1JRG | Genus

Total Genus 128

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	128
sequence length	361
structure length	354
Chain Sequence	AELVSDKALESAPTVGWASQNGFTTGGAAATSDNIYIVTNISEFTSALSAGAEAKIIQIKGTIDISGGTPYTDFADQKARSQINIPANTTVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEPHYEKGDGWNAEWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKRGSDYVTISNSLIDQHDKTMLIGHDKGKLHVTLFNNVFNRVTERAPRVRYGSIHSFNNVFKGDAKDPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASKACKVVKKFNGSIFSDNGSVLNGSAVDLSGCGFSAYTSKIPYIYDVQPMTTELAQSITDNAGSGKL

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

loadScript /static/js/j2s/core/package.js

loadScript /static/js/j2s/core/corejmol.z.js

loadScript /static/js/j2s/core/corescript.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__0229175549350789__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__0229175549350789__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1JRG/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__0229175549350789__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"0229175549350789","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1JRG/A/"

Jmol Version: 14.29.13 2018-04-17 17:17

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor white

backgroundColor = "white"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__0229175549350789__ ready

script 1 started

platformSpeed = 8

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

molecule tags	Lyase
source organism	Erwinia chrysanthemi
publication title	Structure of pectate lyase A: comparison to other isoforms. pubmed doi rcsb
molecule keywords	Pectate lyase
total genus	128
structure length	354
sequence length	361
chains with identical sequence	B
ec nomenclature	ec 4.2.2.2: Pectate lyase.
pdb deposition date	2001-08-13

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00544	Pec_lyase_C	Pectate lyase

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
2.160.20.10	Mainly Beta	3 Solenoid	Pectate Lyase C-like	Single-stranded right-handed beta-helix, Pectin lyase-like	1jrgA00

1OOCA 4EW9A 1BHEA 2QY1A 1XG2A 4XMYA 4XLFA 2UVEA 3VMVA 1O8FA 1DBOA 2X6XA 4I84A 2NT9A 4YZ0A 3KRGA 2O0VA 3JURA 1PXZA 3SUCA 4MR0A 4XORA 4OJ6A 4OJ5A 2X6WA 4XOTA 2X3HA 3VSUA 3GQ9A 2NSTA 3GQAA 4U4BA 4YZAA 2INVA 1VBLA 2VBEA 4NK6A 2VJIA 5C1EA 1IA5A 1H80A 4W8SA 1O88A 2IQ7A 1GQ8A 3B90A 3EQOA 4NK8A 1RU4A 2NT6A 1O8HA 4YELA 4YEJA 2NTQA 4Z03A 1OFLA 4OJOA 4MXNA 3ZSCA 1RMGA 3GQ8A 1EE6A 1O8EA 2INUA 1K5CA 4AVZA 4YZQA 1OFMA 4XLCA 1CZFA 2QXZA 3VMWA 2PYGA 4HWVA 1KCCA 4OZYA 1WMRA 4XKVA 4XONA 4Z05A 2ODLA 1IDJA 4XN0A 1QJVA 2QX3A 4XR6A 2VBMA 1O8MA 2PECA 3ZPPA 4YZXA 3GQ7A 2NSPA 4OJPA 3B4NA 1JTAA 3GRHA 1PE9A 1BN8A 1O8LA 1O8JA 2X6YA 3WWGA 1O8IA 1AIRA 1JRGA 4W8TA 4OZZA 2EWEA 2NZMA 3VSTA 1PLUA 3UW0A 2UVFA 4XQFA 4XKWA 1HG8A 2O04A 2O17A 4XOPA 4XLEA 4XN3A 1KCDA 4U49A 1O8GA 4XM3A 4OJLA 4XL9A 1IDKA 1DBGA 4PMHA 3T9GA 1OGOX 1O8DA 3VSVA 1KTWA 4XNFA 2O0WA 2NTBA 2O1DA 2PYHA 2VBKA 4Z06A 1NHCA 4W8QA 1IB4A 2NTPA 3EQNA 1O8KA 1OGMX 4W8RA 3B8YA 4C2LA 4URRA 2X85A 4XLHA 1RWRA 2BSPA 2Z8GA 4XLAA 2VJJA 3FY3A 1QCXA 5C1CA 5AMVA 3LMWA 1X0CA
chains in the Genus database with same CATH superfamily

2BM4A 1OOCA 4EW9A 1BHEA 2QY1A 1EZGA 1XG2A 4XMYA 2B0RA 4XLFA 2UVEA 3H09A 1QRBA 3VMVA 1O8FA 1DBOA 2X6XA 1HF2A 2NT9A 4I84A 4YZ0A 3KRGA 2O0VA 2VFQA 1QA3A 3JURA 1PXZA 3SUCA 2W7ZA 3N90A 4MR0A 4YCQA 3ML3A 3PETA 4XORA 4OJ6A 4OJ5A 2X6WA 4XOTA 2X3HA 3VSUA 3GQ9A 4YDTA 2NSTA 3GQAA 2XT2A 1CLWA 4U4BA 4YZAA 2INVA 1VBLA 2QZAA 2VBEA 3BH6B 2J8KA 4KH3A 4NK6A 2VJIA 5C1EA 1TYUA 1IA5A 1H80A 3PSZA 4W8SA 1O88A 1LM1A 1GQ8A 2IQ7A 3B90A 3EQOA 4NK8A 1RU4A 2NT6A 1O8HA 4YELA 1TYWA 3N6ZA 4YEJA 2NTQA 4Z03A 1QA2A 1OFLA 4OJOA 4MXNA 3ZSCA 3SQVA 1RMGA 3GQ8A 1EE6A 1O8EA 2INUA 1K5CA 4AVZA 4YZQA 1OFMA 1DABA 1OFEA 2BX6A 4XLCA 1CZFA 2QXZA 4V02C 3VMWA 2BM5A 1OFDA 2XTXA 2BM7A 2PYGA 1L1IA 2F3LA 3PSSA 4HWVA 5JLVC 1KCCA 4OZYA 1WMRA 4XKVA 4XONA 4Z05A 1IDJA 2ODLA 4XN0A 3SYJA 1QJVA 2QX3A 4XR6A 2VBMA 1O8MA 2PECA 3DU1X 3ZPPA 1K4ZA 4YC5A 4YZXA 5DNSA 3GQ7A 2NSPA 4OJPA 2BM6A 2VFNA 1KQ5A 3B4NA 3SZEA 3RIQA 1JTAA 2YUHA 5JMCB 4YFOA 2V5IA 3GRHA 1PE9A 1BN8A 1O8LA 1O8JA 2X6YA 3WWGA 3AK5A 1O8IA 1AIRA 1JRGA 4W8TA 3JX8A 2EWEA 2NZMA 4OZZA 3VSTA 4YEIA 1PLUA 1TYVA 3NB2A 2VFOA 3UW0A 2UVFA 4XQFA 4XKWA 1HG8A 2O04A 2O17A 4JRAC 4XOPA 4XLEA 2XT4A 4XN3A 1KCDA 1EA0A 4U49A 1O8GA 4XM3A 2IOUG 3P4GA 4OJLA 4XL9A 1QQ1A 1IDKA 1DBGA 4PMHA 3T9GA 1OGOX 1O8DA 3VSVA 1TYXA 4OPWA 1KTWA 4OM9A 2J8IA 4XNFA 2O0WA 2QYUA 2NTBA 3SY2A 3LYCA 2G0YA 2O1DA 2PYHA 2VBKA 4Z06A 1NHCA 2VFMA 1WXRA 4W8QA 1IB4A 2NTPA 1LLZA 3EQNA 1O8KA 1OGMX 3NAWA 4W8RA 3B8YA 3TH0A 4URRA 4C2LA 1K8FA 3LJYA 2VFPA 2X85A 4XLHA 1RWRA 2BSPA 2Z8GA 2XC1A 4XLAA 2VJJA 2XTYA 3FY3A 1QCXA 2O6WA 5C1CA 5AMVA 1TSPA 1LLWA 2XTWA 1QRCA 1QA1A 3BH7B 3LMWA 1X0CA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1OOC A;  4EW9 A;  1BHE A;  2QY1 A;  1XG2 A;  4XMY A;  4XLF A;  2UVE A;  3VMV A;  1O8F A;  1DBO A;  2X6X A;  4I84 A;  2NT9 A;  4YZ0 A;  3KRG A;  2O0V A;  3JUR A;  1PXZ A;  3SUC A;  4MR0 A;  4XOR A;  4OJ6 A;  4OJ5 A;  2X6W A;  4XOT A;  2X3H A;  3VSU A;  3GQ9 A;  2NST A;  3GQA A;  4U4B A;  4YZA A;  2INV A;  1VBL A;  2VBE A;  4NK6 A;  2VJI A;  5C1E A;  1IA5 A;  1H80 A;  4W8S A;  1O88 A;  2IQ7 A;  1GQ8 A;  3B90 A;  3EQO A;  4NK8 A;  1RU4 A;  2NT6 A;  1O8H A;  4YEL A;  4YEJ A;  2NTQ A;  4Z03 A;  1OFL A;  4OJO A;  4MXN A;  3ZSC A;  1RMG A;  3GQ8 A;  1EE6 A;  1O8E A;  2INU A;  1K5C A;  4AVZ A;  4YZQ A;  1OFM A;  4XLC A;  1CZF A;  2QXZ A;  3VMW A;  2PYG A;  4HWV A;  1KCC A;  4OZY A;  1WMR A;  4XKV A;  4XON A;  4Z05 A;  2ODL A;  1IDJ A;  4XN0 A;  1QJV A;  2QX3 A;  4XR6 A;  2VBM A;  1O8M A;  2PEC A;  3ZPP A;  4YZX A;  3GQ7 A;  2NSP A;  4OJP A;  3B4N A;  1JTA A;  3GRH A;  1PE9 A;  1BN8 A;  1O8L A;  1O8J A;  2X6Y A;  3WWG A;  1O8I A;  1AIR A;  1JRG A;  4W8T A;  4OZZ A;  2EWE A;  2NZM A;  3VST A;  1PLU A;  3UW0 A;  2UVF A;  4XQF A;  4XKW A;  1HG8 A;  2O04 A;  2O17 A;  4XOP A;  4XLE A;  4XN3 A;  1KCD A;  4U49 A;  1O8G A;  4XM3 A;  4OJL A;  4XL9 A;  1IDK A;  1DBG A;  4PMH A;  3T9G A;  1OGO X;  1O8D A;  3VSV A;  1KTW A;  4XNF A;  2O0W A;  2NTB A;  2O1D A;  2PYH A;  2VBK A;  4Z06 A;  1NHC A;  4W8Q A;  1IB4 A;  2NTP A;  3EQN A;  1O8K A;  1OGM X;  4W8R A;  3B8Y A;  4C2L A;  4URR A;  2X85 A;  4XLH A;  1RWR A;  2BSP A;  2Z8G A;  4XLA A;  2VJJ A;  3FY3 A;  1QCX A;  5C1C A;  5AMV A;  3LMW A;  1X0C A; 
#chains in the Genus database with same CATH topology
 2BM4 A;  1OOC A;  4EW9 A;  1BHE A;  2QY1 A;  1EZG A;  1XG2 A;  4XMY A;  2B0R A;  4XLF A;  2UVE A;  3H09 A;  1QRB A;  3VMV A;  1O8F A;  1DBO A;  2X6X A;  1HF2 A;  2NT9 A;  4I84 A;  4YZ0 A;  3KRG A;  2O0V A;  2VFQ A;  1QA3 A;  3JUR A;  1PXZ A;  3SUC A;  2W7Z A;  3N90 A;  4MR0 A;  4YCQ A;  3ML3 A;  3PET A;  4XOR A;  4OJ6 A;  4OJ5 A;  2X6W A;  4XOT A;  2X3H A;  3VSU A;  3GQ9 A;  4YDT A;  2NST A;  3GQA A;  2XT2 A;  1CLW A;  4U4B A;  4YZA A;  2INV A;  1VBL A;  2QZA A;  2VBE A;  3BH6 B;  2J8K A;  4KH3 A;  4NK6 A;  2VJI A;  5C1E A;  1TYU A;  1IA5 A;  1H80 A;  3PSZ A;  4W8S A;  1O88 A;  1LM1 A;  1GQ8 A;  2IQ7 A;  3B90 A;  3EQO A;  4NK8 A;  1RU4 A;  2NT6 A;  1O8H A;  4YEL A;  1TYW A;  3N6Z A;  4YEJ A;  2NTQ A;  4Z03 A;  1QA2 A;  1OFL A;  4OJO A;  4MXN A;  3ZSC A;  3SQV A;  1RMG A;  3GQ8 A;  1EE6 A;  1O8E A;  2INU A;  1K5C A;  4AVZ A;  4YZQ A;  1OFM A;  1DAB A;  1OFE A;  2BX6 A;  4XLC A;  1CZF A;  2QXZ A;  4V02 C;  3VMW A;  2BM5 A;  1OFD A;  2XTX A;  2BM7 A;  2PYG A;  1L1I A;  2F3L A;  3PSS A;  4HWV A;  5JLV C;  1KCC A;  4OZY A;  1WMR A;  4XKV A;  4XON A;  4Z05 A;  1IDJ A;  2ODL A;  4XN0 A;  3SYJ A;  1QJV A;  2QX3 A;  4XR6 A;  2VBM A;  1O8M A;  2PEC A;  3DU1 X;  3ZPP A;  1K4Z A;  4YC5 A;  4YZX A;  5DNS A;  3GQ7 A;  2NSP A;  4OJP A;  2BM6 A;  2VFN A;  1KQ5 A;  3B4N A;  3SZE A;  3RIQ A;  1JTA A;  2YUH A;  5JMC B;  4YFO A;  2V5I A;  3GRH A;  1PE9 A;  1BN8 A;  1O8L A;  1O8J A;  2X6Y A;  3WWG A;  3AK5 A;  1O8I A;  1AIR A;  1JRG A;  4W8T A;  3JX8 A;  2EWE A;  2NZM A;  4OZZ A;  3VST A;  4YEI A;  1PLU A;  1TYV A;  3NB2 A;  2VFO A;  3UW0 A;  2UVF A;  4XQF A;  4XKW A;  1HG8 A;  2O04 A;  2O17 A;  4JRA C;  4XOP A;  4XLE A;  2XT4 A;  4XN3 A;  1KCD A;  1EA0 A;  4U49 A;  1O8G A;  4XM3 