CATH Domain: 2nyiA01 XML data for domain: 2nyiA01

Molscript image for 2nyiA01
2nyiA01
PDB coordinates for domain 2nyiA01

PDB 2nyi, Chain A, Domain 1

CATH CodeLevel DescriptionLinks
3 Alpha Beta
3.30 2-Layer Sandwich
3.30.70 Alpha-Beta Plaits
3.30.70.260 Gene3D
3.30.70.260.4
3.30.70.260.4.1
3.30.70.260.4.1.1
3.30.70.260.4.1.1.1
3.30.70.260.4.1.1.1.1

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Segment boundaries for domain 2nyiA01

Chopping figure for domain 2nyiA01
DomainStart PDB ResidueStop PDB Residue
2nyiA01 2 82
2nyiA02 87 176

Structural Neighbourhood (60 entries)

There are 60 matching structural neighberhood comparisons for CATH ID 3.30.70.260.4.1.1.1.1 (SIMAX score < 5)

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Displaying entries 1 to 60 (page 1 of 1)
Match Depth Match SSAP score Match Keywords Match Superfamily Length Sequence Id Overlap RMSD SIMAX
2nyiA02 88.85 3.30.70.260 89 20 85 1.70 1.99
1u8sA01 88.18 Glycine cleavage system transcriptional repressor, putativeGlycine cleavage system transcriptional repressorVibrio cholerae 3.30.70.260 86 22 89 2.30 2.57
1zpvB00 87.67 ACT domain-containing proteinUPF0237 protein SP_0238Streptococcus pneumoniae 3.30.70.260 81 19 91 2.15 2.35
1sc6A03 87.35 Glycine, serine and threonine metabolismMetabolic pathwaysD-3-phosphoglycerate dehydrogenase [EC:1.1.1.95]D-3-phosphoglycerate dehydrogenaseEscherichia coli K-12 3.30.70.260 79 5 89 2.96 3.29
1u8sA02 87.18 Glycine cleavage system transcriptional repressor, putativeGlycine cleavage system transcriptional repressorVibrio cholerae 3.30.70.260 84 12 90 2.25 2.49
1y7pB01 86.85 Archaeoglobus fulgidusUncharacterized protein AF_1403 3.30.70.260 80 9 88 2.04 2.30
1u0sA00 86.36 Thermotoga maritimaBacterial chemotaxisTwo-component systemTwo-component system, chemotaxis family, sensor kinase CheA [EC:2.7.13.3]Protein binding 3.30.70.1110 86 11 86 2.45 2.85
2nzcA00 85.59 Thermotoga maritimaPutative uncharacterized protein 3.30.70.1150 77 11 96 2.76 2.87
2qmwA03 84.62 Phenylalanine, tyrosine and tryptophan biosynthesisMetabolic pathwaysPrephenate dehydratase [EC:4.2.1.51]Similar to chorismate mutaseStaphylococcus aureus subsp. aureus Mu50 3.30.70.260 73 13 88 2.69 3.05
2qmxA03 82.30 Prephenate dehydratase [EC:4.2.1.51]Phenylalanine, tyrosine and tryptophan biosynthesisChlorobaculum tepidumMetabolic pathwaysPrephenate dehydratase 3.30.70.260 90 7 82 2.83 3.44
1vr6A01 81.47 Phenylalanine, tyrosine and tryptophan biosynthesisMetabolic pathwaysThermotoga maritima3-deoxy-7-phosphoheptulonate synthase [EC:2.5.1.54]Phospho-2-dehydro-3-deoxyheptonate aldolase 3.30.70.1140 75 6 88 3.82 4.33
1eayD00 80.83 Bacterial chemotaxisTwo-component systemTwo-component system, chemotaxis family, sensor kinase CheA [EC:2.7.13.3]Escherichia coli K-12Chemotaxis protein cheA 3.30.70.400 69 11 89 3.28 3.66
2hiyB01 80.62 Streptococcus pneumoniaePutative uncharacterized protein 3.30.70.1280 87 11 82 3.03 3.66
1i1gA02 80.49 Pyrococcus furiosusHTH-type transcriptional regulator lrpALrp/AsnC family transcriptional regulator, regulator for asnA, asnC and gidA 3.30.70.920 77 5 90 3.83 4.21
