADDEEEEE 87
LRR_4 pfam12799
Leucine Rich repeats (2 copies); Leucine rich repeats are short sequence motifs present in a ...
644-675 7.27e-04

Leucine Rich repeats (2 copies); Leucine rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains.


Pssm-ID: 463713 [Multi-domain]  Cd Length: 44  Bit Score: 38.00  E-value: 7.27e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 528520254  644 PQLRMLSIKHTKVSDVSALAELKNLQTLHLDG 675
Cdd:pfam12799   1 PNLEVLDLSNNQITDIPPLAKLPNLETLDLSG 32
UBA_VP13D cd14306
UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar ...
14-46 9.39e-04

UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins; VP13D is a chorea-acanthocytosis (CHAC)-similar protein encoded by gene VPS13D. it contains two putative domains, ubiquitin-associated (UBA) domain and lectin domain of ricin B chain profile (ricin-B-lectin), suggesting it may interact with, and be involved in the trafficking of, proteins modified with ubiquitin and/or carbohydrate molecules. Further investigation is required.


Pssm-ID: 270491  Cd Length: 36  Bit Score: 37.42  E-value: 9.39e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 528520254  14 LTEMGFSHDQIQAAMQAGFFSVTEAAEWLLQGG 46
Cdd:cd14306    4 LMELGFPEEDCIRALRACGGNVEEAANWLLENA 36
YqiK COG2268
Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];
118-163 9.91e-04

Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];


Pssm-ID: 441869 [Multi-domain]  Cd Length: 439  Bit Score: 42.55  E-value: 9.91e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 528520254 118 EQQRQKVAQEARAERRQKKQERElVLKRIAEDRRSQQEKAQTEATA 163
Cdd:COG2268  287 EREREIELQEKEAEREEAELEAD-VRKPAEAEKQAAEAEAEAEAEA 331
UBA1_Rad23_like cd14280
UBA1 domain of Rad23 proteins found in eukaryotes; The Rad23 family includes the yeast ...
11-43 1.23e-03

UBA1 domain of Rad23 proteins found in eukaryotes; The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA1 domain.


Pssm-ID: 270466  Cd Length: 39  Bit Score: 37.21  E-value: 1.23e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 528520254  11 ISTLTEMGFSHDQIQAAMQAGFFSVTEAAEWLL 43
Cdd:cd14280    6 INNIMSMGFEREQVVRALRAAFNNPDRAVEYLL 38
UBA smart00165
Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 ...
11-43 1.58e-03

Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.


Pssm-ID: 197551 [Multi-domain]  Cd Length: 37  Bit Score: 36.70  E-value: 1.58e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 528520254    11 ISTLTEMGFSHDQIQAAMQAGFFSVTEAAEWLL 43
Cdd:smart00165   5 IDQLLEMGFSREEALKALRAANGNVERAAEYLL 37
CCDC66 pfam15236
Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil ...
100-178 1.63e-03

Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil domain-containing protein 66 (CCDC) refers to a protein domain found in eukaryotes, and is approximately 160 amino acids in length. CCDC66 protein is detected mainly in the inner segments of photoreceptors in many vertebrates including mice and humans. It has been found in dogs, that a mutation in the CCDC66 gene causes generalized progressive retinal atrophy (gPRA). This shows that the protein encoded for by this gene is vital for healthy vision and guards against photoreceptor cell degeneration. The structure of CCDC66 proteins includes a heptad repeat pattern which contains at least one coiled-coil domain. There are at least two or more alpha-helices which form a cable-like structure.


Pssm-ID: 434558 [Multi-domain]  Cd Length: 154  Bit Score: 40.16  E-value: 1.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254  100 KEQLPLETRIKQdksnfHEQQRQKvaQEARAERRQKKQERELVLKRIAEDRRSQQEK--AQTEATADTSPSSAQGQRLGG 177
Cdd:pfam15236  62 KKQLEEKERQKK-----LEEERRR--QEEQEEEERLRREREEEQKQFEEERRKQKEKeeAMTRKTQALLQAMQKAQELAQ 134

                  .
gi 528520254  178 R 178
Cdd:pfam15236 135 R 135
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
100-158 2.69e-03

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 41.06  E-value: 2.69e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528520254  100 KEQLPLETRIKQD---KSNFHEQQRQKVAQEARaERRQKKQERELVLKRIAEDRRSQQEKAQ 158
Cdd:pfam13868 222 KEREEAEKKARQRqelQQAREEQIELKERRLAE-EAEREEEEFERMLRKQAEDEEIEQEEAE 282
sucrsPsyn_pln TIGR02468
sucrose phosphate synthase/possible sucrose phosphate phosphatase, plant; Members of this ...
133-204 2.77e-03

sucrose phosphate synthase/possible sucrose phosphate phosphatase, plant; Members of this family are sucrose-phosphate synthases of plants. This enzyme is known to exist in multigene families in several species of both monocots and dicots. The N-terminal domain is the glucosyltransferase domain. Members of this family also have a variable linker region and a C-terminal domain that resembles sucrose phosphate phosphatase (SPP) (EC 3.1.3.24) (see TIGR01485), the next and final enzyme of sucrose biosynthesis. The SPP-like domain likely serves a binding and not a catalytic function, as the reported SPP is always encoded by a distinct protein.


Pssm-ID: 274147 [Multi-domain]  Cd Length: 1050  Bit Score: 41.69  E-value: 2.77e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528520254   133 RQKKQ-ERELVlKRIAEdRRSQQEKAQTEATADTSPSSAQGQRLGGRVETSVDnhcilmirlPSGESMRERFP 204
Cdd:TIGR02468   89 RKKKQlEWEEA-QRLAK-RRLERERGRREATADMSEDLSEGEKGDVAGDISVA---------GGEPSTKGRLP 150
UBA2_UBP5 cd14386
UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5); UBP5, also called ...
11-47 3.02e-03

UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5); UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. This model corresponds to the UBA2 domain.


Pssm-ID: 270569 [Multi-domain]  Cd Length: 43  Bit Score: 36.16  E-value: 3.02e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 528520254  11 ISTLTEMGFSHDQIQAAMQAGFFSVTEAAEWLLQGGS 47
Cdd:cd14386    6 VAMLVSMGFTRDQAIKALKATDNNVERAADWIFSHPD 42
YqiK COG2268
Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];
106-164 3.12e-03

Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];


Pssm-ID: 441869 [Multi-domain]  Cd Length: 439  Bit Score: 41.01  E-value: 3.12e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528520254 106 ETRIKQDKSNfheqQRQKVAQEAR----AERRQKKQERELVLKRIAEDRRSQQEKAQTEATAD 164
Cdd:COG2268  211 ETEIAIAQAN----REAEEAELEQereiETARIAEAEAELAKKKAEERREAETARAEAEAAYE 269
UBA pfam00627
UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes ...
11-42 3.45e-03

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.


Pssm-ID: 395502 [Multi-domain]  Cd Length: 37  Bit Score: 35.88  E-value: 3.45e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 528520254   11 ISTLTEMGFSHDQIQAAMQAGFFSVTEAAEWL 42
Cdd:pfam00627   6 IQRLVEMGFDREQVREALRATGNNVERAAEYL 37
UBA1_Rad23 cd14377
UBA1 domain of Rad23 proteins found in metazoa; The family includes mammalian orthologs of ...
11-45 4.35e-03

UBA1 domain of Rad23 proteins found in metazoa; The family includes mammalian orthologs of yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe). Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA1 domain.


Pssm-ID: 270560  Cd Length: 40  Bit Score: 35.84  E-value: 4.35e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 528520254  11 ISTLTEMGFSHDQIQAAMQAGFFSVTEAAEWLLQG 45
Cdd:cd14377    6 VTEIMSMGFERDQVVRALRASFNNPDRAVEYLLSG 40
UBA1_scUBP14_like cd14296
UBA1 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 ...
10-44 5.65e-03

UBA1 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 (scUBP14) and similar proteins; scUBP14, also called deubiquitinating enzyme 14, glucose-induced degradation protein 6, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is the yeast ortholog of human Isopeptidase T (USP5), a deubiquitinating enzyme known to bind the 29-linked polyubiquitin chains. scUBP14 has been identified as a K29-linked polyubiquitin binding protein as well. It is involved in K29-linked polyubiquitin metabolism by binding to the 29-linked Ub4 resin and serving as an internal positive control in budding yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.


Pssm-ID: 270482 [Multi-domain]  Cd Length: 39  Bit Score: 35.30  E-value: 5.65e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 528520254  10 FISTLTEMGFSHDQIQAAMQA-GFFSVTEAAEWLLQ 44
Cdd:cd14296    3 AVSQLMSMGFSENAAKRALYYtGNSSVEAAMNWLFE 38
PPP1R42 cd21340
protein phosphatase 1 regulatory subunit 42; Protein phosphatase 1 regulatory subunit 42 ...
758-891 8.09e-03

protein phosphatase 1 regulatory subunit 42; Protein phosphatase 1 regulatory subunit 42 (PPP1R42), also known as leucine-rich repeat-containing protein 67 (lrrc67) or testis leucine-rich repeat (TLRR) protein, plays a role in centrosome separation. PPP1R42 has been shown to interact with the well-conserved signaling protein phosphatase-1 (PP1) and thereby increasing PP1's activity, which counters centrosome separation. Inhibition of PPP1R42 expression increases the number of centrosomes per cell while its depletion reduces the activity of PP1 leading to activation of NEK2, the kinase responsible for phosphorylation of centrosomal linker proteins promoting centrosome separation.


Pssm-ID: 411060 [Multi-domain]  Cd Length: 220  Bit Score: 39.00  E-value: 8.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528520254 758 ITQLSSMTRLKKLSLSNTQVSDsgLQGLIRLKELQELCLDRTAVTSR-----GVAALITHLPHLQVMGLASTQVGDTvir 832
Cdd:cd21340   61 IENLENLVNLKKLYLGGNRISV--VEGLENLTNLEELHIENQRLPPGekltfDPRSLAALSNSLRVLNISGNNIDSL--- 135
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 528520254 833 RGLVHCPQLLKLNLSRTRITDqgLKFLCRM-----QLSQVNLDGTGVTLVGI--ANLISACPHLSS 891
Cdd:cd21340  136 EPLAPLRNLEQLDASNNQISD--LEELLDLlsswpSLRELDLTGNPVCKKPKyrDKIILASKSLEV 199
UBA2_spUBP14_like cd14297
UBA2 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 ...
11-45 8.35e-03

UBA2 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins; spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain.


Pssm-ID: 270483 [Multi-domain]  Cd Length: 39  Bit Score: 34.76  E-value: 8.35e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 528520254  11 ISTLTEMGFSHDQIQAAMQAGFFSVTEAAEWLLQG 45
Cdd:cd14297    4 VKQLVDMGFTEAQARKALRKTNNNVERAVDWLFEG 38
LRR_4 pfam12799
Leucine Rich repeats (2 copies); Leucine rich repeats are short sequence motifs present in a ...
543-583 8.80e-03

Leucine Rich repeats (2 copies); Leucine rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains.


Pssm-ID: 463713 [Multi-domain]  Cd Length: 44  Bit Score: 34.91  E-value: 8.80e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528520254  543 TCLKHLSfLNSPLITDagLSVLSNLSKLQHLNLSSCSKLTD 583
Cdd:pfam12799   1 PNLEVLD-LSNNQITD--IPPLAKLPNLETLDLSGNNKITD 38
UBX_UBXN3B cd16120
Ubiquitin regulatory domain X (UBX) found in FAS associated factor 2 (FAF2, also known as ...
189-260 9.10e-03

Ubiquitin regulatory domain X (UBX) found in FAS associated factor 2 (FAF2, also known as UBXN3B) and similar proteins; UBX domain-containing protein 3B (UBXN3B), also termed protein ETEA, or FAF2, or UBX domain-containing protein 8 (UBXD8), belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. FAF2 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The p97-UBXD8 complex destabilizes mRNA by promoting release of ubiquitinated the RNA-binding protein HuR from messenger ribonucleoprotein (mRNP). Moreover, FAF2 is the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. A yeast two-hybrid assay showed that FAF2 can interact with Fas.


Pssm-ID: 340537  Cd Length: 80  Bit Score: 36.10  E-value: 9.10e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528520254 189 LMIRLPSGESMRERFPADTPLSQVVEYIASRHPSLPAFSLLQGFPRK-----RFGETELTCSLRSLGLTPNAALCIQ 260
Cdd:cd16120    3 ILFKLPNGTRLERRFLKSDSLKVLYDFVFSHEDSPDKFQLVTNFPRRvlpcqPTEEQPNPPTLEEAGLGKSEVLFVQ 79
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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