A;  2IOU G;  3P4G A;  4OJL A;  4XL9 A;  1QQ1 A;  1IDK A;  1DBG A;  4PMH A;  3T9G A;  1OGO X;  1O8D A;  3VSV A;  1TYX A;  4OPW A;  1KTW A;  4OM9 A;  2J8I A;  4XNF A;  2O0W A;  2QYU A;  2NTB A;  3SY2 A;  3LYC A;  2G0Y A;  2O1D A;  2PYH A;  2VBK A;  4Z06 A;  1NHC A;  2VFM A;  1WXR A;  4W8Q A;  1IB4 A;  2NTP A;  1LLZ A;  3EQN A;  1O8K A;  1OGM X;  3NAW A;  4W8R A;  3B8Y A;  3TH0 A;  4URR A;  4C2L A;  1K8F A;  3LJY A;  2VFP A;  2X85 A;  4XLH A;  1RWR A;  2BSP A;  2Z8G A;  2XC1 A;  4XLA A;  2VJJ A;  2XTY A;  3FY3 A;  1QCX A;  2O6W A;  5C1C A;  5AMV A;  1TSP A;  1LLW A;  2XTW A;  1QRC A;  1QA1 A;  3BH7 B;  3LMW A;  1X0C A; 
#chains in the Genus database with same CATH homology
 1OOC A;  4EW9 A;  1BHE A;  2QY1 A;  1XG2 A;  4XMY A;  4XLF A;  2UVE A;  3VMV A;  1O8F A;  1DBO A;  2X6X A;  4I84 A;  2NT9 A;  4YZ0 A;  3KRG A;  2O0V A;  3JUR A;  1PXZ A;  3SUC A;  4MR0 A;  4XOR A;  4OJ6 A;  4OJ5 A;  2X6W A;  4XOT A;  2X3H A;  3VSU A;  3GQ9 A;  2NST A;  3GQA A;  4U4B A;  4YZA A;  2INV A;  1VBL A;  2VBE A;  4NK6 A;  2VJI A;  5C1E A;  1IA5 A;  1H80 A;  4W8S A;  1O88 A;  2IQ7 A;  1GQ8 A;  3B90 A;  3EQO A;  4NK8 A;  1RU4 A;  2NT6 A;  1O8H A;  4YEL A;  4YEJ A;  2NTQ A;  4Z03 A;  1OFL A;  4OJO A;  4MXN A;  3ZSC A;  1RMG A;  3GQ8 A;  1EE6 A;  1O8E A;  2INU A;  1K5C A;  4AVZ A;  4YZQ A;  1OFM A;  4XLC A;  1CZF A;  2QXZ A;  3VMW A;  2PYG A;  4HWV A;  1KCC A;  4OZY A;  1WMR A;  4XKV A;  4XON A;  4Z05 A;  2ODL A;  1IDJ A;  4XN0 A;  1QJV A;  2QX3 A;  4XR6 A;  2VBM A;  1O8M A;  2PEC A;  3ZPP A;  4YZX A;  3GQ7 A;  2NSP A;  4OJP A;  3B4N A;  1JTA A;  3GRH A;  1PE9 A;  1BN8 A;  1O8L A;  1O8J A;  2X6Y A;  3WWG A;  1O8I A;  1AIR A;  1JRG A;  4W8T A;  4OZZ A;  2EWE A;  2NZM A;  3VST A;  1PLU A;  3UW0 A;  2UVF A;  4XQF A;  4XKW A;  1HG8 A;  2O04 A;  2O17 A;  4XOP A;  4XLE A;  4XN3 A;  1KCD A;  4U49 A;  1O8G A;  4XM3 A;  4OJL A;  4XL9 A;  1IDK A;  1DBG A;  4PMH A;  3T9G A;  1OGO X;  1O8D A;  3VSV A;  1KTW A;  4XNF A;  2O0W A;  2NTB A;  2O1D A;  2PYH A;  2VBK A;  4Z06 A;  1NHC A;  4W8Q A;  1IB4 A;  2NTP A;  3EQN A;  1O8K A;  1OGM X;  4W8R A;  3B8Y A;  4C2L A;  4URR A;  2X85 A;  4XLH A;  1RWR A;  2BSP A;  2Z8G A;  4XLA A;  2VJJ A;  3FY3 A;  1QCX A;  5C1C A;  5AMV A;  3LMW A;  1X0C A;

...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)

...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

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

1JRGA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations