NCBI Conserved Domain Search

first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...

1292-1357

1.08e-21

first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

Pssm-ID: 380736 [Multi-domain] Cd Length: 69 Bit Score: 90.23 E-value: 1.08e-21

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1939203063 1292 KSQLQTYAQKRNFALPVYSCERVGPPHASRFKCKVTVNGHTFESLEYFPILNKAENAAAKAALMSL 1357
Cdd:cd19907      3 KSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNSL 68

DSRM_AtDRB-like_rpt1

first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...

857-920

3.42e-18

Pssm-ID: 380736 [Multi-domain] Cd Length: 69 Bit Score: 80.21 E-value: 3.42e-18

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1939203063  857 MYKSKLQELCQQRSWELPTYESSRQGQAHNPRFLATVTVNDISFHSPSPSNTSKKAQNDAAKLA 920
Cdd:cd19907      1 MYKSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVA 64

Rnc

dsRNA-specific ribonuclease [Transcription];

1369-1438

1.65e-16

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 80.53 E-value: 1.65e-16

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1939203063 1369 YKNLLQELAQREGCGLPTYS-TNKSGEAHIPTFTSTVEIKGEIF-TGQGaKTKKQAEMSAAKTAYTALKQRN 1438
Cdd:COG0571    159 YKTALQEWLQARGLPLPEYEvVEEEGPDHAKTFTVEVLVGGKVLgEGTG-RSKKEAEQAAAKAALEKLGKKE 229

dsrm

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...

858-923

5.12e-14

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.

Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 68.41 E-value: 5.12e-14

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1939203063  858 YKSKLQELCQQRSWELPTYESSRQGQAHNPRFLATVTVNDISFHSPSPSNTsKKAQNDAAKLAYEH 923
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSK-KEAEQLAAEKALEK 65

DSRM

Double-stranded RNA binding motif;

1369-1435

6.90e-14

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 68.06 E-value: 6.90e-14

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1939203063  1369 YKNLLQELAQREGCgLPTYSTNK-SGEAHIPTFTSTVEIKGEI-FTGQGaKTKKQAEMSAAKTAYTALK 1435
Cdd:smart00358    1 PKSLLQELAQKRKL-PPEYELVKeEGPDHAPRFTVTVKVGGKRtGEGEG-SSKKEAKQRAAEAALRSLK 67

dsrm

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...

1369-1434

1.01e-13

Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 67.26 E-value: 1.01e-13

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1939203063 1369 YKNLLQELAQREGCGLPTYSTNKSGEAHIPTFTSTVEIKGEIFTGQGAKTKKQAEMSAAKTAYTAL 1434
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66

RNaseIII

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...

1369-1434

1.70e-13

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]

Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 71.47 E-value: 1.70e-13

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1939203063 1369 YKNLLQELAQREGCGLPTYSTNK-SGEAHIPTFTSTVEIKGEIF-TGQGaKTKKQAEMSAAKTAYTAL 1434
Cdd:TIGR02191  154 YKTALQEWAQARGKPLPEYRLIKeEGPDHDKEFTVEVSVNGEPYgEGKG-KSKKEAEQNAAKAALEKL 220

DSRM

Double-stranded RNA binding motif;

858-922

7.62e-13

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 64.98 E-value: 7.62e-13

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1939203063   858 YKSKLQELCQQRSWElPTYES-SRQGQAHNPRFLATVTVNDISFhsPSPSNTSKK-AQNDAAKLAYE 922
Cdd:smart00358    1 PKSLLQELAQKRKLP-PEYELvKEEGPDHAPRFTVTVKVGGKRT--GEGEGSSKKeAKQRAAEAALR 64

Rnc

dsRNA-specific ribonuclease [Transcription];

858-922

2.24e-11

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 65.51 E-value: 2.24e-11

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1939203063  858 YKSKLQELCQQRSWELPTYE-SSRQGQAHNPRFLATVTVNDISFHspSPSNTSKK-AQNDAAKLAYE 922
Cdd:COG0571    159 YKTALQEWLQARGLPLPEYEvVEEEGPDHAKTFTVEVLVGGKVLG--EGTGRSKKeAEQAAAKAALE 223

RNaseIII

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...

858-922

3.69e-09

Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 58.75 E-value: 3.69e-09

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1939203063  858 YKSKLQELCQQRSWELPTYE-SSRQGQAHNPRFLATVTVNDISFhsPSPSNTSKK-AQNDAAKLAYE 922
Cdd:TIGR02191  154 YKTALQEWAQARGKPLPEYRlIKEEGPDHDKEFTVEVSVNGEPY--GEGKGKSKKeAEQNAAKAALE 218

dsrm

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...

1291-1335

4.44e-08

Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 51.46 E-value: 4.44e-08

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1939203063 1291 SKSQLQTYAQKRNFALPVYSCERVGPPHASRFKCKVTVNGHTFES 1335
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGS 45

DSRM

Double-stranded RNA binding motif;

1292-1333

1.98e-07

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 49.57 E-value: 1.98e-07

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 1939203063  1292 KSQLQTYAQKRNFaLPVYSC-ERVGPPHASRFKCKVTVNGHTF 1333
Cdd:smart00358    2 KSLLQELAQKRKL-PPEYELvKEEGPDHAPRFTVTVKVGGKRT 43

PHA03103

double-strand RNA-binding protein; Provisional

862-920

1.49e-06

double-strand RNA-binding protein; Provisional

Pssm-ID: 222987 [Multi-domain] Cd Length: 183 Bit Score: 50.53 E-value: 1.49e-06

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1939203063  862 LQELCQ--QRSWelpTYESSRQGQAHNPRFLATVTVNDISFhSPSPSNTSKKAQNDAAKLA 920
Cdd:PHA03103   115 INEYCQitSRDW---SINITSSGPSHSPTFTASVIISGIKF-KPAIGSTKKEAKNNAAKLA 171

Rnc

dsRNA-specific ribonuclease [Transcription];

1292-1330

3.36e-06

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 50.10 E-value: 3.36e-06

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1939203063 1292 KSQLQTYAQKRNFALPVYSC-ERVGPPHASRFKCKVTVNG 1330
Cdd:COG0571    160 KTALQEWLQARGLPLPEYEVvEEEGPDHAKTFTVEVLVGG 199

PHA03103

double-strand RNA-binding protein; Provisional

1392-1430

2.08e-03

double-strand RNA-binding protein; Provisional

Pssm-ID: 222987 [Multi-domain] Cd Length: 183 Bit Score: 40.90 E-value: 2.08e-03

                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1939203063 1392 SGEAHIPTFTSTVEIKGEIFTGQGAKTKKQAEMSAAKTA 1430
Cdd:PHA03103   133 SGPSHSPTFTASVIISGIKFKPAIGSTKKEAKNNAAKLA 171

Name

Accession

Description

Interval

E-value

PLN02475

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

61-825

0e+00

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

Pssm-ID: 215264 [Multi-domain] Cd Length: 766 Bit Score: 1659.52 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063   61 MASHIVGYPRMGPKRELKFALESFWDGKSSAQDLQKVAADLRESIWKQMSDAGIKYIPSNTFSYYDQMLDTTAMLGAVPP 140
Cdd:PLN02475     1 MASHIVGYPRMGPKRELKFALESFWDGKSSAEDLQKVAADLRSSIWKQMSAAGIKYIPSNTFSYYDQVLDTTAMLGAVPP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  141 RYGWNGGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHFIVPELGPEVNFSYASHKAVTEYKEAKALGVDTVPVLVGPVS 220
Cdd:PLN02475    81 RYGWTGGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHYIVPELGPEVKFSYASHKAVNEYKEAKALGVDTVPVLVGPVS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  221 YLLLSKPAKGVEKTFSLLSLLGKILPIYKEVISELKEAGASWIQFDEPTLVMDLESHKLEAFTEAYSELESTLSGLNVLI 300
Cdd:PLN02475   161 YLLLSKPAKGVDKSFDLLSLLDKILPVYKEVIAELKAAGASWIQFDEPALVMDLESHKLQAFKTAYAELESTLSGLNVLV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  301 ETYFADIPAQQYKTLTSLKGVTAFGFDLIRGTKTLDLIK-GEFPEGKHLFAGVVDGRNIWANDLAASLSTLEALESIVGK 379
Cdd:PLN02475   241 ETYFADVPAEAYKTLTSLKGVTAFGFDLVRGTKTLDLIKkAGFPSGKYLFAGVVDGRNIWANDLAASLATLQALEGIVGK 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  380 DKLVVSTSCSLLHTAVDLVNETKLDKEIKSWLAFAAQKVVEVNALAKALAGEKDEEFFSANAAAQASRKSSPRVNNEAVQ 459
Cdd:PLN02475   321 DKLVVSTSCSLLHTAVDLVNETKLDKELKSWLAFAAQKVVEVVALAKALAGQKDEAFFSANAAAQASRRSSPRVTNEAVQ 400

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  460 KAAAALKGSDHRRATNVSARLDAQQKKLNLPILPTTTIGSFPQTMELRKVRREYKAKKVSEDDYIKAIKEEISKVVKLQE 539
Cdd:PLN02475   401 KAAAALKGSDHRRATPVSARLDAQQKKLNLPILPTTTIGSFPQTVELRRVRREYKAKKISEEDYVKAIKEEIAKVVKLQE 480

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  540 EFDIDVLVHGEPERNDMVEYFGEQLSGFAFSANGWVQSYGSRCVKPPIIYGDVSRPKSMTVFWSALAQSMTSRPMKGMLT 619
Cdd:PLN02475   481 ELDIDVLVHGEPERNDMVEYFGEQLSGFAFTANGWVQSYGSRCVKPPIIYGDVSRPKAMTVFWSSVAQSMTKRPMKGMLT 560

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  620 GPVTILNWSFVRNDQPRFETCYQIALAIKDEVEDLEKNGITVIQIDEAALREGLPLRKSEQAFYLDWAVHSFRITNCGVQ 699
Cdd:PLN02475   561 GPVTILNWSFVRNDQPRHETCYQIALAIKDEVEDLEKAGITVIQIDEAALREGLPLRKSEHAFYLDWAVHSFRITNCGVQ 640

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  700 DTTQIHTHMCYSNFNDIIHSIIDMDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEEIADRINKML 779
Cdd:PLN02475   641 DTTQIHTHMCYSNFNDIIHSIIDMDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEEIADRINKML 720

                          730       740       750       760
                   ....*....|....*....|....*....|....*....|....*.
gi 1939203063  780 AVLETNILWVNPDCGLKTRKYTEVKPALKNMVDAAKLLRTQLASAK 825
Cdd:PLN02475   721 AVLESNILWVNPDCGLKTRKYPEVKPALKNMVAAAKLLRAQLASAK 766

PRK05222

5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional

61-823

0e+00

5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional

Pssm-ID: 235367 [Multi-domain] Cd Length: 758 Bit Score: 1345.15 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063   61 MASHIVGYPRMGPKRELKFALESFWDGKSSAQDLQKVAADLRESIWKQMSDAGIKYIPSNTFSYYDQMLDTTAMLGAVPP 140
Cdd:PRK05222     2 IKTHILGFPRIGPRRELKKALESYWAGKISEEELLATARELRARHWQRQKEAGLDLIPVGDFSYYDHVLDTAVLLGAIPE 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  141 RYGWNGGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHFIVPELGPEVNFSYASHKAVTEYKEAKALGVDTVPVLVGPVS 220
Cdd:PRK05222    82 RFGNLGGSVDLDTYFAMARGGKDVAALEMTKWFNTNYHYIVPEFDPDTQFKLTSNKLLDEFEEAKALGINTKPVLLGPVT 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  221 YLLLSKpakGVEKTFSLLSLLGKILPIYKEVISELKEAGASWIQFDEPTLVMDLESHKLEAFTEAYSELESTLSGLNVLI 300
Cdd:PRK05222   162 FLWLSK---SKGEGFDRLDLLDDLLPVYAELLAELAAAGAEWVQIDEPALVLDLPQEWLEAFKRAYEALAAAKPRPKLLL 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  301 ETYFADIpAQQYKTLTSLkGVTAFGFDLIRGTKTLDLIKGEFPEGKHLFAGVVDGRNIWANDLAASLSTLEALESIVgkD 380
Cdd:PRK05222   239 ATYFGSL-NDALDLLASL-PVDGLHLDLVRGPEQLAALLKYFPADKVLSAGVIDGRNIWRADLEAALALLEPLAAKV--D 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  381 KLVVSTSCSLLHTAVDLVNETKLDKEIKSWLAFAAQKVVEVNALAKALAGEKD--EEFFSANAAAQASRKSSPRVNNEAV 458
Cdd:PRK05222   315 RLWVAPSCSLLHVPVDLDAETKLDPELKSWLAFAKQKLEELALLARALNGGRGavAEALAANRAAIAARRTSPRVHNPAV 394

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  459 QKAAAALKGSDHRRATNVSARLDAQQKKLNLPILPTTTIGSFPQTMELRKVRREYKAKKVSEDDYIKAIKEEISKVVKLQ 538
Cdd:PRK05222   395 RARLAALTEADFQRQSPYAERAAAQRARLNLPLLPTTTIGSFPQTTEIRKARAAFKKGELSEEEYEAFIREEIARAIRLQ 474

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  539 EEFDIDVLVHGEPERNDMVEYFGEQLSGFAFSANGWVQSYGSRCVKPPIIYGDVSRPKSMTVFWSALAQSMTSRPMKGML 618
Cdd:PRK05222   475 EELGLDVLVHGEFERNDMVEYFGEQLDGFAFTQNGWVQSYGSRCVKPPIIYGDVSRPEPMTVEWIKYAQSLTDKPVKGML 554

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  619 TGPVTILNWSFVRNDQPRFETCYQIALAIKDEVEDLEKNGITVIQIDEAALREGLPLRKSEQAFYLDWAVHSFRITNCGV 698
Cdd:PRK05222   555 TGPVTILNWSFVRDDQPREETARQIALAIRDEVLDLEAAGIKIIQIDEPALREGLPLRRSDWDAYLDWAVEAFRLATSGV 634

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  699 QDTTQIHTHMCYSNFNDIIHSIIDMDADVITIENSRSDEKLLSVFREgVKYGAGIGPGVYDIHSPRIPSTEEIADRINKM 778
Cdd:PRK05222   635 KDETQIHTHMCYSEFNDIIDAIAALDADVISIETSRSDMELLDAFED-FGYPNEIGPGVYDIHSPRVPSVEEIEELLRKA 713

                          730       740       750       760
                   ....*....|....*....|....*....|....*....|....*
gi 1939203063  779 LAVLETNILWVNPDCGLKTRKYTEVKPALKNMVDAAKLLRTQLAS 823
Cdd:PRK05222   714 LEVIPAERLWVNPDCGLKTRGWEETIAALKNMVAAAKELRAELAA 758

met_syn_B12ind

TIGR01371

5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; This model describes ...

