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Conserved domains on  [gi|115527833|gb|AAI24741|]
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Wu:fb15e04 protein, partial [Danio rerio]

Protein Classification

intermediate filament family protein( domain architecture ID 705869)

intermediate filament (IF) family protein is a primordial component of the cytoskeleton and the nuclear envelope; such as type I keratins

CATH:  1.20.5.170
Gene Ontology:  GO:0005882
PubMed:  2183847|12596228|28101862

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
Filament super family cl25641
Intermediate filament protein;
171-486 1.49e-70

Intermediate filament protein;


The actual alignment was detected with superfamily member pfam00038:

Pssm-ID: 459643 [Multi-domain]  Cd Length: 313  Bit Score: 230.19  E-value: 1.49e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  171 EKEELQALNDKFASFIDKARSLEQHNAVLRAKISMFTNPEQGGPANTSVLLTSAIGAYKSQIDSLSSTKEAIIAEIEHFK 250
Cdd:pfam00038   2 EKEQLQELNDRLASYIDKVRFLEQQNKLLETKISELRQKKGAEPSRLYSLYEKEIEDLRRQLDTLTVERARLQLELDNLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  251 AIIEDNQARYEEETSQTKSLELDWTALKEEVDNLYLTLFELQTSICGLEDQIALSKQVYDAKVKEVRTIVTGGVksaVSI 330
Cdd:pfam00038  82 LAAEDFRQKYEDELNLRTSAENDLVGLRKDLDEATLARVDLEAKIESLKEELAFLKKNHEEEVRELQAQVSDTQ---VNV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  331 SVDNAAQaQDLTSALTEVKAHYETLAQRSKQEALVSVQDSLSMMSVSSQPSSQTLTSAKDELRAYKLQIDSVQREIERLK 410
Cdd:pfam00038 159 EMDAARK-LDLTSALAEIRAQYEEIAAKNREEAEEWYQSKLEELQQAAARNGDALRSAKEEITELRRTIQSLEIELQSLK 237

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 115527833  411 SLNLQLESQVEEAECHSNSHTETYQDQVLTLKSQLDDLRKQITQYGQEYQELLASKMSLDVEITAYKKLLDSEENR 486
Cdd:pfam00038 238 KQKASLERQLAETEERYELQLADYQELISELEAELQETRQEMARQLREYQELLNVKLALDIEIATYRKLLEGEECR 313
 
Name Accession Description Interval E-value
Filament pfam00038
Intermediate filament protein;
171-486 1.49e-70

Intermediate filament protein;


Pssm-ID: 459643 [Multi-domain]  Cd Length: 313  Bit Score: 230.19  E-value: 1.49e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  171 EKEELQALNDKFASFIDKARSLEQHNAVLRAKISMFTNPEQGGPANTSVLLTSAIGAYKSQIDSLSSTKEAIIAEIEHFK 250
Cdd:pfam00038   2 EKEQLQELNDRLASYIDKVRFLEQQNKLLETKISELRQKKGAEPSRLYSLYEKEIEDLRRQLDTLTVERARLQLELDNLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  251 AIIEDNQARYEEETSQTKSLELDWTALKEEVDNLYLTLFELQTSICGLEDQIALSKQVYDAKVKEVRTIVTGGVksaVSI 330
Cdd:pfam00038  82 LAAEDFRQKYEDELNLRTSAENDLVGLRKDLDEATLARVDLEAKIESLKEELAFLKKNHEEEVRELQAQVSDTQ---VNV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  331 SVDNAAQaQDLTSALTEVKAHYETLAQRSKQEALVSVQDSLSMMSVSSQPSSQTLTSAKDELRAYKLQIDSVQREIERLK 410
Cdd:pfam00038 159 EMDAARK-LDLTSALAEIRAQYEEIAAKNREEAEEWYQSKLEELQQAAARNGDALRSAKEEITELRRTIQSLEIELQSLK 237

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 115527833  411 SLNLQLESQVEEAECHSNSHTETYQDQVLTLKSQLDDLRKQITQYGQEYQELLASKMSLDVEITAYKKLLDSEENR 486
Cdd:pfam00038 238 KQKASLERQLAETEERYELQLADYQELISELEAELQETRQEMARQLREYQELLNVKLALDIEIATYRKLLEGEECR 313
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 220-489 3.61e-08

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 56.61  E-value: 3.61e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   220 LLTSAIGAYKSQIDSLSSTKEAIIAEIEHFKAIIEDNQARYEEETSQTKSLELDWTAL-KEEVDNLYLTLFELQTSICGL 298
Cdd:TIGR02169  227 ELLKEKEALERQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLgEEEQLRVKEKIGELEAEIASL 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   299 EDQIALSK-QVYDAKVKEVRTIVTGGVKSAVSISVDNAAQAQD-----LTSALTEVKAHYETLAQRSKQEalvsvqdsls 372
Cdd:TIGR02169  307 ERSIAEKErELEDAEERLAKLEAEIDKLLAEIEELEREIEEERkrrdkLTEEYAELKEELEDLRAELEEV---------- 376

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   373 mmSVSSQPSSQTLTSAKDELRAYKLQIDSVQREIERLKSLNLQLESQVEEAechsNSHTETYQDQVLTLKSQLDDLRKQI 452
Cdd:TIGR02169  377 --DKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSEELADL----NAAIAGIEAKINELEEEKEDKALEI 450

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 115527833   453 TQYGQEYQELLASKMSLDVEITAYKKLLDSEENRLKS 489
Cdd:TIGR02169  451 KKQEWKLEQLAADLSKYEQELYDLKEEYDRVEKELSK 487
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 220-491 4.58e-05

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 46.47  E-value: 4.58e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 220 LLTSAIGAYKSQIDSLSSTKEAIIAEIEHFKAIIEDNQARYEEETSQTKSLELDWTALKEEVDNLYLTLFELQTSICGLE 299
Cdd:COG1196  250 ELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELE 329

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 300 DQIALSKQVYDAKVKEVRTIvtggvKSAVSISVDNAAQAQDLTSALTEVKAHYETLAQRSKQEALVSVQDSLSMMSVSSQ 379
Cdd:COG1196  330 EELEELEEELEELEEELEEA-----EEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEE 404

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 380 PsSQTLTSAKDELRAYKLQIDSVQREIERLKSLNLQLESQVEEAEchsnSHTETYQDQVLTLKSQLDDLRKQITQYGQEY 459
Cdd:COG1196  405 L-EEAEEALLERLERLEEELEELEEALAELEEEEEEEEEALEEAA----EEEAELEEEEEALLELLAELLEEAALLEAAL 479

                        250       260       270
                 ....*....|....*....|....*....|..
gi 115527833 460 QELLASKMSLDVEITAYKKLLDSEENRLKSGG 491
Cdd:COG1196  480 AELLEELAEAAARLLLLLEAEADYEGFLEGVK 511
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
162-462 9.38e-04

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 42.33  E-value: 9.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 162 DTVQVTRMKEKEELQALNDKFASFIDKARSLEQHNAVLRAKismftnpeqggpANTsvlLTSAIGAYKSQIDSLSSTKEA 241
Cdd:PRK02224 324 EELRDRLEECRVAAQAHNEEAESLREDADDLEERAEELREE------------AAE---LESELEEAREAVEDRREEIEE 388

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 242 IIAEIEhfkaiieDNQARYEEETSQTKSLELDWTALKEEVDNLYLTLFELQTSICGLEDQIALSKQVYDA-KVKEVRTIV 320
Cdd:PRK02224 389 LEEEIE-------ELRERFGDAPVDLGNAEDFLEELREERDELREREAELEATLRTARERVEEAEALLEAgKCPECGQPV 461

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 321 TGgvKSAVSISVDNAAQAQDLTSALTEVKAHYETLAQRSKQ-EALVSVQDSLSMMSVSSQPSSQTLTSAKDELRAYKLQI 399
Cdd:PRK02224 462 EG--SPHVETIEEDRERVEELEAELEDLEEEVEEVEERLERaEDLVEAEDRIERLEERREDLEELIAERRETIEEKRERA 539

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 115527833 400 DSVQREIERLKSLNLQLESQVEEAECHSNSHTE---TYQDQVLTLKSQLDDLRK------QITQYGQEYQEL 462
Cdd:PRK02224 540 EELRERAAELEAEAEEKREAAAEAEEEAEEAREevaELNSKLAELKERIESLERirtllaAIADAEDEIERL 611
 
Name Accession Description Interval E-value
Filament pfam00038
Intermediate filament protein;
171-486 1.49e-70

Intermediate filament protein;


Pssm-ID: 459643 [Multi-domain]  Cd Length: 313  Bit Score: 230.19  E-value: 1.49e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  171 EKEELQALNDKFASFIDKARSLEQHNAVLRAKISMFTNPEQGGPANTSVLLTSAIGAYKSQIDSLSSTKEAIIAEIEHFK 250
Cdd:pfam00038   2 EKEQLQELNDRLASYIDKVRFLEQQNKLLETKISELRQKKGAEPSRLYSLYEKEIEDLRRQLDTLTVERARLQLELDNLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  251 AIIEDNQARYEEETSQTKSLELDWTALKEEVDNLYLTLFELQTSICGLEDQIALSKQVYDAKVKEVRTIVTGGVksaVSI 330
Cdd:pfam00038  82 LAAEDFRQKYEDELNLRTSAENDLVGLRKDLDEATLARVDLEAKIESLKEELAFLKKNHEEEVRELQAQVSDTQ---VNV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  331 SVDNAAQaQDLTSALTEVKAHYETLAQRSKQEALVSVQDSLSMMSVSSQPSSQTLTSAKDELRAYKLQIDSVQREIERLK 410
Cdd:pfam00038 159 EMDAARK-LDLTSALAEIRAQYEEIAAKNREEAEEWYQSKLEELQQAAARNGDALRSAKEEITELRRTIQSLEIELQSLK 237

