1FKMA

Crystal structure of the ypt/rab-gap domain of gyp1p
Total Genus 127

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
127
sequence length
382
structure length
322
Chain Sequence
NSIIQRISKFDNILKDKTIINQQDLRQISWNGIPKIHRPVVWKLLIGYLPVNTKRQEGFLQRKRKEYRDSLKHTFSDQHSRDIPTWHQIEIDIPRTNPHIPLYQFKSVQNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLPPSQIDDVEIKDPSTYMVDEQITDLEADTFWCLTKLLEQITDNYIHGQPGILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWDTYLSETSSLNEFHVFVCAAFLIKWSDQLMEMDFQETITFLQNPPTKDWTETDIEMLLSEAFIWQSLYK
5010015020025030030025020015010050
020406080100120Genus Matrix

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.


  Genus data interpretation
Chord Diagram
EMPTYTIV3 (295-298)AH1 (251-262)AH4 (304-322)TIV2 (265-268)TIV1 (262-265)AH3 (286-294)3H2 (301-303)TVIII1 (298-301)AH2 (270-278)3H1 (283-285)Updating...
connected with : NaN
molecule tags Endocytosis/exocytosis
source organism Saccharomyces cerevisiae
publication title Crystal structure of the GAP domain of Gyp1p: first insights into interaction with Ypt/Rab proteins.
pubmed doi rcsb
molecule keywords PROTEIN (GYP1P)
total genus 127
structure length 322
sequence length 382
ec nomenclature
pdb deposition date 2000-08-09