1kn6A00 80.09 Mus musculusPeptide hormone processingSerine-type endopeptidase activityNeuroendocrine convertase 1Proprotein convertase subtilisin/kexin type 1 [EC:3.4.21.93] 3.30.70.850 73 5 87 3.36 3.86
1s99A02 79.98 Bacillus subtilisPutative HMP/thiamine-binding protein ykoF 3.30.70.930 81 7 85 3.35 3.93
1q5yD00 79.97 CopG family transcriptional regulator, nickel-responsive regulatorNickel-responsive regulatorProtein bindingEscherichia coli K-12 3.30.70.1150 80 2 90 4.07 4.52
2w25A02 79.61 Lrp/AsnC family transcriptional regulator, leucine-responsive regulatory proteinLeucine-responsive regulatory proteinMycobacterium tuberculosis 3.30.70.920 81 10 86 3.51 4.06
1earA02 79.44 Sporosarcina pasteuriiUrease accessory protein ureE 3.30.70.790 69 7 81 3.98 4.86
1fjeB01 79.36 NucleolinMesocricetus auratus 3.30.70.330 81 10 92 4.52 4.88
1harA02 79.31 Human immunodeficiency virus type 1 BH10Gag-Pol polyprotein 3.30.70.270 69 10 76 3.33 4.35
2hfvA01 79.00 Rhodopseudomonas palustrisPutative uncharacterized protein 3.30.70.790 77 10 90 4.17 4.59
1xmbA02 78.95 Auxin metabolic processArabidopsis thalianaIAA-Ala conjugate hydrolase activityIAA-amino acid hydrolase ILR1-like 2 3.30.70.360 101 10 72 2.90 4.01
1no8A00 78.95 THO complex subunit 4Mus musculusSpliceosomeSingle-stranded DNA bindingRNA binding 3.30.70.330 78 11 85 3.41 3.97
1konA03 78.77 UPF0082 protein yebCEscherichia coli K-12 3.30.70.980 75 14 87 3.42 3.93
1gmuA01 78.65 Klebsiella aerogenesUrease accessory protein ureE 3.30.70.790 67 11 77 3.30 4.24
1s99A01 78.55 Bacillus subtilisPutative HMP/thiamine-binding protein ykoF 3.30.70.930 77 7 90 3.05 3.35
1lfpA03 78.52 UPF0082 protein aq_1575Aquifex aeolicus 3.30.70.980 73 5 81 3.77 4.61
1u7lA01 78.47 V-type H+-transporting ATPase subunit C [EC:3.6.3.14]Oxidative phosphorylationVacuolar acidificationProtein bindingVacuolar proton-transporting V-type ATPase, V1 domain 3.30.70.1180 91 12 78 3.30 4.23
1in0A01 78.32 Hypothetical proteinHaemophilus influenzaeUPF0234 protein HI_1034 3.30.70.860 70 11 89 3.79 4.23
1l3kA01 78.14 Heterogeneous nuclear ribonucleoprotein A1NucleolusProtein bindingCytoplasmSpliceosome 3.30.70.330 84 6 88 4.30 4.88
2do0A01 78.10 Protein domain specific bindingIntegral to plasma membraneParaspecklesAlternative nuclear mRNA splicing, via spliceosomeHeterogeneous nuclear ribonucleoprotein M 3.30.70.330 76 7 92 4.27 4.63
2gx8C02 77.97 Bacillus cereus ATCC 14579NIF3-related protein 3.30.70.830 102 11 70 3.07 4.35
1fxlA02 77.95 AU-rich element bindingELAV like protein 2/3/4MRNA processingHomo sapiensELAV-like protein 4 3.30.70.330 77 5 87 4.21 4.84
2epiB00 77.90 Methanocaldococcus jannaschiiUPF0045 protein MJ1052 3.30.70.930 96 10 72 2.99 4.10
2iboA00 77.61 Streptococcus pneumoniaePutative uncharacterized protein 3.30.70.930 87 9 79 3.45 4.35
2rb7A02 77.46 Peptidase, M20/M25/M40 familyDesulfovibrio desulfuricans subsp. desulfuricans str. G20 3.30.70.360 98 5 74 3.20 4.30
1mw7A03 77.31 Helicobacter pyloriUPF0082 protein HP_0162 3.30.70.980 75 10 90 3.74 4.11
