current user: public

anford Burnham Prebys Medical Discovery Institute
We are hiring bioinformatics experts and software developers. Join us!

Query: 3lvz_A mol:protein length:294 Blr6230 protein, from PDB0516

Results of FFAS03 search in COG0516
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.
    .   10    .   20    .   30    .   40    .   50    .   60    .   70    .   80    .   90    .  100    .  110    .  120    .  130    .  140    .  150    .  160    .  170    .  180    .  190    .  200    .  210    .  220    .  230    .  240    .  250    .  260    .  270    .  280    .  290
# Score Template Links and tools%idFirst MRRLTAALCALTLLSTGAQAQTIKDFLAVAMKKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALEKKLast
1 -48.000[R] COG0491 Zn-dependent hydrolases, including glyoxylases  ali follow..  21  5..............................................GFAAGPYKTNCYVVRGENEVAIIDPG-MHAHDDLVEYITTNNLS---VDKIVLTHGHIDHTRDAGVVAKRFNAPVYIHPDDAFFLEVYKGSGTKTAMLFDADNMVSLRDLVDGETITLAGEEFTLKHAPGHSPGCTLIVGK--EYCFSGDVLFKGS--------IGRTDFESDADAMNESLRAVLPLDDALILPGHGPTTTMRA------ERTGNPFLLA............................ 212
2 -35.500[R] KOG0814 Glyoxylase  ali follow..  23  55........................................................SYLLADLKNAVIIDP-VLEQAKRDAQLVKDLGFE---LKYAINTHMHADHITGSGWLRKLTGCQSVIAAASGA---------------------KADRHLNEGDRIDFGTHVIDALATPGHTNGCMTYVIKDQGCVFTGDTLLIRGC--------GRTDFQGCPRNLYENVSKIFTLPENFRIPAHDYKGQMESSVWEEKRYNPRLTKDIEEFVKIMENLNLPYPKKI.......... 254
3 -34.900[R] KOG0813 Glyoxylase  ali follow..  18  18..........................................LGCNPSAMTLQGTNTYLLGSGSRRILIDTGDEDVPQYIAHLGDVLQQEKASIDTILLTHWHHDHVGGVKSIVGTKLAEKDCRVFKFGRTDAPDVCPEI-------PTDIKLHPLAHNQEFTTEGANVRVVHTPGHTTDHVVLAMNE-------GTLFSGDCILGEGTAV------EDLFEYMKSLEKILDIKPQRIFPGHGNVIE-------------EPIGKIEYYINHRNQREQQILQFFVQRPNEN... 234
4 -26.100[S] KOG4736 Uncharacterized conserved protein  ali follow..  13  297.......................................................AITLVNDNGYIVLIDTGASSDTERLLHSLAKESVTLDQIDSVVITHASPGHMGNMNFFAQ---KPILYHSMEYIGRHVTPT----------------ELKERPYRKLSGN---VEVWKTPGHTQHDLSVLVHNVAGY--GTMAIVGDLLLSEKRDVMIEEGVWDNAIKRQNANLIVCM-ADWIVPGHGQPFRVLPNYRQKAG..................................... 478
5 -22.500[R] COG1237 Metal-dependent hydrolases of the beta-lactamase superfamily II  ali follow..  17  29........................................................SALVESNGYKVLVDTGTDGKV--LLNNMHELGIDANDIDVLFITHGHYDHTGGLKEFLKERSIEVYAHPLPGFISSGEIKRVTWDRAVGYFPDGRKDPVRDDMALIVEGSKGLVVISGCGHS-GIINIARHAMELRGSKIAALIGGFHLRGAKK----------ELLDDVVTNMKELGVNALYPGH.................................................... 244
6 -20.000[C] COG0426 Uncharacterized flavoproteins  ali follow..  15  3...................SMSTTGNAHTENVQHRLTVETVEIAPNTTAIRCTTYNSYLIR-GEQTVLVDTSHQKFRQLYLETLKGL-INPKAIDYIIVSHTEPDHSGLVEDVLQLARATVLASKIALQFLEGLVHDPFSK------------RIVKSGDRIDIGGHEIEFVSAP-HWPDTIFSYDRKTEVIYTCDA-FGMHFCDNRTFDEDLEAIEADFRFYLNAMKRMGDLKIKIIANGHGPTECYQSWSQRQAKSETTVGLFYVADYGYSNLLVQAIGEGIQKTGVAVE.. 302
7 -18.900[R] COG2248 Predicted hydrolase (metallo-beta-lactamase superfamily)  ali follow..  12  16................................EWRRTVDPQVPGSNVIPLASESLLALFLKIGKVGILIDPGVQAEMKALSLAREKIQEYAKKAQIVTISHYHYDHHTPFESSSVEKAREIYAGKLLLIKHPTENINNSQKKRAHEFKEIAKDIKFADSQSFDFGSFTIEFSPPVPHGRSKLGYVLMVLVDDGKKSVLHASDTQLINDKAVEAHRVGNVKEIGMKNINRIISETNAIVLDHHIIRDKGYERFFSELDER---PLTFAEFLGKESAPLEAYRRELHKLEKGEEVE 339
8 -17.800[A] KOG1137 mRNA cleavage and polyadenylation factor II complex, BRR5 (CPSF subunit)  ali follow..  11  23.............................................IVTPLGAGGRSCVYMSFRGKNILFDCGIHPAYSGMAALPYFDEIDPSSIDVLLITHFHIDHAASLPYFLEKTTGRVFMTHADYVKVSKVSVEDMLFDEQDINKSMDKIEVIDFHQTVEVNGIKFWCYTA-GHVLGAAMFMVDIAGV----RILYTGDYSREEDRHLRAAELPIREKRFTDVIHSTVAQGGRVLIPAFA----LDEYWANHPDLHNIPIYYASPLAKKCMAVYQTYILSMNDRIRNQFAN 309
9 -17.700[A] KOG1135 mRNA cleavage and polyadenylation factor II complex, subunit CFT2 (CPSF subunit)  ali follow..  16  19.......................................................LCYLLQVDGDYILLDCGWDERFG--LQYFEELKPFIPKISAVLISHPDPLHLGGLPYLVSKCGAPVYATVPDMVYSHLDVEEFEHYTLDDVDTAFEKVEQVKYNQTVVLSGVHFTALPA-GHMLGGSIWRICRVTGE---DIVYCVDFNHKKERHLNGCSFDNFNEQLVTKILRTVRQKGDCMIVIDTELAHLLDQLWSNADAGLSTY--ASSVVQFAKSQLEWMNEKLFKYDSSSARY 300
10 -17.300[A] KOG1136 Predicted cleavage and polyadenylation specificity factor (CPSF subunit)  ali follow..  13  5.............................................KITPLGAGGRSCLLLSMGGKNIMLDCGMHMGYNDERRYIVPEGPITSHIDCVIISHFHLDHCGALPYMSEIVGGPIYMTHPDMRKVAVERKGESNFFTTQMIDCMKKVIPVTLHQSMMVDTDLEIKAYYAGHVLGAAMFWIKVGS----QSVVYTGDYNMTPDRHLGAAWIDCRERDFLKKVHECVAKGGKVLIPGRAQELCILLETYWERMNLKYPIYFALGLTEKANTYYKMFITWTNQKIRKTFVH 296
11 -16.600[T] COG5212 Low-affinity cAMP phosphodiesterase  ali follow..  14  26.............................................TLYSLGQNGCSSHLISDFQEIISLDGGS--HLSALVELIQSKHLSEQRIKTFLITHCHLDHIYGAVINSAMVGLNYVIDTLKKHVFNNLLWPSLDKAGFINFQVVEPSMYTSLTTTLSILPFPVNHGSSFGQELKSSAFLFRNNLSDRY--FLAFGDVEPDMVASEPLNIHIWRACSSLIAQRKLSHILIECSTPGHFCPRHLVNELCILQSLVQSYGVIMPTLTCLLTHLKSHPLDVILEQLESLSSK 328
12 -16.400[R] COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain  ali follow..  14  179.............................................RVTFLGGSRESCYLLQTPESRILIDCGVNVSNLSSTPLYVPEVQPLDALDAVVITHAHLDHCGLVPLLKFGYRGPIYLTPPDFLEVAGREGTNPPYSSNLIREALKHTITLDYGVVTDISPDVRLTFYNAGHILGSAIAHFHIGEGHY--NIAFTGDFKFEKTRLFDQPSRKEAEERLIEVINRTLDRGGKVLIPTFA-MIVLEEAMREKRLRETYVYLDGMIHTAYPEYLNAQLRDLIFYHGINP... 473
13 -15.200[R] COG1235 Metal-dependent hydrolases of the beta-lactamase superfamily I  ali follow..  12  34.......................................PVSGENFRKYGGN--TICIEVRCGDHVLLFDAGSG-----LHPAGLALRAEGITDVNLFFSHCHYDHIVGFPYFKAIWSGHLAGSMTTREMLKDFMSPPWFPVPLEICCAKIATRDFKAGDVLVHPGLSIRTGML-NHPGNAIGYRLDWEGKSLAI-----------------ITDTEHEPSSIDETVLDLIR-DVDLFL-GHSSWQQAIRLAKLADAKN-APSRSDEELDDIEKQAKAEFNGAFAAMDGQV... 289
14 -15.200[R] COG0595 Predicted hydrolase of the metallo-beta-lactamase superfamily  ali follow..  12  1.....................................MSNIKITP-LGGVREFGKNMYLVEVEEQIFVLDAGLK-GVDFVIPDITYLLENADRVAGIFLTHGHADSIGALPYIVSELKVPVFGSELTIELAKINVKNYADSRKFNDFHVVTEDTEIDDGNIVYTGDFRFDPAVAKGYNSGVLALLSSSPNALSTMQSASEHEIYEKIYDYIDDNEGRVIIACNAGNLGRIQQTGRRVAFTGEDQIIETATRLNKLQIVDKKSIIKPAEIKKYADNELVILETGRMGEPLKSLGD 308
15 -14.300[R] COG2333 Predicted hydrolase (metallo-beta-lactamase superfamily)  ali follow..  15  84.............................................QVDTLDVGQGLATLIVKNGKGILYDTGSSMAELEILPYLQREGIV---LEKLILSHDDNDHAGGASTILKAYPNVELITPSRKNYGENYRTF------------------CTAGRDWHWQGLHFQILSPHNRADNSHSCVILVDDGK--NSVLLTGDAEAKNEQIFAR-----------------TLGKIDVLQVGHHGSKTSTSEYLLSQVRPDVAIISSGRWNPWKFPHYSVMER............ 288
16 -14.000[J] COG1236 Predicted exonuclease of the beta-lactamase fold involved in RNA processing  ali follow..  16  44...........................................................NAGELRTFSIDTTRSPG-------------KQPQPDAYLITHAHSDHHGKSAMLSP----RAVCTDKTATALE------------IRHDRKYVGSMCRLGDEIEIEGVRVKTYPT-AHTAGAAAFYWENDVGTR---ILVTGDVKLITEANYGDPEDPCHFADDLESMKCALFESGPVAFGAYEFGKAQRAVELMRGFGYEGAIRMEARTRALTRSMLEDAGELAGIDSRGEDE. 255
17 -12.800[Q] COG2015 Alkyl sulfatase and related hydrolases  ali follow..  16  114........................................YKVTDRIYQVGYDLANITFVKGDTGWIVFDPLTVPATAKAALDFVNQELGERPVKAVVYSHAHADHFGGVKGIVSQEQVPIIAPKAENVLAGNAMSRRTTYQYGNVLPKAPTKVISEQTETVVIDGVTMEFQNTPGESPAEMNTYFPQFKALWMAENTVGGLHNVYTLRGAEVRDAKAWSKYINESIHMYAK-EADVMFASHTWPRWGNDNINHFLRKQRDMY............................... 371
18 -9.780[R] KOG3798 Predicted Zn-dependent hydrolase (beta-lactamase superfamily)  ali follow..  10  85.............................................FATWLGH---ATVLVDLEGVKFVTDPVWADRASFTSKRYRPPPMKLEDLDFAVVSHDHYDH------LDADAVKRITNLNPQIKWFVPLGLKKWMKNQGIGADGSNTVTELNESSEFVKNGKTITIWCLPAHSGQNHRLWSGWAVIGENRRFYFPGDTGF---CDVEFKKIGEKLGPFDLAAIPIGAYEPRWFMKSHINPDEAVEVHKLVRARNSIGI-----WGTYPMGTTEYYLEPRDKLKELMDAR 334
19 -9.700[R] KOG2121 Predicted metal-dependent hydrolase (beta-lactamase superfamily)  ali follow..  15  482.........................................RDDMEIVILGTRNVSAIFIDFSRGSLLLDCG-EGTLGQLKRGLDGADEAVRKLRCIWISHIHADHHTGLARIKGVTHEPVIVEAEGSLFTQGSPMQSVFKRSDISMDNSSVLLCLKNLKKVEIGLNDLISFPV--HCPQAYGVVIKAAERVNSWKMVYSGDSEATFEDALIEEALAKNHSTTKEAIDVGSAANVYRIVLTHFSQESHMHNTCIAFDLMSINMADLHVLPKVLPYFKTLFRDEMVEDEDADDVA 828
20 -9.590[L] KOG1361 Predicted hydrolase involved in interstrand cross-link repair  ali follow..  13  124................TTSALGKRRRDSSFSNDSPRPCPFYKKLPGT-------------------FTVDA------------------CVQGCSAYFLTHFHADHYIGLT--KAWSHGPIYCSSLTSRLLRLSLSVNPSS------------HPLELDVEYTINGIKVTLIEA-NHCPGAALIHFRLLDG---TCYLHTGD-TTYCNPRYKFPSKEDVLSYVVRITKDFLRKQPKTLI----GSYSIGKELAIAKALGVKIFANASRRRILQSFGWDDISKNLSTDGKATC.. 374

FFAS is supported by the NIH grant R01-GM087218-01
1 1 8 0 3 2   jobs submitted since Jan 1, 2011
Comments and questions to: webmaster

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.

Alexey M. Eroshkin, Andrew LeBlanc, Dana Weekes, Kai Post, Zhanwen Li, Akhil Rajput, Sal T. Butera, Dennis R. Burton, Adam Godzik. bNAber: database of broadly neutralizing HIV antibodies. Nucl. Acids Res. 2013; published on November 7, 2013.

Ye Y, Godzik A. Comparative analysis of protein domain organization. Genome Res. 2004 Mar;14(3):343-53.