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00566 RabGAP-TBC Rab-GTPase-TBC domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.472.80 Mainly Alpha Orthogonal Bundle Cyclin A; domain 1 Cyclin A; domain 1 1fkmA02
5EJCA 2QFZA 2G77A 3QWLA 2QQ8A 4HL4A 3HZJA 4Z6YA 4HLQA 3QYEA 4NC6A 1FKMA 3QYBA
chains in the Genus database with same CATH superfamily
1H25B 3DTOA 3MY1B 1O9KB 3QXEB 2UZBB 1OIUB 2WIHB 1VOLA 2C5OB 5L2WB 3HB9A 3X24B 3BG3A 4OB2B 2QF7A 1VINA 3A8GB 3QHWB 2PHGA 4CFWB 2C5VB 3BLRB 4BCMB 3RGFB 1VYWB 1GUXA 2IW9B 3QZ5B 5LQFB 5IHYA 4TTHA 3BLHB 2ZPBB 1O9KA 1AD6A 2C5XB 2ZPGB 4BCKB 3G33B 4BCJB 4BBRM 2ZCFB 4EOQB 3EJ1B 5IDPB 3VKHA 4OGRB 1H28B 3TNIB 3QZ9B 1UGRB 1XO2A 2CZ1B 4MFDA 4BCQD 2W9FA 2W99A 3DJBA 2PK2A 2DD5B 5FGKB 5ACBA 1IREB 4BXXX 2JGZB 2QGSA 4CXAB 2BS4A 1C9BA 1H1RB 2WMAB 4BCIB 3HBLA 3EIDB 4BCQB 3QYGB 3MI9B 4HNVA 4IMYB 4F7LB 5IF1B 5HVYB 1ENWA 4BCND 4F6UB 4F7JB 3TN8B 4ELLA 1G3NC 2LW4A 4YOSA 4OB0B 3HHTB 1URCB 1GH6B 5BNJB 4BCOB 3MY5B 5CYIB 4CFUD 4ROCA 3BHUB 2DXCB 3F5XB 3A8HB 4YOOA 4F70B 2WPAB 3QYHB 1OL2B 5LMKB 4FM4B 4NC6A 1H1SB 3QHRB 2ZPEB 4F6WB 2KR6A 4JX5A 4NSTB 2W96A 1H26B 4JX4A 3MIAB 2B9RA 4BCFB 2CJMB 2X1NB 3GTMS 2BKZB 3A8LB 2ZPFB 4ELJA 2ZPHB 4CFMB 4UN0A 1AHJB 1P5EB 5HBHB 2W9ZA 3QYBA 1UNGD 1BU2A 1GY3B 1N4MA 3A8MB 2BS2A 2BPMB 4HNUA 4KRDB 3WVEB 2PJQA 3BHVB 5HQ0B 1OIYB 4Y72B 5I5ZB 3HO8A 5EJCA 4HNTA 4MIMA 1E9HB 3TW6A 1PKDB 4AI6A 3A8OB 1JSTB 4BCHB 4II5B 2I53A 3DDPB 2QFZA 1W98B 2WHBB 4QSHA 4OB1B 5HNBB 3BG9A 2CZ7B 2G77A 4HLQA 4EOKB 3VKGA 2WEVB 4ROEA 3BHTB 1H1PB 1TFBA 5ICPB 4EOJB 4CFNB 2UZLB 3B57A 4G6LB 4ZGDB 5IDNB 2I40B 3X28B 2R7GA 4JX6A 3NDQA 3TNHB 2IVXA 1F5QB 4BCNB 4CFVB 4RODA 2C4GB 1TD6A 4KRCB 2BS3A 2WIPB 4BY1X 4CFUB 3KHIA 1UGSB 4EOSB 4HL4A 4OB3B 2CCIB 4F6SB 2DXBB 5HBEB 4Z6YA 4BBSM 2PMIB 5DQVA 2WFYB 2IN3A 3K7AM 2WJ9A 3POMA 2D0QB 4YC3B 1KXUA 2CYZB 1V29B 4ZGEB 1D3UB 1UNHD 2UZEB 2W2HA 4AKHA 4I3ZB 4F7NB 2ZPIB 1OKVB 1FINB 3TW7A 2G9XB 2IW8B 4AKIA 1H4LD 4BCMD 1FVVB 1H27B 3X26B 3O0GD 2DMEA 4EOMB 1UNLD 1QLBA 2CZ0B 2PK9B 1OGUB 3QWLA 2DD4B 2C6TB 4CFXB 1JOWA 1AISB 3DDQB 3EOCB 4F7SB 5HBJB 2KMGA 3DL1A 1OKWB 2DPPB 4AKGA 2UUEB 3M03A 4M6VA 2CZ6B 3WVDB 4EC8B 1JKWA 5CEIB 3H4CA 4EOOB 3PO3S 2WXVB 2F2CA 4EOIB 3X20B 1UGPB 3HZJA 1ZP2A 3LQ5B 4EC9B 4EOPB 1FKMA 1JSUB 3TNWB 1E7PA 1H1QB 2QDJA 4LOCA 2IW6B 4ZGJB 4FX3B 4MFEA 1OI9B 4EONB 3QYEA 2ZZDB 1OL1B 3VYHB 4BCGB 3X25B 4BY7X 4EOLB 5DQWA 2C5NB 3VYGB 3BLQB 2CCHB 2UZDB 1H24B 4OR5B 1UGQB 4BCPB 4CRLB 2QQ8A 3DOGB 2EUFA 1QMZB 3BG5A 2AHJB 2V22B 4EORB 2QDYB 4YOZA 1GUXB 5EFQB 2WMBB
chains in the Genus database with same CATH topology
3VKGA 3QYHB 2KMGA 3DL1A 3QXEB 4FM4B 4NC6A 2ZPEB 2DPPB 2KR6A 4AKGA 4JX5A 4ZGDB 3HB9A 3X24B 3BG3A 4OB2B 2QF7A 3X28B 4JX4A 4M6VA 2CZ6B 3WVDB 3A8GB 4JX6A 3H4CA 3A8LB 2ZPFB 4ELJA 2ZPHB 3QZ5B 1AHJB 2BS3A 3X20B 1UGPB 3HZJA 3KHIA 2ZPBB 3QYBA 1UGSB 2ZPGB 4HL4A 4BBRM 4OB3B 2ZCFB 1FKMA 2DXBB 4Z6YA 3A8MB 2BS2A 4BBSM 3VKHA 4HNUA 1E7PA 3WVEB 2QDJA 2WJ9A 4LOCA 4ZGJB 3QZ9B 1UGRB 4MFEA 2D0QB 2CZ1B 3QYEA 2ZZDB 2CYZB 4MFDA 3HO8A 5EJCA 1V29B 3VYHB 4ZGEB 2DD5B 1IREB 3X25B 4HNTA 4AKHA 4MIMA 3TW6A 3VYGB 2ZPIB 2BS4A 4AI6A 3A8OB 3TW7A 3HBLA 1UGQB 3QYGB 4AKIA 4HNVA 2QFZA 2QQ8A 4QSHA 3BG5A 4OB0B 3X26B 3HHTB 2AHJB 4OB1B 2QDYB 2CZ0B 1QLBA 3BG9A 3QWLA 2CZ7B 2DD4B 2G77A 2DXCB 4HLQA 3A8HB
chains in the Genus database with same CATH homology

  
#chains in the Genus database with same CATH superfamily
 5EJC A;  2QFZ A;  2G77 A;  3QWL A;  2QQ8 A;  4HL4 A;  3HZJ A;  4Z6Y A;  4HLQ A;  3QYE A;  4NC6 A;  1FKM A;  3QYB A; 
#chains in the Genus database with same CATH topology
 1H25 B;  3DTO A;  3MY1 B;  1O9K B;  3QXE B;  2UZB B;  1OIU B;  2WIH B;  1VOL A;  2C5O B;  5L2W B;  3HB9 A;  3X24 B;  3BG3 A;  4OB2 B;  2QF7 A;  1VIN A;  3A8G B;  3QHW B;  2PHG A;  4CFW B;  2C5V B;  3BLR B;  4BCM B;  3RGF B;  1VYW B;  1GUX A;  2IW9 B;  3QZ5 B;  5LQF B;  5IHY A;  4TTH A;  3BLH B;  2ZPB B;  1O9K A;  1AD6 A;  2C5X B;  2ZPG B;  4BCK B;  3G33 B;  4BCJ B;  4BBR M;  2ZCF B;  4EOQ B;  3EJ1 B;  5IDP B;  3VKH A;  4OGR B;  1H28 B;  3TNI B;  3QZ9 B;  1UGR B;  1XO2 A;  2CZ1 B;  4MFD A;  4BCQ D;  2W9F A;  2W99 A;  3DJB A;  2PK2 A;  2DD5 B;  5FGK B;  5ACB A;  1IRE B;  4BXX X;  2JGZ B;  2QGS A;  4CXA B;  2BS4 A;  1C9B A;  1H1R B;  2WMA B;  4BCI B;  3HBL A;  3EID B;  4BCQ B;  3QYG B;  3MI9 B;  4HNV A;  4IMY B;  4F7L B;  5IF1 B;  5HVY B;  1ENW A;  4BCN D;  4F6U B;  4F7J B;  3TN8 B;  4ELL A;  1G3N C;  2LW4 A;  4YOS A;  4OB0 B;  3HHT B;  1URC B;  1GH6 B;  5BNJ B;  4BCO B;  3MY5 B;  5CYI B;  4CFU D;  4ROC A;  3BHU B;  2DXC B;  3F5X B;  3A8H B;  4YOO A;  4F70 B;  2WPA B;  3QYH B;  1OL2 B;  5LMK B;  4FM4 B;  4NC6 A;  1H1S B;  3QHR B;  2ZPE B;  4F6W B;  2KR6 A;  4JX5 A;  4NST B;  2W96 A;  1H26 B;  4JX4 A;  3MIA B;  2B9R A;  4BCF B;  2CJM B;  2X1N B;  3GTM S;  2BKZ B;  3A8L B;  2ZPF B;  4ELJ A;  2ZPH B;  4CFM B;  4UN0 A;  1AHJ B;  1P5E B;  5HBH B;  2W9Z A;  3QYB A;  1UNG D;  1BU2 A;  1GY3 B;  1N4M A;  3A8M B;  2BS2 A;  2BPM B;  4HNU A;  4KRD B;  3WVE B;  2PJQ A;  3BHV B;  5HQ0 B;  1OIY B;  4Y72 B;  5I5Z B;  3HO8 A;  5EJC A;  4HNT A;  4MIM A;  1E9H B;  3TW6 A;  1PKD B;  4AI6 A;  3A8O B;  1JST B;  4BCH B;  4II5 B;  2I53 A;  3DDP B;  2QFZ A;  1W98 B;  2WHB B;  4QSH A;  4OB1 B;  5HNB B;  3BG9 A;  2CZ7 B;  2G77 A;  4HLQ A;  4EOK B;  3VKG A;  2WEV B;  4ROE A;  3BHT B;  1H1P B;  1TFB A;  5ICP B;  4EOJ B;  4CFN B;  2UZL B;  3B57 A;  4G6L B;  4ZGD B;  5IDN B;  2I40 B;  3X28 B;  2R7G A;  4JX6 A;  3NDQ A;  3TNH B;  2IVX A;  1F5Q B;  4BCN B;  4CFV B;  4ROD A;  2C4G B;  1TD6 A;  4KRC B;  2BS3 A;  2WIP B;  4BY1 X;  4CFU B;  3KHI A;  1UGS B;  4EOS B;  4HL4 A;  4OB3 B;  2CCI B;  4F6S B;  2DXB B;  5HBE B;  4Z6Y A;  4BBS M;  2PMI B;  5DQV A;  