66-820

0e+00

Pssm-ID: 273583 [Multi-domain] Cd Length: 750 Bit Score: 1297.70 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063   66 VGYPRMGPKRELKFALESFWDGKSSAQDLQKVAADLRESIWKQMSDAGIKYIPSNTFSYYDQMLDTTAMLGAVPPRYGWN 145
Cdd:TIGR01371    1 LGFPRIGPKRELKKALESYWAGKITKEELLKVAKDLRKKNWKLQKEAGVDFIPSNDFSLYDHVLDTAVMLGAIPERFGNY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  146 GGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHFIVPELGPEVNFSYASHKAVTEYKEAKALGVDTVPVLVGPVSYLLLS 225
Cdd:TIGR01371   81 GGDLDLDTYFAMARGNKDVPALEMTKWFNTNYHYIVPELSPTTEFKLTSNKPLEEYLEAKELGIETKPVLLGPITFLKLS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  226 KpakGVEKTFSLLSLLGKILPIYKEVISELKEAGASWIQFDEPTLVMDLESHKLEAFTEAYSELESTLSGLNVLIETYFA 305
Cdd:TIGR01371  161 K---AVEEPFEPLSLLEKLLPVYKEVLKKLAEAGATWVQIDEPALVTDLSKEDLAAFKEAYTELSEALSGLKLLLQTYFD 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  306 DIPAQqYKTLTSLKgVTAFGFDLIRGTKTLDLIKGEFPEGKHLFAGVVDGRNIWANDLAASLSTLEALESIVGKdkLVVS 385
Cdd:TIGR01371  238 SVGDA-LEALVSLP-VKGIGLDFVHGKGTLELVKAGFPEDKVLSAGVIDGRNIWRNDLEASLSLLKKLLAHVGK--LVVS 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  386 TSCSLLHTAVDLVNETKLDKEIKSWLAFAAQKVVEVNALAKALAGEKDEEFFSANAAAQA--SRKSSPRVNNEAVQKAAA 463
Cdd:TIGR01371  314 TSCSLLHVPVDLELETKLDPELKSWLAFAKEKLEELKALKRALNGNDDAVAFALEANAAAiaARKSSPRVNDAQVKARLA 393

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  464 ALKGSDHRRATNVSARLDAQQKKLNLPILPTTTIGSFPQTMELRKVRREYKAKKVSEDDYIKAIKEEISKVVKLQEEFDI 543
Cdd:TIGR01371  394 NLKEDDFRRRSPFKERLPLQQKRLNLPLLPTTTIGSFPQTPEVRKARAAYRKGEISEEEYEKFIKEEIKKVIKIQEELGL 473

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  544 DVLVHGEPERNDMVEYFGEQLSGFAFSANGWVQSYGSRCVKPPIIYGDVSRPKSMTVFWSALAQSMTSRPMKGMLTGPVT 623
Cdd:TIGR01371  474 DVLVHGEFERNDMVEYFGEKLAGFAFTQNGWVQSYGSRCVRPPIIYGDVSRPKPMTVKWSVYAQSLTSKPVKGMLTGPVT 553

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  624 ILNWSFVRNDQPRFETCYQIALAIKDEVEDLEKNGITVIQIDEAALREGLPLRKSEQAFYLDWAVHSFRITNCGVQDTTQ 703
Cdd:TIGR01371  554 ILNWSFVRDDIPRKEIAYQIALAIRDEVLDLEEAGIKIIQIDEPALREGLPLRKSDWPEYLDWAVEAFRLATSGVKDETQ 633

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  704 IHTHMCYSNFNDIIHSIIDMDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLE 783
Cdd:TIGR01371  634 IHTHMCYSEFNEIIESIADLDADVISIEASRSDMELLSAFKNGFGYPNGIGPGVYDIHSPRVPSVEEMADLIEKALQVLP 713

                          730       740       750
                   ....*....|....*....|....*....|....*..
gi 1939203063  784 TNILWVNPDCGLKTRKYTEVKPALKNMVDAAKLLRTQ 820
Cdd:TIGR01371  714 AERLWVNPDCGLKTRNWEEVIASLKNMVEAAKEAREQ 750

CIMS_N_terminal_like

cd03312

CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many ...

63-427

0e+00

Pssm-ID: 239428 [Multi-domain] Cd Length: 360 Bit Score: 600.67 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063   63 SHIVGYPRMGPKRELKFALESFWDGKSSAQDLQKVAADLRESIWKQMSDAGIKYIPSNTFSYYDQMLDTTAMLGAVPPRY 142
Cdd:cd03312      2 THILGFPRIGANRELKKALESYWKGKISEEELLATAKELRLRHWKLQKEAGIDLIPVGDFSLYDHVLDTSVLLGAIPERF 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  143 GWNGGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHFIVPELGPEVNFSYASHKAVTEYKEAKALGVDTVPVLVGPVSYL 222
Cdd:cd03312     82 GALGGLVDLDTYFAMARGNQDVPALEMTKWFDTNYHYIVPELSPDTEFKLASNKLLDEYLEAKALGINTKPVLLGPVTFL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  223 LLSKPAKGvekTFSLLSLLGKILPIYKEVISELKEAGASWIQFDEPTLVMDLESHKLEAFTEAYSELESTLSGLNVLIET 302
Cdd:cd03312    162 KLSKAKGG---GFDRLSLLDKLLPVYKELLKKLAAAGAEWVQIDEPALVLDLPEEWLAAFKRAYEELAKAAPGLKLLLAT 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  303 YFADIpAQQYKTLTSLkGVTAFGFDLIRGTKTLDLIKGEFPEGKHLFAGVVDGRNIWANDLAASLSTLEALESIVGkDKL 382
Cdd:cd03312    239 YFGSL-GENLDLLASL-PVDGLHLDLVRGPENLEAVLKAGFADKVLSAGVVDGRNIWRADLAASLALLETLAAILG-DRL 315

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*
gi 1939203063  383 VVSTSCSLLHTAVDLVNETKLDKEIKSWLAFAAQKVVEVNALAKA 427
Cdd:cd03312    316 VVSPSCSLLHVPVDLENETKLDPELKSWLAFAKQKLEELALLARA 360

Meth_synt_2

pfam01717

Cobalamin-independent synthase, Catalytic domain; This is a family of vitamin-B12 independent ...

492-815

0e+00

Pssm-ID: 366771 [Multi-domain] Cd Length: 323 Bit Score: 564.75 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  492 LPTTTIGSFPQTMELRKVRREYKAKKVSEDDYIKAIKEEISKVVKLQEEFDIDVLVHGEPERNDMVEYFGEQLSGFAFSA 571
Cdd:pfam01717    1 FPTTTIGSFPQTAEIRAARVEFKKGEISLEEYELRIRGEIEDAVRRQERLGLDVLVHGEPERGDMVEYFGEALGGFAFTK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  572 NGWVQSYGSRCVKPPIIYGDVSRPKSMTVFWSALAQSMTSRPMKGMLTGPVTILNWSFVRNDQPRFETCYQIALAIKDEV 651
Cdd:pfam01717   81 NGWVQSYGSRCVRPPIIYGDVSRPAPMTVKWSAYAQSTTDKPVKGMLTGPVTILNWSFVRDDQPRAAIAMQIALALRDEV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  652 EDLEKNGITVIQIDEAALREGLPLRKSEQAFYLDWAVHSFRITNCGVQDTTQIHTHMCYSNFNDIIHSIIDMDADVITIE 731
Cdd:pfam01717  161 ADLEAAGIAVIQIDEPALREGLPLKKLDWAAYLDWAVAAFRLDTCGAADDTQIHTHMCYSDFNDILSAIAALDADVITIE 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  732 NSRSDEKLLSVFREgVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNILWVNPDCGLKTRKYTEVKPALKNMV 811
Cdd:pfam01717  241 ASRSDMELLEAFEE-WGYGRGIGPGVYDIHSPRVPSMEEIAALIVAALDVVPAERLWVNPDCGLKTRGWEEARAALRNMV 319


                   ....
gi 1939203063  812 DAAK 815
Cdd:pfam01717  320 DAAK 323

Meth_synt_1

pfam08267

Cobalamin-independent synthase, N-terminal domain; The N-terminal domain and C-terminal ...

63-377

1.21e-163

Cobalamin-independent synthase, N-terminal domain; The N-terminal domain and C-terminal domains of cobalamin-independent synthases together define a catalytic cleft in the enzyme. The N-terminal domain is thought to bind the substrate, in particular, the negatively charged polyglutamate chain. The N-terminal domain is also thought to stabilize a loop from the C-terminal domain.

