3BRY | Genus

Total Genus 77

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	77
sequence length	434
structure length	389
Chain Sequence	VFNLEGFGPVSRAMGGTGAAFDIGPAAMMENPATLGLMGEGRHFSLGLDVVSTDIKVTTASSGNHGNNNGPYFAPQTAFVYRQGRYAFGAGIFAEGGLGTQYGGSSFLSRTSNGVDTGLDQFSRLLVLRVPFSAAYHVTDKLTVGASVDAVWTSLNLGTLLDVSQIGTLAGQGRVSGTLVPTLLGVPGLSGGYIDFSGVQAWGIGGRLGLTYQVTPDTRIGAAYQAKTHVGDLTGQATLSAVGNIPLKGDVTVRNFQMPAQLTVGISHQFNDQLSVSADYQRVFWSSVMKDMNVGFVQSGSAANLDLSLPQNYRDISVFGIGAEYRYNAKWTFRGGFHYAQETTSLTGGVSYAIGKNDVIDFALSVALRKTSVTHSQVNAVIAYQKRFH

Loading diagram...

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__176035093052021__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__176035093052021__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3BRY/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__176035093052021__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"176035093052021","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3BRY/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__176035093052021__ 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

Chord Diagram

molecule tags	Transport protein
source organism	Ralstonia pickettii
publication title	Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation. pubmed doi rcsb
molecule keywords	TbuX
total genus	77
structure length	389
sequence length	434
chains with identical sequence	B
ec nomenclature
pdb deposition date	2007-12-21

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

cath code	Class	Architecture	Topology	Homology	Domain
2.40.160.60	Mainly Beta	Beta Barrel	Porin	Outer membrane protein transport protein (OMPP1/FadL/TodX)	3bryA00

2R8AA 3PF1A 2R89A 3PGUA 3BS0A 3DWNA 3PGRA 2R4OA 3DWOX 3PGSA 1T16A 2R4NA 1T1LA 2R4PA 3BRZA 3BRYA 2R88A 2R4LA
chains in the Genus database with same CATH superfamily

3PQUA 5IYUA 4FZNA 5G3AA 3RBHA 4C69X 2YNKA 3LK42 4N75A 4FZLA 1OSMA 3A0BO 4KRAA 4RJXA 5AFUL 2X9KA 4O3XB 4GHBA 1GFOA 4C4VA 1QJ8A 3K19A 1MPFA 2KC0A 4BUMX 4O3YA 1ZHXA 3UPGA 4RLCA 3DWOX 4UB6O 2F1VA 3A2SX 4FRXA 4O3ZA 1BXWA 2AXTO 3HOLA 5KAIO 2JQYA 3BRYA 2R88A 2R4LA 3LK3A 1ZHWA 3SY7A 4N74A 4AYID 1GFNA 1GFMA 2F1TA 3T0SA 4PR7A 4AKRB 2LHFA 2MHLA 2XG6A 3KVDD 2O4VA 3NJTA 3VY9X 3T24A 3DA3A 3HW9A 4FESA 3WU2O 3QRAA 2WVPA 1MM4A 3BS0A 3C5OA 4AKMA 2ERVA 4RL9A 1BH3A 5EE2A 4FQEA 3DZMA 3VZTX 2R4PA 2OMFA 1QJ9A 4AYEC 1P4TA 2LFUA 1QJPA 4AUIA 2XE1A 4FZMA 4XNLA 4G75A 4E1SA 7PRNA 5GV0A 2Y0HA 1ORMA 2K0LA 4D5UA 4E1TA 3AA0B 2J1NA 3VE1A 5FVNA 1S5LO 4FT6A 1GFQA 3AA6B 3SYBA 2IWWA 4LSIA 3DA4A 2IWVA 3HOEA 4XNKA 3G7GA 3JCUO 4G76A 4B61A 2FGRA 4K3CA 2J4UP 5DL7A 2F1CX 3FYXA 3SY9A 4GCQA 4JCHA 5PRNA 8PRNA 1ZHZA 3O0EA 4UB8O 3AA1B 5G38A 3A0HO 4GCSA 2R8AA 3SYSA 4FSOA 4AFKA 3POQA 3LK41 4D65A 4AKRA 4FRTA 2KXPA 1IZNB 2KDYA 2R4OA 3AA7B 3AAAB 3AAEA 2W80C 4JFBA 4O4UA 4O3WA 4F4BA 4C4VB 1E54A 4FOZA 4LSFA 4LSEA 2XE3A 2KZ7B 3PF1A 3SZVA 2YPVA 4FMSA 3VY8X 3PGSA 3UAQA 4AYMC 3WI4A 4K3BA 5H2FO 4C00A 2M07A 1Q9FA 4GF4A 4IL6O 1YS5A 2MNHA 3VZUX 3KZIO 2K4TA 2Y7SA 1HXUA 2WJQA 3JTYA 3AA0A 5TISO 2Y0LA 3AA6A 3VZWX 4Z3TA 2PORA 1G90A 4LSHA 3SZDA 3LK2B 1H6S1 5G26A 2R4NA 5ADXL 2XE2A 2R89A 2QTKA 4O49A 2Y2XA 2ODJA 2ZLDA 3PRNA 3UU2A 2FGQX 4QQ1A 2W81C 3EMNX 3POUA 4KR8A 5T5FA 4AZLA 1MM5A 5GTHO 2XE5A 2PRNA 1HXXA 3DWNA 5B5EO 1ZHYA 3HWBA 3TZGA 6PRNA 1OPFA 5DL8A 1IZNA 3QRCA 3AAAA 3AA7A 3PORA 2N2MA 3NSGA 4AYNA 1BT9A 1T16A 3PQSA 4RLBA 1GFPA 1PHOA 2ZFGA 5G39A 2KZ7A 3LK3B 3PGUA 3POXA 1THQA 2JMMA 5GTIO 2XTRA 4FUVA 3PGRA 2X27X 5JDPA 2N2LA 1Q9GA 4PJ0O 5ADXK 5DL5A 2WJRA 1ZHTA 4U9CA 3WI5A 3V8UA 4N58A 2Y0KA 5D5DA 2M06A 2KXPB 3AAEB 4FSPA 4RJWA 4D64A 4N59A 2GE4A 4O4XA 3BRZA 5E79O 4KR4A 3GP6A 5DL6A 4CTDA 3VE2A 3LK2A 4GCPA 3T20A 4PUXA 5AFUK 5B66O 4AYDC 2XMXA 2XTQA 1T1LA 1HXTA 3AA1A 1PRNA 5KAFO
chains in the Genus database with same CATH topology

2R8AA 3PF1A 2R89A 3PGUA 3BS0A 3DWNA 3PGRA 2R4OA 3DWOX 3PGSA 1T16A 2R4NA 1T1LA 2R4PA 3BRZA 3BRYA 2R88A 2R4LA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2R8A A;  3PF1 A;  2R89 A;  3PGU A;  3BS0 A;  3DWN A;  3PGR A;  2R4O A;  3DWO X;  3PGS A;  1T16 A;  2R4N A;  1T1L A;  2R4P A;  3BRZ A;  3BRY A;  2R88 A;  2R4L A; 
#chains in the Genus database with same CATH topology
 3PQU A;  5IYU A;  4FZN A;  5G3A A;  3RBH A;  4C69 X;  2YNK A;  3LK4 2;  4N75 A;  4FZL A;  1OSM A;  3A0B O;  4KRA A;  4RJX A;  5AFU L;  2X9K A;  4O3X B;  4GHB A;  1GFO A;  4C4V A;  1QJ8 A;  3K19 A;  1MPF A;  2KC0 A;  4BUM X;  4O3Y A;  1ZHX A;  3UPG A;  4RLC A;  3DWO X;  4UB6 O;  2F1V A;  3A2S X;  4FRX A;  4O3Z A;  1BXW A;  2AXT O;  3HOL A;  5KAI O;  2JQY A;  3BRY A;  2R88 A;  2R4L A;  3LK3 A;  1ZHW A;  3SY7 A;  4N74 A;  4AYI D;  1GFN A;  1GFM A;  2F1T A;  3T0S A;  4PR7 A;  4AKR B;  2LHF A;  2MHL A;  2XG6 A;  3KVD D;  2O4V A;  3NJT A;  3VY9 X;  3T24 A;  3DA3 A;  3HW9 A;  4FES A;  3WU2 O;  3QRA A;  2WVP A;  1MM4 A;  3BS0 A;  3C5O A;  4AKM A;  2ERV A;  4RL9 A;  1BH3 A;  5EE2 A;  4FQE A;  3DZM A;  3VZT X;  2R4P A;  2OMF A;  1QJ9 A;  4AYE C;  1P4T A;  2LFU A;  1QJP A;  4AUI A;  2XE1 A;  4FZM A;  4XNL A;  4G75 A;  4E1S A;  7PRN A;  5GV0 A;  2Y0H A;  1ORM A;  2K0L A;  4D5U A;  4E1T A;  3AA0 B;  2J1N A;  3VE1 A;  5FVN A;  1S5L O;  4FT6 A;  1GFQ A;  3AA6 B;  3SYB A;  2IWW A;  4LSI A;  3DA4 A;  2IWV A;  3HOE A;  4XNK A;  3G7G A;  3JCU O;  4G76 A;  4B61 A;  2FGR A;  4K3C A;  2J4U P;  5DL7 A;  2F1C X;  3FYX A;  3SY9 A;  4GCQ A;  4JCH A;  5PRN A;  8PRN A;  1ZHZ A;  3O0E A;  4UB8 O;  3AA1 B;  5G38 A;  3A0H O;  4GCS A;  2R8A A;  3SYS A;  4FSO A;  4AFK A;  3POQ A;  3LK4 1;  4D65 A;  4AKR A;  4FRT A;  2KXP A;  1IZN B;  2KDY A;  2R4O A;  3AA7 B;  3AAA B;  3AAE A;  2W80 C;  4JFB A;  4O4U A;  4O3W A;  4F4B A;  4C4V B;  1E54 A;  4FOZ A;  4LSF A;  4LSE A;  2XE3 A;  2KZ7 B;  3PF1 A;  3SZV A;  2YPV A;  4FMS A;  3VY8 X;  3PGS A;  3UAQ A;  4AYM C;  3WI4 A;  4K3B A;  5H2F O;  4C00 A;  2M07 A;  1Q9F A;  4GF4 A;  4IL6 O;  1YS5 A;  2MNH A;  3VZU X;  3KZI O;  2K4T A;  2Y7S A;  1HXU A;  2WJQ A;  3JTY A;  3AA0 A;  5TIS O;  2Y0L A;  3AA6 A;  3VZW X;  4Z3T A;  2POR A;  1G90 A;  4LSH A;  3SZD A;  3LK2 B;  1H6S 1;  5G26 A;  2R4N A;  5ADX L;  2XE2 A;  2R89 A;  2QTK A;  4O49 A;  2Y2X A;  2ODJ A;  2ZLD A;  3PRN A;  3UU2 A;  2FGQ X;  4QQ1 A;  2W81 C;  3EMN X;  3POU A;  4KR8 A;  5T5F A;  4AZL A;  1MM5 A;  5GTH O;  2XE5 A;  2PRN A;  1HXX A;  3DWN A;  5B5E O;  1ZHY A;  3HWB A;  3TZG A;  6PRN A;  1OPF A;  5DL8 A;  1IZN A;  3QRC A;  3AAA A;  3AA7 A;  3POR A;  2N2M A;  3NSG A;  4AYN A;  1BT9 A;  1T16 A;  3PQS A;  4RLB A;  1GFP A;  1PHO A;  2ZFG A;  5G39 A;  2KZ7 A;  3LK3 B;  3PGU A;  3POX A;  1THQ A;  2JMM A;  5GTI O;  2XTR A;  4FUV A;  3PGR A;  2X27 X;  5JDP A;  2N2L A;  1Q9G A;  4PJ0 O;  5ADX K;  5DL5 A;  2WJR A;  1ZHT A;  4U9C A;  3WI5 A;  3V8U A;  4N58 A;  2Y0K A;  5D5D A;  2M06 A;  2KXP B;  3AAE B;  4FSP A;  4RJW A;  4D64 A;  4N59 A;  2GE4 A;  4O4X A;  3BRZ A;  5E79 O;  4KR4 A;  3GP6 A;  5DL6 A;  4CTD A;  3VE2 A;  3LK2 A;  4GCP A;  3T20 A;  4PUX A;  5AFU K;  5B66 O;  4AYD C;  2XMX A;  2XTQ A;  1T1L A;  1HXT A;  3AA1 A;  1PRN A;  5KAF O; 
#chains in the Genus database with same CATH homology
 2R8A A;  3PF1 A;  2R89 A;  3PGU A;  3BS0 A;  3DWN A;  3PGR A;  2R4O A;  3DWO X;  3PGS A;  1T16 A;  2R4N A;  1T1L A;  2R4P A;  3BRZ A;  3BRY A;  2R88 A;  2R4L 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...

3BRYA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN