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Query: 3gis_X mol:protein length:121 Thrombomodulin, from PDB0516

Results of FFAS03 search in PDB0516
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
# Score Template Links and tools%idFirst VEPVDPCFRANCEYQCQPLNQTSYLCVCAEGFAPIPHEPHRCQLFCNQTACPADCDPNTQASCECPEGYILDDGFICTDIDECENGGFCSGVCHNLPGTFECICGPDSALAGQIGTDCDSGLast
1 -55.2003gis_X mol:protein length:121 Thrombomodulin  ali model  100  1VEPVDPCFRANCEYQCQPLNQTSYLCVCAEGFAPIPHEPHRCQLFCNQTACPADCDPNTQASCECPEGYILDDGFICTDIDECENGGFCSGVCHNLPGTFECICGPDSALAGQIGTDCDSG 121
2 -50.3001dx5_I mol:protein length:118 THROMBOMODULIN  ali model follow..  98  1VEPVDPCFRANCEYQCQPLDQTSYLCVCAEGFAPIPHEPHRCQMFCNQTACPADCDPNTQASCECPEGYILDDGFICTDIDECENGGFCSGVCHNLPGTFECICGPDSALAGQIGTDC... 118
3 -32.6001dqb_A mol:protein length:83 THROMBOMODULIN  ali model follow..  98  3.EPVDPCFRANCEYQCQPLNQTSYLCVCAEGFAPIPHEPHRCQMFCNQTACPADCDPNTQASCECPEGYILDDGFICTDIDE....................................... 83
4 -31.9002w86_A mol:protein length:147 FIBRILLIN-1  ali model follow..  25  3..DIDECESSPCINGVCKNSPGSFICECSSESTLDP-TKTICIETIKGGAAWGSPCTLCQVDPICGKGYSRIKGTQCEDIDECEVFPGKNGLCVNTRGSFKCQCPSGMTLDATGRICL... 147
5 -30.1002w2m_E mol:protein length:107 LOW-DENSITY LIPOPROTEIN RECEPTOR  ali model follow..  25  3...................PMSDYDIPTTENL-----YFQGAMGTNECGGCSHVCDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKAC.... 100
6 -27.9001z1y_A mol:protein length:186 ookinete surface protein Pvs25  ali model follow..  21  42.EEKNECKKGQCIENPDPAQVNMYKCGCIEGYTLKEDTCVLDVCQYKNCGESGECSEIQSAGCSCAIGKVPNDEKKCTKTGETACQLKCNEVCKNVEGVYKCQCMEGFTFDKEKNVCLGP. 180
7 -27.5001uzj_A mol:protein length:162 FIBRILLIN-1  ali model follow..  23  2..DVNECLDPTISGNCVN-TPGSYICDCPPDFELNP-TRVGCVDTRSGNCYLDIRGDNGDTACSNEIGVGVSITVILEDIDECQELPGQGGKCINTFGSFQCRCPTGYYLNEDTRVC.... 161
8 -25.6003gcw_E mol:protein length:83 Low-density lipoprotein receptor  ali model follow..  30  2.........................................AMGTNECGGCSYVCDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKAC.... 82
9 -24.9002bo2_A mol:protein length:143 EGF-LIKE MODULE CONTAINING MUCIN-LIKE HORMONE  ali model follow..  23  1..DSRGCARWPQDSSCVN----ATACRCNPGFSSFSEPMETCDDINECATLSKVSNTEGSYDCVCSPGYEPESENTCQDVDECSSGQH-STVCFNTVGSYSCRCRPGWKPRHGIPNNQK.. 138
10 -21.4001lmj_A mol:protein length:86 fibrillin 1  ali model follow..  24  2..DIDECRPDLCGRGQCVNTPGDFECKCDEGYESGFMMMKNCMDIDECQRDPLLC---------------------------------RGGVCHNTEGSYRCECPPGHQLSPNISACI... 86
11 -21.0001z6c_A mol:protein length:87 Vitamin K-dependent protein S  ali model follow..  28  1....................................KDVDECSLKPSICGTAVCKNIPGDFECECPEGYRYNKSKSCEDIDECSENM-CAQLCVNYPGGYTCYCKKGFKLAQDQKSCEV.. 85
12 -18.9003v65_B mol:protein length:386 Low-density lipoprotein receptor-related prot  ali model follow..  30  1....................................TGEENCNV--NNGGCAQKCMIRGAVQCTCHTGYRLEDGRTCQDVNECAEEGYCSQGCTNSEGAFQCWCEAGYELRPDRRSCKALG 85
13 -18.7001emn_A mol:protein length:82 FIBRILLIN  ali model follow..  31  1........................................SAVDMDECKEPDVCKNTDGSYRCECPFGYIL-AGNECVDTDECSVGNPGNGTCKNVIGGFECTCEEGFEPGPMM....... 79
14 -17.5001gl4_A mol:protein length:285 NIDOGEN-1  ali model follow..  12  3.LAQQTCANNQCSVECRD-YATGFCCRCVANYT---GNGRQCVAEGSPQRVNGKVQVPVVFENTDLHSYVVMHGRSYTAISTIPETGYSLLAPIGGIIGWMFAVEQDGFKNG......... 126
15 -16.8001aut_L mol:protein length:114 ACTIVATED PROTEIN C  ali model follow..  20  5.....................................DGDQCLVLPLEHPCASLCDGIGSFSCDCRSGWEGRFCQREVSFLNCSDNGGCTHYCLEEVGWRRCSCAPGYKLGDDLLQCHP.. 94
16 -16.2001nfu_B mol:protein length:195 COAGULATION FACTOR XA, LIGHT CHAIN  ali model follow..  16  2.EMKKGHLERECEETCSYEEAREVFEDSDKTNEFWNKYKDGDQCETSPCQNQGKCDGLGEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIP.. 121
17 -15.3002mgp_A mol:protein length:99 Merozoite surface protein 1  ali model follow..  13  9.VDTRDIPKNA---GCFRDDDGTEEWRCLLGYKKGEGNTCVENNNPTCDINNGGCDPTKKIICTCKEPTPYYEGVFCSSSS........................................ 99
18 -15.0001apq_A mol:protein length:53 COMPLEMENT PROTEASE C1R  ali model follow..  31  1............................................................................AVDLDECASRSKCQHLCHNYVGGYFCSCRPGYELQEDRHSC.... 50
19 -14.7001pfx_L mol:protein length:146 FACTOR IXA  ali model follow..  17  8.EFVRGNLERECEEKCSFEEAREVFENTEKTNEFWKQYVDGDQCEPNPCLNGGLCDDINSYECWCQVGF---EGKNCEDATCNIKNGRCKQCKTGADSKVLCSCTTGYRLAPDQKSCKP.. 126
20 -14.5002mgr_A mol:protein length:99 Merozoite surface protein 1  ali model follow..  13  9.VDTRDIPKNA---GCFRDDDGTKEWRCLLGYKKGEGNTCVENNNPTCDINNGGCDPTKKIICTCKEPTPYYEGVFCSSSS........................................ 99
21 -14.4001p0s_L mol:protein length:138 Coagulation factor X precursor  ali model follow..  15  7.....EMKKGHLERECMEETCSYEEAR-TNEFWNKYKDGDQCET-SPCQNQGKCKDGLGEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIP.. 126
22 -14.3003s94_A mol:protein length:619 Low-density lipoprotein receptor-related prot  ali model follow..  20  556.................................................................LMGLKATNVHRVIGSNPCAENGGCSHLCLYRPQGLRCACPIGFELISDMKTCIVP. 611
23 -14.2002kl7_A mol:protein length:71 Fibulin-4  ali model follow..  25  1.SDVNECLTIPCEMKCIN-HYGGYLCLPRSAAVINDLHGEGPPPP----------VPPAQHPNPCPPGYEPDDQDSCVD.......................................... 71
24 -13.6003v64_C mol:protein length:349 agrin  ali model follow..  30  1...............................................................................VNECAEEGYCSQGCTNSEGAFQCWCEAGYELRPDRRSCKALG 42
25 -13.3004cbz_A mol:protein length:312 PROTEIN JAGGED-1  ali model follow..  22  196....PECNRAICRQGCSPKHKLPGDCRCQYGWQGLYCDKCIPHPGCVHGICN------EPWQCLCETNWG---GQLCDDLNYCGTHQPCLNTCSNTPDKYQCSCPEGYS............ 298
26 -13.2001yo8_A mol:protein length:634 thrombospondin-2  ali model follow..  22  2..DPDGCLSNPCFPQCSSFPDGSWSCFCPVGFL---GNGTHCEDLDECALVPDICNTQPGFHCPCPPRYR-TEKQVCEPENPCHKHAECIYLGHFSDPMYKCECQTGYA............ 138
27 -13.1004xbm_A mol:protein length:531 Delta-like protein 1  ali model follow..  22  346..SAMTCADGPCFNRCSDSPDGGYSCRCPVGYSGFNCEKKIDYCSSSPCSNGAKCDLGDAYLCRCQAGF---SGRHCDNVDDCASSP--GGTCRDGVNDFSCTCPPGYT............ 454
28 -13.0003kl6_B mol:protein length:57 Coagulation Factor X light chain  ali model follow..  20  2.............................................................................RARKLCSDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPT. 45
29 -12.9003m0c_C mol:protein length:791 Low-density lipoprotein receptor  ali model follow..  25  253.DREYDCKDMSDEVGCVNVTPNKFKCHCRDWSDEPIKECGTNECLDNNGGCSHVCDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAVG 393
30 -12.6004d90_A mol:protein length:143 EGF-like repeat and discoidin I-like domain-c  ali model follow..  30  1....DICDPNPCENICLPLADGSFSCECPDGFTAGPCTPNPCHNGGTCEISEAYRDTFIGYVCKCPRGFN---GIHCQNINECEVEP--GGICTDLVANYSCECPGEFM............ 127
31 -12.6001n1i_A mol:protein length:105 Merozoite surface protein-1  ali model follow..  17  7MSSAHKCIDTNVPEACYRYLDGTEEWRCLLGFK---EVGGKCVPASICEENNGGCAPEKEVECKCTKEGSLFEGVFCSSSSG....................................... 98
32 -12.4004xlw_B mol:protein length:261 Delta-like protein  ali model follow..  16  149.....VCSDNSCSRLCKKRDDPDGSPSCLPGWTGKYCDQPICLS----GCHEQNGYCSKPDECNCRPGWQ---GPLC---NECIPHKGCRHTCTI---PWQCACDEGWG............ 252
33 -12.4002gd4_L mol:protein length:58 Coagulation factor X, Stuart factor, Stuart-P  ali model follow..  21  2...............................................................................RKLCSDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPT. 43
34 -12.4001b9w_A mol:protein length:95 PROTEIN (MEROZOITE SURFACE PROTEIN 1)  ali model follow..  17  1MSSEHRCIDTNVPEACYRYLDGTEEWRCLLYFKEDAGPNMTCKDKNGGCAPEAECNDKNEIVCKCTKEGSLFEGVFCS........................................... 89
35 -12.3004fbr_A mol:protein length:267 Myxobacterial hemagglutinin  ali model follow..  12  31.QNVVALDIKSDDGGKTLKGTMTYNGEGPIGFRGTLSSANNYTVENQWGGTSAPWQPGGTYNGEGPIGFK---SEVTDSAAPWHSGGVWGGKTLSGTMTYNGEGPIGFR............ 196
36 -12.3002ygq_A mol:protein length:324 WNT INHIBITORY FACTOR 1  ali model follow..  26  176....PHCEKALCTPRCMNGGLTPGFCICPPGFY-----GVNCDKANCSTTCFNGGTCFYPGKCICPPGLEGEQCEISKCPQPCRNGGKC-------IGKSKCKCSKGYQ............ 270
37 -12.3003s2k_A mol:protein length:629 Low-density lipoprotein receptor-related prot  ali model follow..  17  578....HPCANGGCSHICLVKGDGTTRCSCPMHLVLLQ-DELSCGE............................................................................. 618
38 -12.2001fax_L mol:protein length:96 FACTOR XA  ali model follow..  26  2.KDGDQCETSPCQNKCKD-GLGEYTCTCLEGFE------------------GKNCELFTRKLCS-------------------LDNGDCDQFCHEEQASVVCSCARGYTLADNGKAC.... 81
39 -12.2004a0p_A mol:protein length:628 LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROT  ali model follow..  17  580....HPCANGGCSHICLVKGDGTTRCSCPMHLVLLQ-DELSCGGT............................................................................ 621
40 -12.2001dan_L mol:protein length:152 BLOOD COAGULATION FACTOR VIIA light chain  ali model follow..  25  46..DGDQCASSPCQNSCKD-QLQSYICFCLPAFEGRNCETHK-ICVNENGGCEQYCHTGTKRSCRCHEGYSLADGVSCTPTVECGKIPILE--------KRNASKPQG.............. 151
41 -12.2001cej_A mol:protein length:96 PROTEIN (MEROZOITE SURFACE PROTEIN 1)  ali model follow..  16  1..NISQHQKKQCPQGCFRHLDEREECKCLLNYKQEGDPNPTCNENNGGCDADAKCSNGKKITCECTKPDSYPDGIFCSSSN........................................ 96
42 -12.1004gk9_A mol:protein length:279 agglutinin (BOA)  ali model follow..  12  109.QQVVALDIESGDQGATLAGTMTYAGEGPIGFKSQQADGGVYAVENQWGGSSAPWHNGGTYAGEGPIGFK---GNSVATSAPWHPGGIWNGNTFHGSMTYSGEGPIGFR............ 273
43 -12.1003s8v_A mol:protein length:623 Low-density lipoprotein receptor-related prot  ali model follow..  18  577....HPCANGGCSHICLVKGDGTTRCSCPMHLVLLQ-DELSC............................................................................... 615
44 -11.9002vj3_A mol:protein length:135 NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1  ali model follow..  24  3.QDVDECSANPCEHKCINTL-GSFECQCLQGYTGPRCEIDVNECVSNPCQNDATCDQIGEFQCICMPGYE---GVHCEVNTDECASSPCLHRCLDKINEFQCECPTGFT............ 113