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 115527833  411 SLNLQLESQVEEAECHSNSHTETYQDQVLTLKSQLDDLRKQITQYGQEYQELLASKMSLDVEITAYKKLLDSEENR 486
Cdd:pfam00038 238 KQKASLERQLAETEERYELQLADYQELISELEAELQETRQEMARQLREYQELLNVKLALDIEIATYRKLLEGEECR 313
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 220-489 3.61e-08

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 56.61  E-value: 3.61e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   220 LLTSAIGAYKSQIDSLSSTKEAIIAEIEHFKAIIEDNQARYEEETSQTKSLELDWTAL-KEEVDNLYLTLFELQTSICGL 298
Cdd:TIGR02169  227 ELLKEKEALERQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLgEEEQLRVKEKIGELEAEIASL 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   299 EDQIALSK-QVYDAKVKEVRTIVTGGVKSAVSISVDNAAQAQD-----LTSALTEVKAHYETLAQRSKQEalvsvqdsls 372
Cdd:TIGR02169  307 ERSIAEKErELEDAEERLAKLEAEIDKLLAEIEELEREIEEERkrrdkLTEEYAELKEELEDLRAELEEV---------- 376

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   373 mmSVSSQPSSQTLTSAKDELRAYKLQIDSVQREIERLKSLNLQLESQVEEAechsNSHTETYQDQVLTLKSQLDDLRKQI 452
Cdd:TIGR02169  377 --DKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSEELADL----NAAIAGIEAKINELEEEKEDKALEI 450

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 115527833   453 TQYGQEYQELLASKMSLDVEITAYKKLLDSEENRLKS 489
Cdd:TIGR02169  451 KKQEWKLEQLAADLSKYEQELYDLKEEYDRVEKELSK 487
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 169-470 1.38e-05

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 48.09  E-value: 1.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  169 MKEKE-ELQALNDKFASFIDKARSLEQHNAVLRAKISMFTNPEQggpantsvlltsaigAYKSQIDSLSSTKEAIIAEIE 247
Cdd:TIGR04523 365 LEEKQnEIEKLKKENQSYKQEIKNLESQINDLESKIQNQEKLNQ---------------QKDEQIKKLQQEKELLEKEIE 429

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  248 HFKAIIEDNQaryeeetSQTKSLELDWTALKEEVDNLYLTLFELQTSICGLEDQIALSKQVYDAKVKEVrtivtggvksa 327
Cdd:TIGR04523 430 RLKETIIKNN-------SEIKDLTNQDSVKELIIKNLDNTRESLETQLKVLSRSINKIKQNLEQKQKEL----------- 491

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  328 vsisVDNAAQAQDLTSALTEVKAHYETLAQrsKQEALVSVQDSLSmmSVSSQPSSQtLTSAKDEL---------RAYKLQ 398
Cdd:TIGR04523 492 ----KSKEKELKKLNEEKKELEEKVKDLTK--KISSLKEKIEKLE--SEKKEKESK-ISDLEDELnkddfelkkENLEKE 562

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 115527833  399 IDSVQREIERLKSLNLQLESQVEEAEchsnSHTETYQDQVLTLKSQL-------DDLRKQITQYGQEYQELLASKMSLD 470
Cdd:TIGR04523 563 IDEKNKEIEELKQTQKSLKKKQEEKQ----ELIDQKEKEKKDLIKEIeekekkiSSLEKELEKAKKENEKLSSIIKNIK 637
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 170-461 3.10e-05

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 47.37  E-value: 3.10e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   170 KEKEELQALNDKFASFIDKARSLEQHNAVLRAKISMftnpeqggpantsvlLTSAIGAYKSQIDSLS-----STKEAIIA 244
Cdd:TIGR02169  734 KLKERLEELEEDLSSLEQEIENVKSELKELEARIEE---------------LEEDLHKLEEALNDLEarlshSRIPEIQA 798

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   245 EIEHFKAIIEDNQARYEEETSQTKSLELDWTALKEEVDNLYLTLFELQTSICGLEDQIALS---KQVYDAKVKEVRTIVT 321
Cdd:TIGR02169  799 ELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLngkKEELEEELEELEAALR 878

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   322 GGVKSAVSIS--VDNA-AQAQDLTSALTEVKAHYETLAQRSKQ--EALVSVQDSLSMMSvSSQPSSQTLTSAKDELRAYK 396
Cdd:TIGR02169  879 DLESRLGDLKkeRDELeAQLRELERKIEELEAQIEKKRKRLSElkAKLEALEEELSEIE-DPKGEDEEIPEEELSLEDVQ 957

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 115527833   397 LQIDSVQREIERLKSLNLQLESQVEEAECHSNShtetYQDQVLTLKSQLDDLRKQITQYGQEYQE 461
Cdd:TIGR02169  958 AELQRVEEEIRALEPVNMLAIQEYEEVLKRLDE----LKEKRAKLEEERKAILERIEEYEKKKRE 1018
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 163-485 3.19e-05