1cvjA01 77.18 Poly(A) RNA bindingTranslation activator activityProtein C-terminus bindingMRNA polyadenylationPolyadenylate-binding protein 1 3.30.70.330 77 11 90 4.04 4.44
1j4wA01 76.95 Transcription from RNA polymerase II promoterFar upstream element-binding proteinSequence-specific DNA binding transcription factor activityFar upstream element-binding protein 1Nucleus 3.30.1370.10 74 6 84 4.17 4.94
1rwuA00 76.70 Hypothetical proteinUPF0250 protein ybeDEscherichia coli K-12 3.30.70.1460 87 7 77 3.74 4.86
1nzaA00 76.60 Thermus thermophilus HB8Divalent-cation tolerance protein cutAPeriplasmic divalent cation tolerance protein 3.30.70.830 103 10 71 3.48 4.84
1kohA01 76.60 Nuclear RNA export factor 1Homo sapiensProtein binding 3.30.70.330 97 7 74 3.61 4.86
1cg2A02 76.51 Pseudomonas sp. RS-16Carboxypeptidase G2 3.30.70.360 110 12 70 3.06 4.37
2qrrA00 76.43 D-methionine transport system ATP-binding proteinMethionine import ATP-binding protein MetNVibrio parahaemolyticusABC transporters 3.30.70.260 93 12 77 3.45 4.46
1fxlA01 76.19 AU-rich element bindingELAV like protein 2/3/4MRNA processingHomo sapiensELAV-like protein 4 3.30.70.330 71 9 75 3.32 4.41
2nuhA00 76.12 Xylella fastidiosaPeriplasmic divalent cation tolerance proteinPeriplasmic divalent cation tolerance protein 3.30.70.830 104 11 71 3.37 4.74
2v8hA02 75.80 Beta-alanine synthaseLachancea kluyveri 3.30.70.360 116 12 66 3.22 4.85
2ia0B02 75.79 Pyrococcus furiosusUncharacterized HTH-type transcriptional regulator PF0864 3.30.70.920 99 18 71 2.88 4.02
1x5uA01 75.69 SpliceosomeSpliceosomal complexHomo sapiensSplicing factor 3B subunit 4Splicing factor 3B subunit 4 3.30.70.330 80 16 92 4.47 4.83
1ufwA00 75.62 Phosphatidylinositol signaling systemSynaptojanin-2Phosphatidylinositol-bisphosphatase [EC:3.1.3.36]Homo sapiensInositol phosphate metabolism 3.30.70.330 95 9 74 3.49 4.67
2pd1A01 75.61 Nitrosomonas europaeaPutative uncharacterized protein 3.30.70.900 93 5 81 3.83 4.69
1lfwA03 75.54 Lactobacillus delbrueckii subsp. lactisBeta-Ala-Xaa dipeptidase 3.30.70.360 88 9 72 3.18 4.37
1mwqA00 75.52 Hypothetical proteinHaemophilus influenzaeUncharacterized protein HI_0828 3.30.70.1060 98 9 74 3.58 4.81
3ct9A02 75.14 Bacteroides thetaiotaomicronAcetylornithine deacetylase 3.30.70.360 104 12 66 3.29 4.96
2pehA01 74.82 Splicing factor 45SpliceosomeHomo sapiensProtein bindingSplicing factor 45 3.30.70.330 83 2 91 4.43 4.84
1kr4A00 74.60 Thermotoga maritimaDivalent-cation tolerance protein cutAPeriplasmic divalent cation tolerance protein 3.30.70.830 107 6 67 3.30 4.90
1vk8A00 74.59 Thermotoga maritimaPutative uncharacterized protein 3.30.70.930 91 6 71 3.43 4.80
3cedA00 74.28 ABC transportersD-methionine transport system ATP-binding proteinMethionine import ATP-binding protein MetN 2Staphylococcus aureus subsp. aureus Mu50 3.30.70.260 97 7 74 3.18 4.28
1yqhB00 74.01 IG hypothetical 16092Bacillus cereus ATCC 14579 3.30.70.930 98 11 69 3.09 4.45
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Displaying entries 1 to 60 (page 1 of 1)


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Domain ATOM Sequence 

>pdb|2nyiA01
ETQSFVVSVAGSDRVGIVHDFSWALKNISANVESSRACLGGDFAIVLVSLNAKDGKLIQSALESALPGFQISTRRASSV
BLAST against CATH

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Domain COMBS Sequence 

>pdb|2nyiA01
SETQSFVVSVAGSDRVGIVHDFSWALKNISANVESSRXACLGGDFAXIVLVSLNAKDGKLIQSALESALPGFQISTRRAS
SV
BLAST against CATH

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Domain History Events (55)

Domain assigned by cuff on 14 Feb 2008 15:49

same superfamily

Domain assignment manual match h by cuff on 14 Feb 2008 15:48

scores good enough for homology

Domain assignment manual match t by tronnberg on 10 Sep 2007 12:26

SSAP: 88.18 OV: 89 SEQ: 22. Very similar linkage and structure. The function for the query is unknown.

Homcheck review by tronnberg on 10 Sep 2007 12:26

SSAP: 88.18 OV: 89 SEQ: 22. Very similar linkage and structure. The function for the query is unknown.

Flow stage update by tronnberg on 10 Sep 2007 12:26

SSAP: 88.18 OV: 89 SEQ: 22. Very similar linkage and structure. The function for the query is unknown.

Homcheck allotment by tronnberg on 10 Sep 2007 12:24

User 'tronnberg' has allocated a domain to themselves for HomChecking with comment : Grabbed this domain via HomCheck's "Get Me A Domain" button.

Flow stage update by tronnberg on 10 Sep 2007 12:24

User 'tronnberg' has allocated a domain to themselves for HomChecking with comment : Grabbed this domain via HomCheck's "Get Me A Domain" button.

Flow stage update by auto on 09 Sep 2007 08:49

Domain "2nyiA01" SCOP scan with no results - no SCOP mapping

Domain scan scop cath by auto on 09 Sep 2007 08:48

Adding scan of type "DOMAIN_SCAN_SCOP_CATH" with 0 results for 2nyiA01

Flow stage update by auto on 09 Sep 2007 08:35

Retrieved PRC_PFAMCATH results for job ID SID2796411511007712 and results inserted.

Domain scan prc pfamcath by auto on 09 Sep 2007 08:34

Adding scan of type "DOMAIN_SCAN_PRC_PFAMCATH" with 11 results for 2nyiA01

Update comment by auto on 09 Sep 2007 05:13

PRC_PFAMCATH job SID2796411511007712 is not yet finished.

Prc pfamcath submit by auto on 09 Sep 2007 05:02

The entry "2nyiA01" has been submitted to the PRC_PFAMCATH webservice.

Flow stage update by auto on 09 Sep 2007 05:02

The entry "2nyiA01" has been submitted to the PRC_PFAMCATH webservice.

Flow stage update by auto on 09 Sep 2007 04:05

Retrieved SSAP results for job ID SID4566157120541808 and results inserted.

Domain scan ssap cath by auto on 09 Sep 2007 03:58

Adding scan of type "DOMAIN_SCAN_SSAP_CATH" with 3774 results for 2nyiA01

Update comment by auto on 05 Sep 2007 19:31

SSAP job SID4566157120541808 is not yet finished.

Ssap cath submit by auto on 05 Sep 2007 16:03

The entry "2nyiA01" has been submitted to the SSAP webservice.

Flow stage update by auto on 05 Sep 2007 16:03

The entry "2nyiA01" has been submitted to the SSAP webservice.

Flow stage update by auto on 05 Sep 2007 08:22

Retrieved PRC results for job ID SID7696551019378176 and inserted them into the database.

Domain scan prc cath by auto on 05 Sep 2007 08:21

Adding scan of type "DOMAIN_SCAN_PRC_CATH" with 10 results for 2nyiA01

Prc cath submit by auto on 05 Sep 2007 03:40

The entry "2nyiA01" has been submitted to the PRC webservice.

Flow stage update by auto on 05 Sep 2007 03:40

The entry "2nyiA01" has been submitted to the PRC webservice.

Flow stage update by auto on 04 Sep 2007 17:07

Retrieved HMM(SAM) results for job ID SID4252718584325856 and inserted them into the database.

Domain scan sam cath by auto on 04 Sep 2007 17:07

Adding scan of type "DOMAIN_SCAN_SAM_CATH" with 4 results for 2nyiA01

Update comment by auto on 04 Sep 2007 11:45

HMM(SAM) job SID4252718584325856 is not yet finished.

Flow stage update by auto on 04 Sep 2007 09:52

The entry "2nyiA01" has been submitted to the HMM (SAM) webservice.

Sam cath submit by auto on 04 Sep 2007 09:52

The entry "2nyiA01" has been submitted to the HMM (SAM) webservice.

Flow stage update by auto on 04 Sep 2007 00:19

Retrieved "2nyiA01" CATHEDRAL results for job ID SID0753792463851648 and inserted them into the database.

Domain scan cathedral cath by auto on 04 Sep 2007 00:17

Adding scan of type "DOMAIN_SCAN_CATHEDRAL_CATH" with 167 results for 2nyiA01

Cathedral cath submit by auto on 03 Sep 2007 13:58

The entry "2nyiA01" has been submitted to the CATHEDRAL webservice.

Flow stage update by auto on 03 Sep 2007 13:58

The entry "2nyiA01" has been submitted to the CATHEDRAL webservice.

Flow stage update by auto on 03 Sep 2007 11:57

ScanList with 11099 domains written to "/cath/data/current/scanlists/cathdb_current.fletcher/2nyiA01.scanlist" for "2nyiA01"

Write scan list by auto on 03 Sep 2007 11:56

Writing ScanList containing 11099 domains to file "/cath/data/current/scanlists/cathdb_current.fletcher/2nyiA01.scanlist" for domain "2nyiA01"

Update comment by auto on 03 Sep 2007 10:10

Waiting for 18 new domains (example : 2qg4C01) to be processed so that they can be scanned against too.

Update comment by auto on 03 Sep 2007 06:31

Waiting for 73 new domains (example : 2q3eK03) to be processed so that they can be scanned against too.

Update comment by auto on 03 Sep 2007 02:36

Waiting for 140 new domains (example : 2q08A02) to be processed so that they can be scanned against too.

Update comment by auto on 02 Sep 2007 22:32

Waiting for 188 new domains (example : 2o3jA01) to be processed so that they can be scanned against too.

Update comment by auto on 02 Sep 2007 18:21

Waiting for 279 new domains (example : 2b43C04) to be processed so that they can be scanned against too.

Update comment by auto on 02 Sep 2007 14:21

Waiting for 351 new domains (example : 1sh0B02) to be processed so that they can be scanned against too.

Update comment by auto on 02 Sep 2007 10:14

Waiting for 431 new domains (example : 1r0kA03) to be processed so that they can be scanned against too.

Update comment by auto on 02 Sep 2007 02:27

Waiting for 551 new domains (example : 1bplB01) to be processed so that they can be scanned against too.

Update comment by auto on 01 Sep 2007 22:11

Waiting for 607 new domains (example : 1bplB01) to be processed so that they can be scanned against too.

Update comment by auto on 01 Sep 2007 18:13

Waiting for 686 new domains (example : 1bplB01) to be processed so that they can be scanned against too.

Update comment by auto on 01 Sep 2007 14:15

Waiting for 771 new domains (example : 1bplB01) to be processed so that they can be scanned against too.

Update comment by auto on 01 Sep 2007 11:40

Waiting for 841 new domains (example : 1bplB01) to be processed so that they can be scanned against too.

Update comment by auto on 01 Sep 2007 06:14

Waiting for 903 new domains (example : 1bplB01) to be processed so that they can be scanned against too.

Update comment by auto on 01 Sep 2007 03:31

Waiting for 969 new domains (example : 1bplB01) to be processed so that they can be scanned against too.

Update comment by auto on 31 Aug 2007 20:05

Waiting for 1085 new domains (example : 1bplB01) to be processed so that they can be scanned against too.

Flow stage update by auto on 31 Aug 2007 19:59

No satisfactory AssignClose result found.

Flow stage update by auto on 31 Aug 2007 19:48

No in_process hits for Domain "2nyiA01" ready to be processed

Flow stage update by auto on 31 Aug 2007 19:48

NW result present for Domain "2nyiA01"

Flow stage update by auto on 23 Aug 2007 10:08

All required files are present for Domain "2nyiA01"

Flow stage update by auto on 22 Aug 2007 18:23

Beginning processing for Domain "2nyiA01"

Insertion by cuff on 22 Aug 2007 17:01

nice chopping