2WFY B;  2IN3 A;  3K7A M;  2WJ9 A;  3POM A;  2D0Q B;  4YC3 B;  1KXU A;  2CYZ B;  1V29 B;  4ZGE B;  1D3U B;  1UNH D;  2UZE B;  2W2H A;  4AKH A;  4I3Z B;  4F7N B;  2ZPI B;  1OKV B;  1FIN B;  3TW7 A;  2G9X B;  2IW8 B;  4AKI A;  1H4L D;  4BCM D;  1FVV B;  1H27 B;  3X26 B;  3O0G D;  2DME A;  4EOM B;  1UNL D;  1QLB A;  2CZ0 B;  2PK9 B;  1OGU B;  3QWL A;  2DD4 B;  2C6T B;  4CFX B;  1JOW A;  1AIS B;  3DDQ B;  3EOC B;  4F7S B;  5HBJ B;  2KMG A;  3DL1 A;  1OKW B;  2DPP B;  4AKG A;  2UUE B;  3M03 A;  4M6V A;  2CZ6 B;  3WVD B;  4EC8 B;  1JKW A;  5CEI B;  3H4C A;  4EOO B;  3PO3 S;  2WXV B;  2F2C A;  4EOI B;  3X20 B;  1UGP B;  3HZJ A;  1ZP2 A;  3LQ5 B;  4EC9 B;  4EOP B;  1FKM A;  1JSU B;  3TNW B;  1E7P A;  1H1Q B;  2QDJ A;  4LOC A;  2IW6 B;  4ZGJ B;  4FX3 B;  4MFE A;  1OI9 B;  4EON B;  3QYE A;  2ZZD B;  1OL1 B;  3VYH B;  4BCG B;  3X25 B;  4BY7 X;  4EOL B;  5DQW A;  2C5N B;  3VYG B;  3BLQ B;  2CCH B;  2UZD B;  1H24 B;  4OR5 B;  1UGQ B;  4BCP B;  4CRL B;  2QQ8 A;  3DOG B;  2EUF A;  1QMZ B;  3BG5 A;  2AHJ B;  2V22 B;  4EOR B;  2QDY B;  4YOZ A;  1GUX B;  5EFQ B;  2WMB B; 
#chains in the Genus database with same CATH homology
 3VKG A;  3QYH B;  2KMG A;  3DL1 A;  3QXE B;  4FM4 B;  4NC6 A;  2ZPE B;  2DPP B;  2KR6 A;  4AKG A;  4JX5 A;  4ZGD B;  3HB9 A;  3X24 B;  3BG3 A;  4OB2 B;  2QF7 A;  3X28 B;  4JX4 A;  4M6V A;  2CZ6 B;  3WVD B;  3A8G B;  4JX6 A;  3H4C A;  3A8L B;  2ZPF B;  4ELJ A;  2ZPH B;  3QZ5 B;  1AHJ B;  2BS3 A;  3X20 B;  1UGP B;  3HZJ A;  3KHI A;  2ZPB B;  3QYB A;  1UGS B;  2ZPG B;  4HL4 A;  4BBR M;  4OB3 B;  2ZCF B;  1FKM A;  2DXB B;  4Z6Y A;  3A8M B;  2BS2 A;  4BBS M;  3VKH A;  4HNU A;  1E7P A;  3WVE B;  2QDJ A;  2WJ9 A;  4LOC A;  4ZGJ B;  3QZ9 B;  1UGR B;  4MFE A;  2D0Q B;  2CZ1 B;  3QYE A;  2ZZD B;  2CYZ B;  4MFD A;  3HO8 A;  5EJC A;  1V29 B;  3VYH B;  4ZGE B;  2DD5 B;  1IRE B;  3X25 B;  4HNT A;  4AKH A;  4MIM A;  3TW6 A;  3VYG B;  2ZPI B;  2BS4 A;  4AI6 A;  3A8O B;  3TW7 A;  3HBL A;  1UGQ B;  3QYG B;  4AKI A;  4HNV A;  2QFZ A;  2QQ8 A;  4QSH A;  3BG5 A;  4OB0 B;  3X26 B;  3HHT B;  2AHJ B;  4OB1 B;  2QDY B;  2CZ0 B;  1QLB A;  3BG9 A;  3QWL A;  2CZ7 B;  2DD4 B;  2G77 A;  2DXC B;  4HLQ A;  3A8H B;
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

  
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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