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 46.97  E-value: 3.19e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   163 TVQVTRMKE-KEELQALNDKFASFIDKARSLEQHNAVLRAKISmFTNPEQGGPANTSVLLTSAIGAYKSQIDSLSSTKEA 241
Cdd:TIGR02168  228 ALLVLRLEElREELEELQEELKEAEEELEELTAELQELEEKLE-ELRLEVSELEEEIEELQKELYALANEISRLEQQKQI 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   242 IIAEIEHFKAIIEDNQARYEEETSQTKSLELDWTALKEEvdnlyltLFELQTSICGLEdqialskqvydAKVKEVRtivt 321
Cdd:TIGR02168  307 LRERLANLERQLEELEAQLEELESKLDELAEELAELEEK-------LEELKEELESLE-----------AELEELE---- 364

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   322 ggvksavsisvdnaAQAQDLTSALTEVKAHYETLAQRSKQEalvsvqdslsmmsvssqpsSQTLTSAKDELRAYKLQIDS 401
Cdd:TIGR02168  365 --------------AELEELESRLEELEEQLETLRSKVAQL-------------------ELQIASLNNEIERLEARLER 411

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   402 VQREIERLKSLNLQLESQVEEAECHSNSHT--------ETYQDQVLTLKSQLDDLRKQITQYGQEYQELLASKMSLDVEI 473
Cdd:TIGR02168  412 LEDRRERLQQEIEELLKKLEEAELKELQAEleeleeelEELQEELERLEEALEELREELEEAEQALDAAERELAQLQARL 491

                          330
                   ....*....|..
gi 115527833   474 TAYKKLLDSEEN 485
Cdd:TIGR02168  492 DSLERLQENLEG 503
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 231-472 4.05e-05

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 46.97  E-value: 4.05e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   231 QIDSLSSTKEAIIAEIEHFKAIIEDNQARYEEETSQTKSLELDWTALK-------EEVDNLYLTLFELQTSICGLEDQIa 303
Cdd:TIGR02168  226 ELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEELRlevseleEEIEELQKELYALANEISRLEQQK- 304

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   304 lskQVYDAKVKEVRTivtggvksavsisvdnaaQAQDLTSALTEVKAHYETLaqrskQEALVSVQDSLSMMSVSSQPSSQ 383
Cdd:TIGR02168  305 ---QILRERLANLER------------------QLEELEAQLEELESKLDEL-----AEELAELEEKLEELKEELESLEA 358

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   384 TLTSAKDELRAYKLQIDSVQREIERLKSLNLQLESQVEEAechsnshtetyQDQVLTLKSQLDDLRKQITQYGQEYQELL 463
Cdd:TIGR02168  359 ELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASL-----------NNEIERLEARLERLEDRRERLQQEIEELL 427


                   ....*....
gi 115527833   464 ASKMSLDVE 472
Cdd:TIGR02168  428 KKLEEAELK 436
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 220-491 4.58e-05

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 46.47  E-value: 4.58e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 220 LLTSAIGAYKSQIDSLSSTKEAIIAEIEHFKAIIEDNQARYEEETSQTKSLELDWTALKEEVDNLYLTLFELQTSICGLE 299
Cdd:COG1196  250 ELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELE 329

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 300 DQIALSKQVYDAKVKEVRTIvtggvKSAVSISVDNAAQAQDLTSALTEVKAHYETLAQRSKQEALVSVQDSLSMMSVSSQ 379
Cdd:COG1196  330 EELEELEEELEELEEELEEA-----EEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEE 404

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 380 PsSQTLTSAKDELRAYKLQIDSVQREIERLKSLNLQLESQVEEAEchsnSHTETYQDQVLTLKSQLDDLRKQITQYGQEY 459
Cdd:COG1196  405 L-EEAEEALLERLERLEEELEELEEALAELEEEEEEEEEALEEAA----EEEAELEEEEEALLELLAELLEEAALLEAAL 479

                        250       260       270
                 ....*....|....*....|....*....|..
gi 115527833 460 QELLASKMSLDVEITAYKKLLDSEENRLKSGG 491
Cdd:COG1196  480 AELLEELAEAAARLLLLLEAEADYEGFLEGVK 511
SCP-1 pfam05483
Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major ...
 220-484 1.49e-04

Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.


Pssm-ID: 114219 [Multi-domain]  Cd Length: 787  Bit Score: 44.71  E-value: 1.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  220 LLTSAIGAYKSQIDSLSSTKEAIIAEIEHFKAIIEDNQARYEEETSQTKSLEldwtALKEEVDNLYLTLFELQTSICGLE 299
Cdd:pfam05483 381 IITMELQKKSSELEEMTKFKNNKEVELEELKKILAEDEKLLDEKKQFEKIAE----ELKGKEQELIFLLQAREKEIHDLE 456

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  300 DQIAL---SKQVYDAKVKEVRTIV-------TGGVKSAVSISVDNAAQAQDLTSALTEVKAHYETLAQRSKQEALVSVQd 369
Cdd:pfam05483 457 IQLTAiktSEEHYLKEVEDLKTELekeklknIELTAHCDKLLLENKELTQEASDMTLELKKHQEDIINCKKQEERMLKQ- 535

