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Query: gi|13507742|ref|NP_109691.1| DNA gyrase subunit B MPN003 [Mycoplasma pneumoniae M129], from M.pneumoniae

Results of FFAS03 search in SCOP207
Master-slave alignment(slide right to see more) does not show gaps in the query sequence, use ali links to display alignment between query and templates.
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# Score Template Links and tools%idFirst MEDNNKTQAYDSSSIKILEGLEAVRKRPGMYIGSTGEEGLHHMIWEIIDNSIDEAMGGFASTVKLTLKDNFVTIVEDDGRGIPVDIHPKTNRSTVETVFTVLHAGGKFDNDSYKVSGGLHGVGASVVNALSSSFKVWVAREHQQYFLAFHNGGEVIGDLVNEGKCDKEHGTKVEFVPDFTVMEKSDYKQTVIASRLQQLAFLNKGIQIDFVDERRQNPQSFSWKYDGGLVQYIHHLNNEKEPLFEDIIFGEKTDTVKSVSRDESYTIKVEVAFQYNKTYNQSIFSFCNNINTTEGGTHVEGFRNALVKIINRFAVENKFLKETDEKITRDDICEGLTAIISIKHPNPQYEGQTKKKLGNTEVRPLVNSIVSEIFERFMLENPQEANAIIRKTLLAQEARRRSQEARELTRRKSPFDSGSLPGKLADCTTRDPSISELYIVEGDSAGGTAKTGRDRYFQAILPLRGKILNVEKSHFEQIFNNVEISALVMAVGCGIKPDFELEKLRYNKIIIMTDADVDGAHIRTLLLTFFFRFMYPLVEQGNIYIAQPPLYKVSYSNKDLYMQTDVQLEEWKQQHPNLKYNLQRYKGLGEMDAIQLWETTMDPKVRTLLKVTVEDASIADKAFSLLMGDEVPPRREFIEQNARNVKNIDILast
1 -95.000d3m4ia_ e.78.1.1 (A:) DNA gyrase beta-prime domain {Mycobacterium tuberculosis [TaxId: 1773]}  ali model 3D-neighbors follow..  56  1.............................................................................................................................................................................................................................................................................................................................................................................................................................................TDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGE..................... 207
2 -80.000d4k4oa1 d.122.1.0 (A:18-224) automated matches {Enterococcus faecalis [TaxId: 226185]}  ali model 3D-neighbors follow..  51  1...................GLEAVRKRPGMYIGSTSGEGLHHLVWEIVDNSIDEALAGFAKSIQVIIEPDDSITVIDDGRGIPVGIQAKTGRPAVETVFTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSTSLDVRVYKDGKVYYQEYRRGAVVDDLKVI--EETDRHGTTVHFIPDPEIFTETTYDFDKLATRVRELAFLNRGLHISIEDRREGQEDKKEYHYEG....................................................................................................................................................................................................................................................................................................................................................................................................................................... 207
3 -75.000d3cwva1 d.122.1.0 (A:8-206) automated matches {Myxococcus xanthus [TaxId: 246197]}  ali model 3D-neighbors follow..  26  2..................GIVENVRKRPGMYCGDVGEYGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFCTSRTVTAENLVR-------------VATGAGFLGRPPGDGWGWDSMLVVSLALSSRYQVDIWADGRQWRVMGEHGHPQGETPMEPMPVSAERGVRVHFVPDATIFEVLAFDRARLSRRCNELAALAPGLRVSFADLQRGERTLWHL........................................................................................................................................................................................................................................................................................................................................................................................................................................... 197
4 -71.900d1q1da1 d.122.1.2 (A:7-245) DNA topoisomerase II {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  26  1.........SASDKYQKISQLEHILKRPDTYIGSVEVPGLFKIFDEILVNAADNKVRDPSMKRIDVNAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETANVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINRDINVYLNGKS.................................................................................................................................................................................................................................................................................................................................................................................................................................................... 235
5 -64.300d1s14a_ d.122.1.2 (A:) Topoisomerase IV subunit B {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  36  1..................................TDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPE-----------------------EGVPAVELILCISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCY........................................................................................................................................................................................................................................................................................................................................................................................................................................... 166
6 -57.000d1kija1 d.14.1.3 (A:221-392) DNA gyrase B {Thermus thermophilus [TaxId: 274]}  ali model 3D-neighbors follow..  36  1...................................................................................................................................................................................................................................GVASFAKALAEGEDLLYEKPFLIRG----------THGEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLLEILEENPRIAKAVYEKALRAAQAREAARKARELV................................................................................................................................................................................................................................................. 172
7 -55.500d4wuba2 d.14.1.0 (A:221-392) automated matches {Escherichia coli [TaxId: 83333]}  ali model 3D-neighbors follow..  36  1...................................................................................................................................................................................................................................GIKAFVEYLNKNKTPIHPNIFYFS----------TEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMT................................................................................................................................................................................................................................................. 172
8 -54.100d3lnua2 d.14.1.0 (A:261-422) automated matches {Xanthomonas oryzae [TaxId: 291331]}  ali model 3D-neighbors follow..  25  1..................................................................................................................................................................................................................................NGLRDYLKGEMAEHEMLPADLFVGS----------LKKDTEIVDWAAGWVPEGELVQESYVNLIPTAQHGTHVNGLRSGLTDALREFCDFRN-LLPRGVKLAPEDVWDRVTFVLSLKMTDPQFSGQTKERLSSRQAAGFIEGAAHDAFSLYLNQNVEIGEKIAQIAIDRASAR........................................................................................................................................................................................................................................................... 162
9 -49.700d4hyma2 d.14.1.0 (A:216-377) automated matches {Francisella tularensis [TaxId: 376619]}  ali model 3D-neighbors follow..  29  1..................................................................................................................................................................................................................................TGLKGYLDHKLEAETLPAEPFIIDN----------FSNGDSYLDAVFCWCEDPSESIKSYVNLIPTPQDGTHVTGLKNGIYDAIKAYIEKNS-LSVKNIKITANDSFAQLNYVISVKITNPQFAGQTKEKLSNKDVTNFVATAVKDLLTIWLNQNPDEARQIVENISKVAQK............................................................................................................................................................................................................................................................ 162
10 -48.700d1bjta_ e.11.1.1 (A:) DNA topoisomerase II, C-terminal fragment (residues 410-1202) {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  28  1..........................................................................................................................................................................................................................................................................................................................................................................................................................RKSRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFLGLLDQGFLLEFITPIIKVSITKNTIAFYNMPDYEKWREEESHFTWKQKYYKGLGTSLAQEVREYFLDRHLKIFHSLQGNDKDYIDLAFSK---KKADDRKEWLRQYEPG...... 242
11 -47.300d3cwva2 d.14.1.0 (A:207-356) automated matches {Myxococcus xanthus [TaxId: 246197]}  ali model 3D-neighbors follow..  22  1...................................................................................................................................................................................................................................GVAQWAHVLTEARPQLHPEPVVFD----------FTWDGLRVQCALQWCEDEDSTLLSFANAVRTVRHGAHVKGVTQALRGALAKLSGE------TRGAFPWARVAQGLTAIVAVSGRQMAFAGPTKELLAIPGLEEAIRKQLQPLFIELLREHPVTPALLARR................................................................................................................................................................................................................................................................... 150
12 -45.000d1q1da2 d.14.1.3 (A:246-410) DNA topoisomerase II {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  20  3..........................................................................................................................................................................................................................KNYVELYLKSLEKKRQLDNGEDGAAKSDIPT----------ILYERINNRWEVAFAVSDI-SFQQISFVNSIATTMGGTHVNYITDQIVKKISEILKK-----KKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTD-----LATRMFEIADANEEN........................................................................................................................................................................................................................................................ 165
13 -17.400d2hkja3 d.122.1.2 (A:10-228) Topoisomerase VI-B subunit {Sulfolobus shibatae [TaxId: 2286]}  ali model 3D-neighbors follow..  17  1.................LSPAEFFKRNPELAGFPNPARALYQTVRELIENSLD-DVHGILPNIKITIDLIDDVNVVDNGIGIPPQ---------VPNAFGRVLYSSKYVNRQ---TRGMYGLGVKAAVLYSQEIETSPVNSKRIYTFKLNKNEPIIVERGSVENTRGFHGTSVAI----SIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEG................................................................................................................................................................................................................................................................................................................................................................................................................................................... 201
14 -11.500d2e0aa2 d.122.1.0 (A:188-386) automated matches {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  17  61.......................................LHHMLFELFKNAMRATVEHQENQIEVIVVLGKTIKISDRGGGVPLR--------IIDRLFSYTYSTPVMDNSRNAPLAGF-GYGLPISRLYAKYF.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... 157
15 -11.000d4aoha_ d.5.1.1 (A:) Angiogenin {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  12  13........................................QHYDAKPQGRDDRYGLTSPCKDINTFIHGRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFRR............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. 123
16 -10.800d1th8a1 d.122.1.3 (A:1-136) Anti-sigma factor spoIIab {Bacillus stearothermophilus [TaxId: 1422]}  ali model 3D-neighbors follow..  15  1MRNEMHLQFSARSENESFARVTVAAFVAQLDPTMDELTEIKTVVSEAVTNAIIHGYNNDPNIVSISVIIEDHLTVRDEGVGIP-----------IEEARQPLFTTKPELERS--------GMGFTIMENFMDEVIVES................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ 124
17 -10.400d1h7sa2 d.122.1.2 (A:29-231) DNA mismatch repair protein PMS2 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  19  10..........................................AVKELVENSLDAG----ATNIDLKLKDYGLIEVSDNGCGVEEE---------FEGLTLKHHTSQEFADLTQVETFGFRGEALSSLCALSDTISTCHASAKVGTRLMFDHNGKIIQKTPY----PRPRGTTVSVQ--KEFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNQLGQGKRQ.............................................................................................................................................................................................................................................................................................................................................................................................................................................. 184
18 -10.300d4e01a2 d.122.1.4 (A:186-375) Branched-chain alpha-ketoacid dehydrogenase kinase (BCK) {Norway rat (Rattus norvegicus) [TaxId: 10116]}  ali model 3D-neighbors follow..  17  54.......................................LDYILPELLKNAMRATMESHLDTVVITIANNDIIRISDRGGGIAHKDLDR--------VMDYHFTTAE-SGGQSGPMHGF-GFGLPTSRAYAEYL.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... 165
19 -10.100d1bxda_ d.122.1.3 (A:) Histidine kinase domain of the osmosensor EnvZ {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  23  48...........................................IKRAVANMVVNAARYGNGWIKVSSGTEPNFQVEDDGPGIAPEQRKH--------LFQPF-----VRGDSARTISGT-GLGLAIVQRIVD...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... 125
20 -9.840d1id0a_ d.122.1.3 (A:) Histidine kinase PhoQ domain {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  22  12...............NLTSALNKVYQRKGVNISLDISPEIS--FVEVMGNVLDNACKYCLEFVEISARQTDEIVVEDDGPGIPLSKREV-----------IFDRGQRVD----TLRPG-QGVGLAVAREITE...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... 120
21 -9.430d1b63a2 d.122.1.2 (A:1-216) DNA mismatch repair protein MutL {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  16  18......................EVVERPAS------------VVKELVENSLDAG----ATRIDIDIERGGAIRIRDNGCGIKLARHATSKIASLDDLEAI-------------ISLGFRGEALASISSVSRLTLTSRTAEQQEAWQAYAEG---RDMNVTVKPAAHPVGTTLEVLPARRKFRTEKTEFNHIDEIIRRIALARFDVTINLSHNGK................................................................................................................................................................................................................................................................................................................................................................................................................................................... 194
22 -9.090d1ysra_ d.122.1.3 (A:) automated matches {Mycobacterium tuberculosis [TaxId: 1773]}  ali model 3D-neighbors follow..  19  45.......................................LRLAVDNAIANAVKHGGATLVQLSAVSSRAGVEIAIDDNGSGVPEGERQV--------VF------ERFSRGSTASHSGS-GLGLALVAQQAQ...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... 122
FFAS is supported by the NIH grant R01-GM087218-01
1 4 7 2 5 8   jobs submitted since Jan 1, 2011
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Selected papers from Godzik Lab
Ying Zhang, Ines Thiele, Dana Weekes, Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley Deacon, John Wooley, Scott Lesley, Ian Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik. Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima. Science. 2009 Sep 18;325(5947):1544-9.

Mayya Sedova, Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, Kai W Post, Thomas Hrabe, Eduard Porta-Pardo, Adam Godzik Cancer3D 2.0:: interactive analysis of 3D patterns of cancer mutations in cancer subsets. Nucleic Acids Research, gky1098 2018; Published on November 8 2018.

Pawlowski K, Pio F, Chu Z, Reed JC, Godzik A. PAAD - a new protein domain associated with apoptosis, cancer and autoimmune diseases. Trends Biochem Sci. 2001 Feb;26(2):85-7.