Pssm-ID: 400526 [Multi-domain] Cd Length: 310 Bit Score: 498.26 E-value: 1.21e-163

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063   63 SHIVGYPRMGPKRELKFALESFWDGKSSAQDLQKVAADLRESIWKQMSDAGIKYIPSNTFSYYDQMLDTTAMLGAVPPRY 142
Cdd:pfam08267    1 TSILGFPRIGENRELKKALESYWKGKISEEELLKTAKELRLRHWKKQKEAGIDLIPVGDFSYYDHVLDTAVLLGAIPERF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  143 GWNGGEIGFDVYFSMARGNASVPAMEMTKWFDTNYHFIVPELGPEVNFSYASHKAVTEYKEAKALGVDTVPVLVGPVSYL 222
Cdd:pfam08267   81 GNDGGLDDLDTYFAMARGNKDVPALEMTKWFNTNYHYIVPELDKDTEFKLNSNKLLDEYKEAKALGIETKPVLLGPVTFL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  223 LLSkpaKGVEKTFSLLSLLGKILPIYKEVISELKEAGASWIQFDEPTLVMDLESHKLEAFTEAYSELESTLSGLNVLIET 302
Cdd:pfam08267  161 KLS---KGKGGSFDRLELLPKLLPVYKELLKELAAAGAEWVQIDEPALVLDLPPEWLAAFKEAYQELASAKPGPKLLLAT 237

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1939203063  303 YFADIpAQQYKTLTSLkGVTAFGFDLIRGTKTLDLIKGEFPEGKHLFAGVVDGRNIWANDLAASLSTLEALESIV 377
Cdd:pfam08267  238 YFGSV-ADALELLASL-PVAGLGLDLVRGPENLAALKKGFPADKVLSAGVIDGRNIWRADLEAALELLETLAQKL 310

MetE

COG0620

Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism]; ...

492-820

1.58e-139

Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism]; Methionine synthase II (cobalamin-independent) is part of the Pathway/BioSystem: Methionine biosynthesis

Pssm-ID: 440385 [Multi-domain] Cd Length: 325 Bit Score: 434.18 E-value: 1.58e-139

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  492 LPTTTIGSFPQTMELRKVRREYKAKKVSEDDYIKAIKEEISKVVKLQEEFDIDVLVHGEPERNDMVEYFGEQLSGFAFSA 571
Cdd:COG0620      1 LPTTTVGSFPRPRELKKAREAYWAGEISAEELREAADEAIAEVVRKQEEAGLDVVTDGEFRRYDMVGYFPERLDGYAFAR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  572 NGWVQSYGSRCVKPPIIYGDVSRPKSMTVFWSALAQSMTSRPMKGMLTGPVTILNWSFVRNDQPRFETCYQIALAIKDEV 651
Cdd:COG0620     81 NGWVEWFDTNYHYVPEITGDVSFSGPMTVEEFRFAKSLTGKPVKPVLPGPVTLLLLSKVRDYKDREELLDDLAPAYREEL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  652 EDLEKNGITVIQIDEAALREGLPlrkseqAFYLDWAVHSFRITNCGVQDtTQIHTHMCYSNFNDIIHSIIDMDADVITIE 731
Cdd:COG0620    161 KALEAAGARWIQIDEPALAEDLP------DEYLDWAVEAYNRAAAGVPD-TKIHLHTCYGGYEDILEALAALPVDGIHLE 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  732 NSRSDEKLLSVFREgVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNILWVNPDCGLKTRKYT----EVKPAL 807
Cdd:COG0620    234 FVRSRAGLLEPLKE-LPYDKVLGLGVIDGRNPWVEDPEEVAARIEEALKYVPPERLWVSPDCGLKHRPVDltreEAWAKL 312

                          330
                   ....*....|...
gi 1939203063  808 KNMVDAAKLLRTQ 820
Cdd:COG0620    313 RNMVAFAREVRGE 325

CIMS_C_terminal_like

cd03311

CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many ...

493-816

3.09e-139

CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers the C-terminal barrel, and a few single-barrel sequences most similar to the C-terminal barrel. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Sidechains from both barrels contribute to the binding of the folate substrate.

Pssm-ID: 239427 [Multi-domain] Cd Length: 332 Bit Score: 433.58 E-value: 3.09e-139

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  493 PTTTIGSFPQTMELRKVRREYKAKKVSEDDYIKAIKEEISKVVKLQEEFDIDVLVHGEPERNDMVEYFGEQLSGFAFsaN 572
Cdd:cd03311      1 PTTTVGSFPRPKELREARAKFKKGEISAEELREAEDDAIADAVKDQEEAGLDVVTDGEFRRSDMVEYFLERLDGFEF--T 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  573 GWVQSYGSRCVKPPIIYGDVSRPKSMTVFWSALAQSMT-SRPMKGMLTGPVTILNWSFVRN---DQPRFETCYQIALAIK 648
Cdd:cd03311     79 GWVQSYGSRYYKPPGIVGDVSRRPPMTVEEGKIAQSLThPKPLKGILTGPVTIPSPSFVRFrgyYPSREELAMDLALALR 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  649 DEVEDLEKNGITVIQIDEAALREGLPLRK-SEQAFYLDWAVHSFRitncGVQDTTQIHTHMCYSNF----------NDII 717
Cdd:cd03311    159 EEIRDLYDAGCRYIQIDEPALAEGLPLEPdDLAADYLKWANEALA----DRPDDTQIHTHICYGNFrstwaaeggyEPIA 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  718 HSIIDMDADVITIENSRSDEKLLSVFREgVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNILWVNPDCGLKT 797
Cdd:cd03311    235 EYIFELDVDVFFLEYDNSRAGGLEPLKE-LPYDKKVGLGVVDVKSPEVESPEEVKDRIEEAAKYVPLEQLWVSPDCGFAT 313

                          330
                   ....*....|....*....
gi 1939203063  798 RKYTEVKPALKNMVDAAKL 816
Cdd:cd03311    314 RERGNALTKLENMVKAALV 332

MetE

COG0620

Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism]; ...

62-417

1.12e-80

Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism]; Methionine synthase II (cobalamin-independent) is part of the Pathway/BioSystem: Methionine biosynthesis

Pssm-ID: 440385 [Multi-domain] Cd Length: 325 Bit Score: 269.32 E-value: 1.12e-80

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063   62 ASHIVGYPRMgpkRELKFALESFWDGKSSAQDLQKVAADLRESIWKQMSDAGIKYIPSNTFSYYDqmldttaMLGAVPPR 141
Cdd:COG0620      3 TTTVGSFPRP---RELKKAREAYWAGEISAEELREAADEAIAEVVRKQEEAGLDVVTDGEFRRYD-------MVGYFPER 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  142 ygWNGgeigfdvyFSMARgNASVpamemtKWFDTNYHfIVPELGPEVNFSyaSHKAVTEYKEAKAL-GVDTVPVLVGPVS 220
Cdd:COG0620     73 --LDG--------YAFAR-NGWV------EWFDTNYH-YVPEITGDVSFS--GPMTVEEFRFAKSLtGKPVKPVLPGPVT 132

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  221 YLLLSKpakgVEKTFSLLSLLGKILPIYKEVISELKEAGASWIQFDEPTLVMDLESHKLEAFTEAYSELESTLSGLNVLI 300
Cdd:COG0620    133 LLLLSK----VRDYKDREELLDDLAPAYREELKALEAAGARWIQIDEPALAEDLPDEYLDWAVEAYNRAAAGVPDTKIHL 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  301 ETYFADIPAQqYKTLTSLKgVTAFGFDLIRGT-KTLDLIKgEFPEGKHLFAGVVDGRNIWANDLAASLSTLEALESIVGK 379
Cdd:COG0620    209 HTCYGGYEDI-LEALAALP-VDGIHLEFVRSRaGLLEPLK-ELPYDKVLGLGVIDGRNPWVEDPEEVAARIEEALKYVPP 285

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 1939203063  380 DKLVVSTSCSLLHTAVDLVNEtKLDKEIKSWLAFAAQK 417
Cdd:COG0620    286 ERLWVSPDCGLKHRPVDLTRE-EAWAKLRNMVAFAREV 322

PRK04326

methionine synthase; Provisional

488-821

6.34e-77

methionine synthase; Provisional

Pssm-ID: 179825 [Multi-domain] Cd Length: 330 Bit Score: 258.75 E-value: 6.34e-77

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  488 NLPILPTTTIGSFPQTMELRKVRREYKAKKVSEDDYIKAIKEEISKVVKLQEEFDIDVLVHGEPERNDMVEYFGEQLSGF 567
Cdd:PRK04326     5 KLPFLPTTVVGSYPKPKWLREAIRLHKAGKISEEDLHEAFDDAVRLVVKDHERAGVDIPVDGEMRREEMVEYFAERIEGF 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  568 AFsaNGWVQSYGSRCVKPPIIYGDVSRPKSMTVFWSALAQSMT-SRPMKGMLTGPVTILNWSFVRNDQPRFETCYQIALA 646
Cdd:PRK04326    85 KF--YGPVRVWGNNYFRKPSVVGKIEYKEPMLVDEFEFAKSVTyTRPVKVPITGPYTIAEWSFNEYYKDKEELVFDLAKV 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  647 IKDEVEDLEKNGITVIQIDEAAlregLPLRKSEQAfyldWAVHSFRITNCGVQdtTQIHTHMCYSNFNDIIHSIIDMDAD 726
Cdd:PRK04326   163 INEEIKNLVEAGAKYIQIDEPA----LATHPEDVE----IAVEALNRIVKGIN--AKLGLHVCYGDYSRIAPYILEFPVD 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  727 VITIENSRSDEKLLSVFREgVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNILWVNPDCGLKTRKYTEVKPA 806
Cdd:PRK04326   233 QFDLEFANGNYKLLDLLKE-YGFDKELGLGVIDVHSARVESVEEIKEAIKKGLEYVPPEKLYINPDCGLKLLPREIAYQK 311

                          330
                   ....*....|....*
gi 1939203063  807 LKNMVDAAKLLRTQL 821
Cdd:PRK04326   312 LVNMVKATREVREEL 326

CIMS_like

cd03310

CIMS - Cobalamine-independent methonine synthase, or MetE. Many members have been ...

493-816

1.07e-38

CIMS - Cobalamine-independent methonine synthase, or MetE. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers both the N-and C-terminal barrel, and some single-barrel sequences, mostly from Archaea. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Side chains from both barrels contribute to the binding of the folate substrate.

Pssm-ID: 239426 [Multi-domain] Cd Length: 321 Bit Score: 147.96 E-value: 1.07e-38

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  493 PTTTIGSFPQTMELRKVRREYKAKKVSEDDYIKAIKEEISKVVKLQEEFDIDVLVHGEPERnDMVEYFGEQLSGfafSAN 572
Cdd:cd03310      1 LATGIGSYPLPDGVTKEWSILEKGAIEPEWPEEALFTALGSFFELQLEAGVEVPTYGQLGD-DMIGRFLEVLVD---LET 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  573 GWVQSYGSRCVKPPIIYGDVSRPKSMTVFWSALAQSMTSRPMKGMLTGPVTILNWSFVRNDQP--RFETCYQIALAIKDE 650
Cdd:cd03310     77 GTRFFDNNFFYRPPEAKIEAFLPLELDYLEEVAEAYKEALKVKVVVTGPLTLALLAFLPNGEPdaYEDLAKSLAEFLREQ 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  651 VEDLEKNGITVIQIDEAALREGLPLRKSEQAfYLDWAvhsfrITNCGVQDTTQIHTHMCYsnfNDIIHSIIDMDADVITI 730
Cdd:cd03310    157 VKELKNRGIVVVQIDEPSLGAVGAGAFEDLE-IVDAA-----LEEVSLKSGGDVEVHLCA---PLDYEALLELGVDVIGF 227

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  731 ENSRSD-------EKLLSVFREGVKYGAGIGPGVYDIHSPR--IPSTEEIADRINKMLAVLETnILWVNPDCGLKTRKYT 801
Cdd:cd03310    228 DAAALPskyledlKKLLRIGVRTLILGLVVTDNEAKGRNAWkeIERLEKLVRRLEEPGEVLDE-ILYLTPDCGLAFLPPQ 306

                          330
                   ....*....|....*
gi 1939203063  802 EVKPALKNMVDAAKL 816
Cdd:cd03310    307 EARRKLALLAEAARE 321

PRK00957

methionine synthase; Provisional

491-818

1.67e-34

methionine synthase; Provisional

Pssm-ID: 234875 [Multi-domain] Cd Length: 305 Bit Score: 135.12 E-value: 1.67e-34

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  491 ILPTTTIGSFPQTMELRKVRREYKAKKVS-EDDYIKAIKEeiskVVKLQEEFDIDVLVHGEPeRNDMVEYFGEQLSGFAf 569
Cdd:PRK00957     1 IMITTVVGSYPVVKGEPETLKDKIKGFFGlYDPYKPAIEE----AVADQVKAGIDIISDGQV-RGDMVEIFASNMPGFD- 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  570 sangwvqsyGSRCVkppiiyGDVSRP-KSMTVFWSALAQSMT-----SRPMKGMLTGPVTILNWSFVRN---DQPRFETC 640
Cdd:PRK00957    75 ---------GKRVI------GRVEPPaKPITLKDLKYAKKVAkkkdpNKGVKGIITGPSTLAYSLRVEPfysDNKDEELI 139

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  641 YQIALAIKDEVEDLEKNGITVIQIDEAALREGLP-LRKSEQAfyLDWAVHSFRITNCgvqdttqihTHMCySNFNDIIHS 719
Cdd:PRK00957   140 YDLARALRKEAEALEKAGVAMIQIDEPILSTGAYdLEVAKKA--IDIITKGLNVPVA---------MHVC-GDVSNIIDD 207

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  720 IIDMDADVITIENSRSDEKlLSVFREGVKYGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNILWVNPDCGLKTRK 799
Cdd:PRK00957   208 LLKFNVDILDHEFASNKKN-LEILEEKDLIGKKIGFGCVDTKSKSVESVDEIKALIEEGIEILGAENILIDPDCGMRMLP 286

                          330
                   ....*....|....*....
gi 1939203063  800 YTEVKPALKNMVDAAKLLR 818
Cdd:PRK00957   287 RDVAFEKLKNMVEAAREIR 305

URO-D_CIMS_like

cd00465

The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen ...

493-815

2.61e-30

The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases. Despite their sequence similarities, members of this family have clearly different functions. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway. The methyltransferases represented here are important for ability of methanogenic organisms to use other compounds than carbon dioxide for reduction to methane, and methionine synthases transfer a methyl group from a folate cofactor to L-homocysteine in a reaction requiring zinc.

Pssm-ID: 238261 [Multi-domain] Cd Length: 306 Bit Score: 122.99 E-value: 2.61e-30

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  493 PTTTIGSFPQTMELRKvrreykaKKVSEDDYIKAIKEEISKVVkLQEEFDIDVLVHGEpernDMVEYFGEQLsgfafsaN 572
Cdd:cd00465      1 PVQCEGQTGIMEASET-------MAISEEPGETSKAEWGITLV-EPEEIPLDVIPVHE----DDVLKVAQAL-------G 61

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  573 GWVQSYGSRCVKPPIIYGDVSRPKSMTVFWSA-LAQSMTSRPMKGMLTGPVTILNWSFVRND---------QPRFETCYQ 642
Cdd:cd00465     62 EWAFRYYSQAPSVPEIDEEEDPFREAPALEHItAVRSLEEFPTAGAAGGPFTFTHHSMSMGDalmalyerpEAMHELIEY 141

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  643 IALAIKDEVEDLEKNGITVIQIDEAALREGLPLRKSEqaFYLDWAVHSFR-ITNCGVQDTTQIHTHMCYSNfNDIIHSII 721
Cdd:cd00465    142 LTEFILEYAKTLIEAGAKALQIHEPAFSQINSFLGPK--MFKKFALPAYKkVAEYKAAGEVPIVHHSCYDA-ADLLEEMI 218

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  722 DMDADVITIENSRSDEKLLsvfREGVKYGAGIGPGVYDIHSPRipSTEEIADRINKMLAVLETNIlWVNPDCGLKTRKYT 801
Cdd:cd00465    219 QLGVDVISFDMTVNEPKEA---IEKVGEKKTLVGGVDPGYLPA--TDEECIAKVEELVERLGPHY-IINPDCGLGPDSDY 292

                          330
                   ....*....|....
gi 1939203063  802 EvKPALKNMVDAAK 815
Cdd:cd00465    293 K-PEHLRAVVQLVD 305

DSRM_AtDRB-like_rpt2

cd19908

second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...

1369-1435

2.14e-27

Pssm-ID: 380737 [Multi-domain] Cd Length: 69 Bit Score: 106.41 E-value: 2.14e-27

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1939203063 1369 YKNLLQELAQREGCGLPTYSTNKSGEAHIPTFTSTVEIKGEIFTGQGAKTKKQAEMSAAKTAYTALK 1435
Cdd:cd19908      3 YKNLLQEYAQKAGLPLPLYTTVRSGPGHVPTFTCTVEIAGITFTGEAAKTKKQAEKSAARTAWSSIK 69

PRK01207

methionine synthase; Provisional

489-821

5.87e-23

methionine synthase; Provisional

Pssm-ID: 100814 Cd Length: 343 Bit Score: 102.31 E-value: 5.87e-23

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  489 LPILPTTTIGSF--PQ--TMELRKVRREYKAKKVSEddyiKAIKEeiskVVKLQEEFDID-VLVHGEPERNDMVEYFGEQ 563
Cdd:PRK01207     1 MAALITQEIGSFrkPEylSREFHKIEGTDKFYELAE----RATLE----TLDVFENAGLDnIGIGGEMFRWEMYEHPAER 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  564 LSGFAFSanGWVQSYGSRCVKPPIIYGDVSRPKSMTVFWSALAQSMTSRPMKGMLTGPVTILNWSFVRNDQPRFETCYQI 643
Cdd:PRK01207    73 IKGIIFY--GMVRSFDNRYYRKGSIIDRMERRSSFHLDEVEFVADNTKKPIKVPITGPYTMMDWSFNDFYRDRYDLAMEF 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  644 ALAIKDEVEDLEK------NGITV-IQIDEAAlreglplrKSEQAFYLDWAVHSFRITNCGVQDttQIHTHMCYSNFNDI 716
Cdd:PRK01207   151 ARIINEELKDIKSawdrksPGRKLeIQIDEPA--------TTTHPDEMDIVVDSINKSVYGIDN--EFSIHVCYSSDYRL 220

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  717 IHSII-DMDADVITIENSRSDE----------------KLLSVFREGVKYGAGIGPGVYDIHSPRIPSTEEIADRINKML 779
Cdd:PRK01207   221 LYDRIpELNIDGYNLEYSNRDTlepgtsdekrpgfqdlKYFAEHNESLQRKKFIGLGVTDVHIDYVEPVKLIEDRIRYAL 300

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|...
gi 1939203063  780 AVL-ETNILWVNPDCGLKTRKYTEVKPALKNMVDAAKLLRTQL 821
Cdd:PRK01207   301 KIIkDPELVRLNPDCGLRTRSREIGEQKLRNMVAAKNNILKEL 343

DSRM_AtDRB-like_rpt1

first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...

1292-1357

1.08e-21

Pssm-ID: 380736 [Multi-domain] Cd Length: 69 Bit Score: 90.23 E-value: 1.08e-21

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1939203063 1292 KSQLQTYAQKRNFALPVYSCERVGPPHASRFKCKVTVNGHTFESLEYFPILNKAENAAAKAALMSL 1357
Cdd:cd19907      3 KSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNSL 68

DSRM_AtDRB-like

cd19878

double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...

1369-1435

1.59e-21

double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

Pssm-ID: 380707 [Multi-domain] Cd Length: 67 Bit Score: 89.50 E-value: 1.59e-21

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1939203063 1369 YKNLLQELAQREGCGLPTYSTNKSGEAHIPTFTSTVEIKGEIFTGQGAKTKKQAEMSAAKTAYTALK 1435
Cdd:cd19878      1 YKNLLQEYAQKKKIPLPKYESAKSGPSHQPTFVSTVIVLGVRFSSEGAKNKKQAEQSAAKVALKELG 67

PRK09121

methionine synthase;

490-822

1.82e-19

methionine synthase;

Pssm-ID: 181659 Cd Length: 339 Bit Score: 91.67 E-value: 1.82e-19

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  490 PILPTTTIGSFPQTMELRKVRREYKAKKVSEDDYIKAIKEEISKVVKLQEEFDIDVLVHGEPERNDMVEYFGEQLSGFAF 569
Cdd:PRK09121     1 TLLPTSTAGSLPKPSWLAEPETLWSPWKLQGEELIEGKQDALRLSLQEQEDAGIDIVSDGEQTRQHFVTTFIEHLSGVDF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  570 SANGWVQSYGSRCVKPPIIYGDVSRPKSMTVFWSALAQSMTSRPMKGMLTGPVTILNWSFVRNDQPRFETCYQIALAIKD 649
Cdd:PRK09121    81 EKRETVRIRDRYDASVPTVVGAVSRQKPVFVEDAKFLRQQTTQPIKWALPGPMTMIDTLYDDHYKSREKLAWEFAKILNQ 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  650 EVEDLEKNGITVIQIDEAALReglpLRKSEQAfylDWAVHSFRITNCGVQDTTQIhtHMCYS------------------ 711
Cdd:PRK09121   161 EAKELEAAGVDIIQFDEPAFN----VFFDEVN---DWGVAALERAIEGLKCETAV--HICYGygikantdwkktlgsewr 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  712 NFNDIIHSIIDMDADVITIE--NSRSDEKLLSVFRegvkyGAGIGPGVYDIHSPRIPSTEEIADRINKMLAVLETNILWV 789
Cdd:PRK09121   232 QYEEAFPKLQKSNIDIISLEchNSRVPMDLLELIR-----GKKVMVGAIDVASDTIETPEEVADTLRKALQFVDADKLYP 306

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1939203063  790 NPDCGLK--TRKYTEVKpaLKNMVDAAKLLRTQLA 822
Cdd:PRK09121   307 CTNCGMAplSRDVARGK--LNALSAGAEIVRRELA 339

DSRM_AtDRB-like_rpt1

first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...

857-920

3.42e-18

Pssm-ID: 380736 [Multi-domain] Cd Length: 69 Bit Score: 80.21 E-value: 3.42e-18

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1939203063  857 MYKSKLQELCQQRSWELPTYESSRQGQAHNPRFLATVTVNDISFHSPSPSNTSKKAQNDAAKLA 920
Cdd:cd19907      1 MYKSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVA 64

Rnc

dsRNA-specific ribonuclease [Transcription];

1369-1438

1.65e-16

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 80.53 E-value: 1.65e-16

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1939203063 1369 YKNLLQELAQREGCGLPTYS-TNKSGEAHIPTFTSTVEIKGEIF-TGQGaKTKKQAEMSAAKTAYTALKQRN 1438
Cdd:COG0571    159 YKTALQEWLQARGLPLPEYEvVEEEGPDHAKTFTVEVLVGGKVLgEGTG-RSKKEAEQAAAKAALEKLGKKE 229

DSRM_AtDRB-like_rpt1

first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...

1369-1434

3.41e-16

Pssm-ID: 380736 [Multi-domain] Cd Length: 69 Bit Score: 74.43 E-value: 3.41e-16

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1939203063 1369 YKNLLQELAQREGCGLPTYSTNKSGEAHIPTFTSTVEIKGEIF-TGQGAKTKKQAEMSAAKTAYTAL 1434
Cdd:cd19907      2 YKSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFeSPPGFPTLKAAEHSAAEVALNSL 68

DSRM_RNAse_III_family

cd10845

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...

1369-1434

1.10e-15

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

Pssm-ID: 380682 [Multi-domain] Cd Length: 69 Bit Score: 72.91 E-value: 1.10e-15

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1939203063 1369 YKNLLQELAQREGCGLPTYS-TNKSGEAHIPTFTSTVEIKGEIF-TGQGaKTKKQAEMSAAKTAYTAL 1434
Cdd:cd10845      3 YKTALQEYLQKRGLPLPEYElVEEEGPDHNKTFTVEVKVNGKVIgEGTG-RSKKEAEQAAAKAALEKL 69

dsrm

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...

858-923

5.12e-14

Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 68.41 E-value: 5.12e-14

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1939203063  858 YKSKLQELCQQRSWELPTYESSRQGQAHNPRFLATVTVNDISFHSPSPSNTsKKAQNDAAKLAYEH 923
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSK-KEAEQLAAEKALEK 65

DSRM

Double-stranded RNA binding motif;

1369-1435

6.90e-14

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 68.06 E-value: 6.90e-14

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1939203063  1369 YKNLLQELAQREGCgLPTYSTNK-SGEAHIPTFTSTVEIKGEI-FTGQGaKTKKQAEMSAAKTAYTALK 1435
Cdd:smart00358    1 PKSLLQELAQKRKL-PPEYELVKeEGPDHAPRFTVTVKVGGKRtGEGEG-SSKKEAKQRAAEAALRSLK 67

dsrm

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...

1369-1434

1.01e-13

Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 67.26 E-value: 1.01e-13

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1939203063 1369 YKNLLQELAQREGCGLPTYSTNKSGEAHIPTFTSTVEIKGEIFTGQGAKTKKQAEMSAAKTAYTAL 1434
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66

DSRM_AtDRB-like

cd19878

double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...

858-920

1.24e-13

Pssm-ID: 380707 [Multi-domain] Cd Length: 67 Bit Score: 67.16 E-value: 1.24e-13

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1939203063  858 YKSKLQELCQQRSWELPTYESSRQGQAHNPRFLATVTVNDISFHSPSPSNtSKKAQNDAAKLA 920
Cdd:cd19878      1 YKNLLQEYAQKKKIPLPKYESAKSGPSHQPTFVSTVIVLGVRFSSEGAKN-KKQAEQSAAKVA 62

DSRM_SF

cd00048

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...

863-921

1.61e-13

Pssm-ID: 380679 [Multi-domain] Cd Length: 57 Bit Score: 66.54 E-value: 1.61e-13

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1939203063  863 QELCQQRSWELPTYESSRQGQAHNPRFLATVTVNDISFHSPSPSntSKKAQNDAAKLAY 921
Cdd:cd00048      1 NELCQKNKWPPPEYETVEEGGPHNPRFTCTVTVNGQTFEGEGKS--KKEAKQAAAEKAL 57

DSRM_SF

cd00048

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...

1374-1431

1.69e-13

Pssm-ID: 380679 [Multi-domain] Cd Length: 57 Bit Score: 66.54 E-value: 1.69e-13

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1939203063 1374 QELAQREGCGLPTYSTNKSGEAHIPTFTSTVEIKGEIFTGQGaKTKKQAEMSAAKTAY 1431
Cdd:cd00048      1 NELCQKNKWPPPEYETVEEGGPHNPRFTCTVTVNGQTFEGEG-KSKKEAKQAAAEKAL 57

RNaseIII

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...

1369-1434

1.70e-13

Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 71.47 E-value: 1.70e-13

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1939203063 1369 YKNLLQELAQREGCGLPTYSTNK-SGEAHIPTFTSTVEIKGEIF-TGQGaKTKKQAEMSAAKTAYTAL 1434
Cdd:TIGR02191  154 YKTALQEWAQARGKPLPEYRLIKeEGPDHDKEFTVEVSVNGEPYgEGKG-KSKKEAEQNAAKAALEKL 220

DSRM

Double-stranded RNA binding motif;

858-922

7.62e-13

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 64.98 E-value: 7.62e-13

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1939203063   858 YKSKLQELCQQRSWElPTYES-SRQGQAHNPRFLATVTVNDISFhsPSPSNTSKK-AQNDAAKLAYE 922
Cdd:smart00358    1 PKSLLQELAQKRKLP-PEYELvKEEGPDHAPRFTVTVKVGGKRT--GEGEGSSKKeAKQRAAEAALR 64

DSRM_RNAse_III_family

cd10845

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...

858-924

5.96e-12

Pssm-ID: 380682 [Multi-domain] Cd Length: 69 Bit Score: 62.51 E-value: 5.96e-12

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1939203063  858 YKSKLQELCQQRSWELPTYES-SRQGQAHNPRFLATVTVNDIsFHSPSPSNTSKKAQNDAAKLAYEHF 924
Cdd:cd10845      3 YKTALQEYLQKRGLPLPEYELvEEEGPDHNKTFTVEVKVNGK-VIGEGTGRSKKEAEQAAAKAALEKL 69

PRK08575

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional

65-357

1.96e-11

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional

Pssm-ID: 236299 [Multi-domain] Cd Length: 326 Bit Score: 67.45 E-value: 1.96e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063   65 IVG-YPRmgPKRELKfALESFWDGKSSAQDLQKVAADLRESIWKQMSDAGIKYIpsntfsyydqmldTTAMlgavpprYG 143
Cdd:PRK08575     7 LVGsYPR--PVKLAK-VISWYNSGKISKEKLEKAINENTKRFFELAKDVGIDYT-------------TDGL-------FR 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  144 WNggEIgFDVYFSMARGnasVPAMEMTKWFDTNYHF----IVPELGPEVNFSYA-SHKAVTEYKEAKALGVDTVPVLVGP 218
Cdd:PRK08575    64 WD--DI-FDPTISFISG---VEKGGLQRFYDNNFYYrqpvIKEKINLKEENPYLqWLESAREIKEEVSLESKLKAVLPGP 137

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  219 VSYLLLSkpakgvEKTFslLSLLGKILPIYKEVISEL-KE--AGASWIQFDEPTLVM-DLESHKLEAFTEAYSELESTLS 294
Cdd:PRK08575   138 LTYAVLS------DNEY--YKNLIELMEDYASVVNSLiKElsSVVDAVEIHEPSIFAkGIKRDTLEKLPEVYKTMAKNVN 209

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1939203063  295 GLNVLIeTYFADIPAQQYKTLTSLKgVTAFGFDLIRGTKTLDLIKGEFPeGKHLFAGVVDGRN 357
Cdd:PRK08575   210 IEKHLM-TYFEINNLKRLDILFSLP-VTYFGIDVIENLKKLGRVYTYLK-GRKVYLGILNARN 269

Rnc

dsRNA-specific ribonuclease [Transcription];

858-922

2.24e-11

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 65.51 E-value: 2.24e-11

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1939203063  858 YKSKLQELCQQRSWELPTYE-SSRQGQAHNPRFLATVTVNDISFHspSPSNTSKK-AQNDAAKLAYE 922
Cdd:COG0571    159 YKTALQEWLQARGLPLPEYEvVEEEGPDHAKTFTVEVLVGGKVLG--EGTGRSKKeAEQAAAKAALE 223

DSRM_AtDRB-like

cd19878

double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...

1292-1339

4.70e-11

Pssm-ID: 380707 [Multi-domain] Cd Length: 67 Bit Score: 59.84 E-value: 4.70e-11

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1939203063 1292 KSQLQTYAQKRNFALPVYSCERVGPPHASRFKCKVTVNGHTFESLEYF 1339
Cdd:cd19878      2 KNLLQEYAQKKKIPLPKYESAKSGPSHQPTFVSTVIVLGVRFSSEGAK 49

CIMS_like

cd03310

CIMS - Cobalamine-independent methonine synthase, or MetE. Many members have been ...

75-390

6.84e-11

Pssm-ID: 239426 [Multi-domain] Cd Length: 321 Bit Score: 65.53 E-value: 6.84e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063   75 RELKFALESFWDGKSSAQDLQKVAADLRESIWKQMSDAGIKYIPSNTFsyYDQMLD-TTAMLGAVPPRygwnggeigfdv 153
Cdd:cd03310     12 DGVTKEWSILEKGAIEPEWPEEALFTALGSFFELQLEAGVEVPTYGQL--GDDMIGrFLEVLVDLETG------------ 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  154 yfsmargnasvpamemTKWFDTNYHFIVPELGPEVnFSYASHKAVTEYKEAKALGVDTVPVLVGPVSYLLLSKPAKGveK 233
Cdd:cd03310     78 ----------------TRFFDNNFFYRPPEAKIEA-FLPLELDYLEEVAEAYKEALKVKVVVTGPLTLALLAFLPNG--E 138

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  234 TFSLLSLLGKILPIYKEVISELKEAGASWIQFDEPTLVMDLESHKLE-AFTEAYSELESTLSGLNVLIETYFADIpaqqY 312
Cdd:cd03310    139 PDAYEDLAKSLAEFLREQVKELKNRGIVVVQIDEPSLGAVGAGAFEDlEIVDAALEEVSLKSGGDVEVHLCAPLD----Y 214

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939203063  313 KTLTSLkGVTAFGFDLIRGTKTLDLIKGEFPE--GKHLFAGVVDGRNIWANDLAASL-STLEALESIVGKDKLV------ 383
Cdd:cd03310    215 EALLEL-GVDVIGFDAAALPSKYLEDLKKLLRigVRTLILGLVVTDNEAKGRNAWKEiERLEKLVRRLEEPGEVldeily 293


                   ....*..
gi 1939203063  384 VSTSCSL 390
Cdd:cd03310    294 LTPDCGL 300

DSRM_SF

cd00048

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...

1296-1335

3.58e-09

Pssm-ID: 380679 [Multi-domain] Cd Length: 57 Bit Score: 54.21 E-value: 3.58e-09

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1939203063 1296 QTYAQKRNFALPVYSCERVGPPHASRFKCKVTVNGHTFES 1335
Cdd:cd00048      1 NELCQKNKWPPPEYETVEEGGPHNPRFTCTVTVNGQTFEG 40

RNaseIII

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...

858-922

3.69e-09

Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 58.75 E-value: 3.69e-09

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1939203063  858 YKSKLQELCQQRSWELPTYE-SSRQGQAHNPRFLATVTVNDISFhsPSPSNTSKK-AQNDAAKLAYE 922
Cdd:TIGR02191  154 YKTALQEWAQARGKPLPEYRlIKEEGPDHDKEFTVEVSVNGEPY--GEGKGKSKKeAEQNAAKAALE 218

DSRM_SON-like

cd19870

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...

860-920

1.62e-08

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

Pssm-ID: 380699 Cd Length: 75 Bit Score: 53.05 E-value: 1.62e-08

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1939203063  860 SKLQELCQQRSWELPTYES-SRQGQAHNPRFLATVTVNDISFHSPSPSNTSKKAQNDAAKLA 920
Cdd:cd19870      6 SALMELCNKRKWGPPEFRLvEESGPPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAATVA 67

dsrm

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...

1291-1335

4.44e-08

Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 51.46 E-value: 4.44e-08

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1939203063 1291 SKSQLQTYAQKRNFALPVYSCERVGPPHASRFKCKVTVNGHTFES 1335
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGS 45

DSRM_RNAse_III_family

cd10845

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...

1291-1331

5.24e-08

Pssm-ID: 380682 [Multi-domain] Cd Length: 69 Bit Score: 51.34 E-value: 5.24e-08

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1939203063 1291 SKSQLQTYAQKRNFALPVYSC-ERVGPPHASRFKCKVTVNGH 1331
Cdd:cd10845      3 YKTALQEYLQKRGLPLPEYELvEEEGPDHNKTFTVEVKVNGK 44

DSRM

Double-stranded RNA binding motif;

1292-1333

1.98e-07

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 49.57 E-value: 1.98e-07

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 1939203063  1292 KSQLQTYAQKRNFaLPVYSC-ERVGPPHASRFKCKVTVNGHTF 1333
Cdd:smart00358    2 KSLLQELAQKRKL-PPEYELvKEEGPDHAPRFTVTVKVGGKRT 43

DSRM_STRBP_RED-like_rpt1

cd19865

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...

1373-1430

2.76e-07

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA, but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

Pssm-ID: 380694 Cd Length: 63 Bit Score: 48.88 E-value: 2.76e-07

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1939203063 1373 LQELAQregcGLPTYSTNKSGEAHIPTFTSTVEIKGEIFTGQGaKTKKQAEMSAAKTA 1430
Cdd:cd19865      7 LNELRP----GLQYKLTSQTGPVHAPVFTMSVEVNGQTFEGTG-RSKKKAKLEAAEKA 59

DSRM_AtDRB-like_rpt2

cd19908

second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...

857-921

4.13e-07

Pssm-ID: 380737 [Multi-domain] Cd Length: 69 Bit Score: 48.63 E-value: 4.13e-07

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1939203063  857 MYKSKLQELCQQRSWELPTYESSRQGQAHNPRFLATVTVNDISFhSPSPSNTSKKAQNDAAKLAY 921
Cdd:cd19908      2 LYKNLLQEYAQKAGLPLPLYTTVRSGPGHVPTFTCTVEIAGITF-TGEAAKTKKQAEKSAARTAW 65

DSRM_DGCR8_rpt1

cd19867

first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...

1369-1434

4.30e-07

first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins; DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

Pssm-ID: 380696 Cd Length: 74 Bit Score: 48.87 E-value: 4.30e-07

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1939203063 1369 YKNLLQELAQREGCGLPTYSTNKSGEAHIPtFTSTVEIKGEIFTGQGAKTKKQAEMSAAKTAYTAL 1434
Cdd:cd19867      8 PVCILHEYCQRVLKVQPEYNFTETENAATP-FSAEVFINGVEYGSGEASSKKLAKQKAARATLEIL 72

PHA03103

double-strand RNA-binding protein; Provisional

862-920

1.49e-06

double-strand RNA-binding protein; Provisional

Pssm-ID: 222987 [Multi-domain] Cd Length: 183 Bit Score: 50.53 E-value: 1.49e-06

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1939203063  862 LQELCQ--QRSWelpTYESSRQGQAHNPRFLATVTVNDISFhSPSPSNTSKKAQNDAAKLA 920
Cdd:PHA03103   115 INEYCQitSRDW---SINITSSGPSHSPTFTASVIISGIKF-KPAIGSTKKEAKNNAAKLA 171

DSRM_PRKRA-like_rpt1

cd19862

first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...

860-927

1.81e-06

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

Pssm-ID: 380691 [Multi-domain] Cd Length: 70 Bit Score: 46.87 E-value: 1.81e-06

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1939203063  860 SKLQELCQQRSWElPTYE-SSRQGQAHNPRFLATVTVNDISFHSPSPSNtsKKAQNDAAKLAYEHFSNS 927
Cdd:cd19862      5 SVLQELCAKRGIT-PKYElISSEGAVHEPTFTFRVTVGDITATGSGTSK--KKAKHAAAENALEQLKGS 70

DSRM_DUS2L

cd19871

double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...

1370-1434

3.29e-06

double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) and similar proteins; DUS2L (also known as dihydrouridine synthase 2 (DUS2), up-regulated in lung cancer protein 8 (URLC8), or tRNA-dihydrouridine synthase 2-like) catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. It negatively regulates the activation of EIF2AK2/PKR. DUS2L contains an N-terminal FMN-binding domain and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.

Pssm-ID: 380700 Cd Length: 68 Bit Score: 46.11 E-value: 3.29e-06

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1939203063 1370 KNLLQELAQREGCGLPTYSTNKSGEAHipTFTSTVEIKGEIFT-GQGAKTKKQAEMSAAKTAYTAL 1434
Cdd:cd19871      3 KMILNEWCRKNKLPQPVYETVQRPSDR--LFQSVVTVDGKKYTsSLWEKSKKLAEQAAAIVCLRAL 66

Rnc