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  370 slsmmsvssqpsSQTLTSAKDELRAyklQIDSVQRE-IERLKSLNLQLESQvEEAECHSNSHTETYQDQVLTLKSQLDDL 448
Cdd:pfam05483 536 ------------IENLEEKEMNLRD---ELESVREEfIQKGDEVKCKLDKS-EENARSIEYEVLKKEKQMKILENKCNNL 599

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 115527833  449 RKQITQYGQEYQELLASKMSLDVEITAYKKLLDSEE 484
Cdd:pfam05483 600 KKQIENKNKNIEELHQENKALKKKGSAENKQLNAYE 635
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 387-488 1.62e-04

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 44.63  E-value: 1.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  387 SAKDELRAYKLQIDSVQREIERLKSLNLQLESQVEEAECHSNSHTETYQD---QVLTLKSQLDDLRKQITQYGQEYQELL 463
Cdd:TIGR04523 381 SYKQEIKNLESQINDLESKIQNQEKLNQQKDEQIKKLQQEKELLEKEIERlkeTIIKNNSEIKDLTNQDSVKELIIKNLD 460

                          90       100
                  ....*....|....*....|....*
gi 115527833  464 ASKMSLDVEITAYKKLLDSEENRLK 488
Cdd:TIGR04523 461 NTRESLETQLKVLSRSINKIKQNLE 485
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
334-493 6.49e-04

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 42.83  E-value: 6.49e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 334 NAAQAQDLTSALTEVKAHYETLAQ------------RSKQEALVSVQDSLSMMS--VSSQPSSQTLTSAKDELRAYKLQI 399
Cdd:COG4717   69 NLKELKELEEELKEAEEKEEEYAElqeeleeleeelEELEAELEELREELEKLEklLQLLPLYQELEALEAELAELPERL 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 400 DSVQREIERLKSLNLQLESQVEEAECHSNSHTETYQD-------QVLTLKSQLDDLRKQITQYGQEYQELLASKMSLDVE 472
Cdd:COG4717  149 EELEERLEELRELEEELEELEAELAELQEELEELLEQlslateeELQDLAEELEELQQRLAELEEELEEAQEELEELEEE 228

                        170       180
                 ....*....|....*....|...
gi 115527833 473 ITAY--KKLLDSEENRLKSGGGV 493
Cdd:COG4717  229 LEQLenELEAAALEERLKEARLL 251
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
385-489 6.71e-04

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 42.20  E-value: 6.71e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 385 LTSAKDELRAYKLQIDSVQREIERLKSLNLQLESQVEEAE---CHSNSHTETYQDQVLTLKSQLDDLRKQITQYGQEYQE 461
Cdd:COG4372   47 LEQLREELEQAREELEQLEEELEQARSELEQLEEELEELNeqlQAAQAELAQAQEELESLQEEAEELQEELEELQKERQD 126

                         90       100
                 ....*....|....*....|....*...
gi 115527833 462 LLASKMSLDVEITAYKKLLDSEENRLKS 489
Cdd:COG4372  127 LEQQRKQLEAQIAELQSEIAEREEELKE 154
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
162-462 9.38e-04

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 42.33  E-value: 9.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 162 DTVQVTRMKEKEELQALNDKFASFIDKARSLEQHNAVLRAKismftnpeqggpANTsvlLTSAIGAYKSQIDSLSSTKEA 241
Cdd:PRK02224 324 EELRDRLEECRVAAQAHNEEAESLREDADDLEERAEELREE------------AAE---LESELEEAREAVEDRREEIEE 388

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 242 IIAEIEhfkaiieDNQARYEEETSQTKSLELDWTALKEEVDNLYLTLFELQTSICGLEDQIALSKQVYDA-KVKEVRTIV 320
Cdd:PRK02224 389 LEEEIE-------ELRERFGDAPVDLGNAEDFLEELREERDELREREAELEATLRTARERVEEAEALLEAgKCPECGQPV 461

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 321 TGgvKSAVSISVDNAAQAQDLTSALTEVKAHYETLAQRSKQ-EALVSVQDSLSMMSVSSQPSSQTLTSAKDELRAYKLQI 399
Cdd:PRK02224 462 EG--SPHVETIEEDRERVEELEAELEDLEEEVEEVEERLERaEDLVEAEDRIERLEERREDLEELIAERRETIEEKRERA 539

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 115527833 400 DSVQREIERLKSLNLQLESQVEEAECHSNSHTE---TYQDQVLTLKSQLDDLRK------QITQYGQEYQEL 462
Cdd:PRK02224 540 EELRERAAELEAEAEEKREAAAEAEEEAEEAREevaELNSKLAELKERIESLERirtllaAIADAEDEIERL 611
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 333-485 1.04e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 42.35  E-value: 1.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   333 DNAAQAQDLtsaLTEVKAHYETL-AQRSKQEALVSVQDSLSMMSVSSqpSSQTLTSAKDELRAYKLQIDSVQREIERLKS 411
Cdd:TIGR02168  186 ENLDRLEDI---LNELERQLKSLeRQAEKAERYKELKAELRELELAL--LVLRLEELREELEELQEELKEAEEELEELTA 260

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 115527833   412 LNLQLESQVEEAEC-HSNSHTE--TYQDQVLTLKSQLDDLRKQITQYGQEYQELLASKMSLDVEI-TAYKKLLDSEEN 485
Cdd:TIGR02168  261 ELQELEEKLEELRLeVSELEEEieELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLeELESKLDELAEE 338
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
336-466 1.05e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 41.81  E-value: 1.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 336 AQAQDLTSALTEVKAHYETLAQRSKQealvsVQDSLSMMSVSSQPSSQTLTSAKDELRAYKLQIDSVQREIERLKSLNLQ 415
Cdd:COG4372   59 EELEQLEEELEQARSELEQLEEELEE-----LNEQLQAAQAELAQAQEELESLQEEAEELQEELEELQKERQDLEQQRKQ 133

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 115527833 416 LESQVEEAEchsnSHTETYQDQVLTLKSQLDDLRKQITQYGQEYQELLASK 466
Cdd:COG4372  134 LEAQIAELQ----SEIAEREEELKELEEQLESLQEELAALEQELQALSEAE 180
CusB_dom_1 pfam00529
Cation efflux system protein CusB domain 1; The cation efflux system protein CusB from E. coli ...
 308-466 1.14e-03

Cation efflux system protein CusB domain 1; The cation efflux system protein CusB from E. coli can be divided into four different domains, the first three domains of the protein are mostly beta-strands and the fourth forms an all alpha-helical domain. This entry represents the first beta-domain (domain 1) of CusB and it is formed by the N and C-terminal ends of the polypeptide (residues 89-102 and 324-385). CusB is part of the copper-transporting efflux system CusCFBA. This domain can also be found in other membrane-fusion proteins, such as HlyD, MdtN, MdtE and AaeA. HlyD is a component of the prototypical alpha-haemolysin (HlyA) bacterial type I secretion system, along with the other components HlyB and TolC. HlyD is anchored in the cytoplasmic membrane by a single transmembrane domain and has a large periplasmic domain within the carboxy-terminal 100 amino acids, HlyB and HlyD form a stable complex that binds the recombinant protein bearing a C-terminal HlyA signal sequence and ATP in the cytoplasm. HlyD, HlyB and TolC combine to form the three-component ABC transporter complex that forms a trans-membrane channel or pore through which HlyA can be transferred directly to the extracellular medium. Cutinase has been shown to be transported effectively through this pore.


Pssm-ID: 425733 [Multi-domain]  Cd Length: 322  Bit Score: 41.25  E-value: 1.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  308 VYDAKVKEVRTIVTGGVksaVSISVDNAAQAQ-----------DLTSALTEVKAHY-ETLAQRSKQEALVSVQDSLSMMS 375
Cdd:pfam00529  15 VVSGNAKAVQPQVSGIV---TRVLVKEGDRVKagdvlfqldptDYQAALDSAEAQLaKAQAQVARLQAELDRLQALESEL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  376 VSSQPSSQTLT----SAKDELRAYKLQIDSVQREIERLKSL---NLQLESQVEEAECHSNSHtetyQDQVLTLKSQLDDL 448
Cdd:pfam00529  92 AISRQDYDGATaqlrAAQAAVKAAQAQLAQAQIDLARRRVLapiGGISRESLVTAGALVAQA----QANLLATVAQLDQI 167

                         170
                  ....*....|....*...
gi 115527833  449 RKQITQYGQEYQELLASK 466
Cdd:pfam00529 168 YVQITQSAAENQAEVRSE 185
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 391-487 2.13e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 41.08  E-value: 2.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 391 ELRAYKLQIDSVQREIERLKSLNLQLESQVEEAEchsnshtetyqDQVLTLKSQLDDLRKQITQYGQEYQELLASKMSLD 470
Cdd:COG1196  233 KLRELEAELEELEAELEELEAELEELEAELAELE-----------AELEELRLELEELELELEEAQAEEYELLAELARLE 301

                         90
                 ....*....|....*..
gi 115527833 471 VEITAYKKLLDSEENRL 487
Cdd:COG1196  302 QDIARLEERRRELEERL 318
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 188-460 2.35e-03

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 41.21  E-value: 2.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   188 KARSLEQHNAVLRAKISmFTNPEQGGPANTSVLLTSAIGAYKSQIDSLSST-------KEAIIAEIEHFKAIIEDNQARY 260
Cdd:TIGR02169  295 KIGELEAEIASLERSIA-EKERELEDAEERLAKLEAEIDKLLAEIEELEREieeerkrRDKLTEEYAELKEELEDLRAEL 373

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   261 EEETSQTKSLELDWTALKEEVDNLYLTLFELQTSICGLEDQialsKQVYDAKVKEVRtivtggvksavsisvdnaAQAQD 340
Cdd:TIGR02169  374 EEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQEE----LQRLSEELADLN------------------AAIAG 431

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   341 LTSALTEVKAHYETLAQRSKQ--EALVSVQDSLSmmsvssqpssqtltSAKDELRAYKLQIDSVQREIERLKSLNLQLES 418
Cdd:TIGR02169  432 IEAKINELEEEKEDKALEIKKqeWKLEQLAADLS--------------KYEQELYDLKEEYDRVEKELSKLQRELAEAEA 497

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*
gi 115527833   419 QVEEAECHSNShtetYQDQVLTLKSQLDDLRKQITQ---YGQEYQ 460
Cdd:TIGR02169  498 QARASEERVRG----GRAVEEVLKASIQGVHGTVAQlgsVGERYA 538
rad50 TIGR00606
rad50; All proteins in this family for which functions are known are involvedin recombination, ...
 357-484 3.77e-03

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).


Pssm-ID: 129694 [Multi-domain]  Cd Length: 1311  Bit Score: 40.42  E-value: 3.77e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833   357 QRSKQEALVSVQDSLSMMSVSSQPSSQTLTSAKDELRAYKLQIDSVQREIERLKSLNLQL-ESQVEEAECHSNSHTETYQ 435
Cdd:TIGR00606  421 ERLKQEQADEIRDEKKGLGRTIELKKEILEKKQEELKFVIKELQQLEGSSDRILELDQELrKAERELSKAEKNSLTETLK 500

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 115527833   436 DQVLTLKSQLDDLRKQITQYGQEYQELLASKMSLDVEITAYKKLLDSEE 484
Cdd:TIGR00606  501 KEVKSLQNEKADLDRKLRKLDQEMEQLNHHTTTRTQMEMLTKDKMDKDE 549
GumC COG3206
Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];
333-488 3.98e-03

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442439 [Multi-domain]  Cd Length: 687  Bit Score: 40.39  E-value: 3.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 333 DNAAQAQDLTSALTEVKAHYETLAQRSKQealVSVQDSLSMMSVSSQPSSQTLTSAKDELRAYKLQID-----------S 401
Cdd:COG3206  216 LLLQQLSELESQLAEARAELAEAEARLAA---LRAQLGSGPDALPELLQSPVIQQLRAQLAELEAELAelsarytpnhpD 292

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 402 VQREIERLKSLNLQLESQVEEAECHSNSHTETYQDQVLTLKSQLDDLRKQITQYGQEYQELLAskmsLDVEITAYKKLLD 481
Cdd:COG3206  293 VIALRAQIAALRAQLQQEAQRILASLEAELEALQAREASLQAQLAQLEARLAELPELEAELRR----LEREVEVARELYE 368


                 ....*..
gi 115527833 482 SEENRLK 488
Cdd:COG3206  369 SLLQRLE 375
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 229-489 4.50e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 40.00  E-value: 4.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  229 KSQIDSLSSTKEAIIAEIEHFKAIIEDNQARYEEETSQTKSLELDWTALKEEVDN--------------LYLTLFELQTS 294
Cdd:TIGR04523 130 EKQKKENKKNIDKFLTEIKKKEKELEKLNNKYNDLKKQKEELENELNLLEKEKLNiqknidkiknkllkLELLLSNLKKK 209

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  295 I-----------------CGLEDQIALSKQVYDAKVKEVRTIVTgGVKSAVSISVDNAAQAQDLTSALTEVKAHYETLAQ 357
Cdd:TIGR04523 210 IqknkslesqiselkkqnNQLKDNIEKKQQEINEKTTEISNTQT-QLNQLKDEQNKIKKQLSEKQKELEQNNKKIKELEK 288

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  358 RSKQ-----EALVSVQDSLSMMSVSSQpssqtLTSAKDELRAYKLQIDSVQREIERLKSLNLQLESQVEeaecHSNSHTE 432
Cdd:TIGR04523 289 QLNQlkseiSDLNNQKEQDWNKELKSE-----LKNQEKKLEEIQNQISQNNKIISQLNEQISQLKKELT----NSESENS 359

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 115527833  433 TYQDQVLTLKSQLDDLRKQITQYGQEYQELLASKMSLDVEITAYKKLLDSEENRLKS 489
Cdd:TIGR04523 360 EKQRELEEKQNEIEKLKKENQSYKQEIKNLESQINDLESKIQNQEKLNQQKDEQIKK 416
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
335-487 5.62e-03

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 39.90  E-value: 5.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  335 AAQAQDLTSALTEVKAHYETLAQ--------RSKQEALVSVQDSLsmmsvssqpssQTLTSAKDELRAYKLQIDSVQREI 406
Cdd:COG4913   633 LEALEAELDALQERREALQRLAEyswdeidvASAEREIAELEAEL-----------ERLDASSDDLAALEEQLEELEAEL 701

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  407 ERLKSLNLQLESQVEEAEchsnSHTETYQDQVLTLKSQLDDLRKQIT---------QYGQEYQELLASKMS--LDVEITA 475
Cdd:COG4913   702 EELEEELDELKGEIGRLE----KELEQAEEELDELQDRLEAAEDLARlelralleeRFAAALGDAVERELRenLEERIDA 777

                         170
                  ....*....|..
gi 115527833  476 YKKLLDSEENRL 487
Cdd:COG4913   778 LRARLNRAEEEL 789
46 PHA02562
endonuclease subunit; Provisional
 219-456 5.77e-03

endonuclease subunit; Provisional


Pssm-ID: 222878 [Multi-domain]  Cd Length: 562  Bit Score: 39.61  E-value: 5.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 219 VLLTSAIGAYKSQIDSLSSTKEAIIAEIEHFK-----------AIIEDNQARYEEETSQTKSLELDWTALKEEVDNLYLT 287
Cdd:PHA02562 170 KLNKDKIRELNQQIQTLDMKIDHIQQQIKTYNknieeqrkkngENIARKQNKYDELVEEAKTIKAEIEELTDELLNLVMD 249

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 288 LFELQTSICGLEDQIALSKQVYDAKVKEVRTIVTGGV--------KSAVSISVDNAAQAQDLTSALTEVKAHYETLAQRs 359
Cdd:PHA02562 250 IEDPSAALNKLNTAAAKIKSKIEQFQKVIKMYEKGGVcptctqqiSEGPDRITKIKDKLKELQHSLEKLDTAIDELEEI- 328

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 360 kqealvsvQDSLSMMSVSSQPSSQTLTSAKDELRAYKLQIDSVQREIERLKSLNLQLESQVEEaechsnshtetYQDQVL 439
Cdd:PHA02562 329 --------MDEFNEQSKKLLELKNKISTNKQSLITLVDKAKKVKAAIEELQAEFVDNAEELAK-----------LQDELD 389

                        250
                 ....*....|....*..
gi 115527833 440 TLKSQLDDLRKQITQYG 456
Cdd:PHA02562 390 KIVKTKSELVKEKYHRG 406
COG1340 COG1340
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];
383-489 8.59e-03

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];


Pssm-ID: 440951 [Multi-domain]  Cd Length: 297  Bit Score: 38.35  E-value: 8.59e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 383 QTLTSAKDELRAYKLQIDSVQREIERLKSLNLQLESQVEE--AECHS-NSHTETYQDQVLTLKSQLDDLRKQITQYGQEY 459
Cdd:COG1340    1 SKTDELSSSLEELEEKIEELREEIEELKEKRDELNEELKElaEKRDElNAQVKELREEAQELREKRDELNEKVKELKEER 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 115527833 460 QELLASKMSLDVEITAYKKLLDSEENRLKS 489
Cdd:COG1340   81 DELNEKLNELREELDELRKELAELNKAGGS 110
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 228-478 9.08e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 39.23  E-value: 9.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  228 YKSQIDSLSSTKEAIIAEIEHFKaiiEDNQaryeEETSQTKSLELDWTALKEEVDNLYLTLFELQTSICGLEDQIAlskq 307
Cdd:TIGR04523 382 YKQEIKNLESQINDLESKIQNQE---KLNQ----QKDEQIKKLQQEKELLEKEIERLKETIIKNNSEIKDLTNQDS---- 450

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  308 VYDAKVKEVRTIVTggvksavsisvdnaAQAQDLTSALTEVKAHYETLAQRSKQeaLVSVQDSLSMMSVSSQPSSQTLTS 387
Cdd:TIGR04523 451 VKELIIKNLDNTRE--------------SLETQLKVLSRSINKIKQNLEQKQKE--LKSKEKELKKLNEEKKELEEKVKD 514

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833  388 AKDelrayklQIDSVQREIERLKSLNLQLESQVEEAECHSNShtetyQDQVLT---LKSQLDDLRKQITQYGQEYQELLA 464
Cdd:TIGR04523 515 LTK-------KISSLKEKIEKLESEKKEKESKISDLEDELNK-----DDFELKkenLEKEIDEKNKEIEELKQTQKSLKK 582

                         250
                  ....*....|....
gi 115527833  465 SKMSLDVEITAYKK 478
Cdd:TIGR04523 583 KQEEKQELIDQKEK 596
COG1340 COG1340
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];
385-482 9.14e-03

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];


Pssm-ID: 440951 [Multi-domain]  Cd Length: 297  Bit Score: 38.35  E-value: 9.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115527833 385 LTSAKDELRAYKLQIDSVQREIERL------KSLNL-----------QLESQVEEAE--CHSNSHTETYQDQVLTLKSQL 445
Cdd:COG1340   97 LRKELAELNKAGGSIDKLRKEIERLewrqqtEVLSPeeekelvekikELEKELEKAKkaLEKNEKLKELRAELKELRKEA 176

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 115527833 446 DDLRKQITQYGQEYQELLASKMSLDVEITAYKKLLDS 482
Cdd:COG1340  177 EEIHKKIKELAEEAQELHEEMIELYKEADELRKEADE 213
 
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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