45 -11.8004k0v_A mol:protein length:529 TEK tyrosine kinase variant  ali model follow..  22  188.....RCEAQECNHLCTACMNNGVECICPPGFM-----GRTCEKACELHTCKERCSGQEGYGCSCATGWKGLQGPDCKLRCSCNNGEMCDRF---------CLCSPGWQ............ 314
46 -11.7005fm9_A mol:protein length:157 NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1  ali model follow..  26  3..QADPCASNPCANQCLP-FEASYICHCPPSFPTCRQDVNECGQKPGLCRHGGTCNEVGSYRCVCRATHT---GPNCESPSPCQNGGTCRP---TGDVTHECACLPGFT............ 113
47 -11.5004yzu_B mol:protein length:62 Coagulation factor IX  ali model follow..  20  2...DVTCNNGRCEQFCKNSADNKVVCSCTEGYRL-AENQKSCEPAVPF......................................................................... 47
48 -11.4004xlw_A mol:protein length:124 Neurogenic locus notch homolog protein 1  ali model follow..  24  1..DVDECAANPCEHKCLN-TLGSFECQCLQGYTGPRCEIDVNECISNPCQNDATCDQIGEFQCICMPGYE---GVYCEINTDECASSPCLHRCVDKINEFLCQCPKGFS............ 110
49 -11.4004xl1_B mol:protein length:230 Delta-like protein  ali model follow..  24  146......................SYRVVCSDNYY-----GDSCSRLCKKDDHFGHYECQPDGSPSCLPGWT---GKYCDQ-GCHEQNGYCSK-------PDECNCRPGWQ............ 222
50 -11.3003soq_A mol:protein length:318 Low-density lipoprotein receptor-related prot  ali model follow..  22  257.....................................................................AFSQQRQPNATNPCGDNGGCSHLCLMSPVFYQCACPTGVKLLENGKTCKD.. 309
51 -11.1002npr_A mol:protein length:90 Merozoite surface protein 1  ali model follow..  19  2MSSEHTCIDTNVPDACYRYLDGTEEWRCLLTFK-VPASNVTCKDNNGGCAPEAECTDSNKIVCKCTKEGSLFEGVFCS........................................... 90
52 -10.6001ob1_C mol:protein length:99 MAJOR MEROZOITE SURFACE PROTEIN  ali model follow..  17  21.......................................................HLDEREECKCLLNYK-QEGDKCVENPNCDADAKCTEESGSNGKKITCECTKPDSYPLFDGIFCS.. 93
53 -10.6003u3p_A mol:protein length:313 Tumor necrosis factor receptor superfamily me  ali model follow..  16  27....DKCPAGYVSEHCTNTSLR--VCSCPVGFTRHENGIEKCHDCSQPCP-KLPCAALTDRECTCPPGM-FQSNATCAPHTVCPVGWGVRKKGTETEDVRCKQCARGTFSDVPSSV..... 142
54 -10.5005fma_A mol:protein length:154 NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1  ali model follow..  19  37.QDVNECGEKPGHGGTCHNEVGSYRCVCRATHTNCERPYVPCSPSPCQNGGTCRPTGDVTHECACLPGF---TGQNCEENIDDCPGNNCKNACVDGVNTYNCRCPPEWT............ 148
55 -10.4002ra0_L mol:protein length:51 Coagulation factor X  ali model follow..  22  5....................................................................................DNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPT. 40
56 -10.2001kig_L mol:protein length:51 FACTOR XA  ali model follow..  16  4....................................................................................DNGGCDQFCREERSEVRCSCAHGYVLGDDSKSCVST. 39
57 -10.1002vj2_A mol:protein length:169 JAGGED-1  ali model follow..  22  55....PECNRAICRQGCSPKHKLPGDCRCQYGWQGLYCDKCIPHPGCVHGICNE------PWQCLCETNW---GGQLCDDLNYCGTHQPCLNTCSNTPDKYQCSCPEGYS............ 157
58 -9.9601rfn_B mol:protein length:57 PROTEIN (COAGULATION FACTOR IX)  ali model follow..  20  7........NGRCEQFCKNSADNKVVCSCTEGYRL-AENQKSCEPAVPF......................................................................... 45
59 -9.8304bxs_A mol:protein length:423 FACTOR X-LIKE PROTEASE  ali model follow..  17  5...VEEFKSGNIERECIEE-----RCSKEEAREVFEDDEKTETDQCSSNPCHYICDGIGSYTCTCLSGYEGKNCERVLYKSCRVDNGNCWHFCKHVQNDIQCSCAEGYLLGEDGHSCVAG. 127
60 -9.6801dgj_A mol:protein length:907 ALDEHYDE OXIDOREDUCTASE  ali model follow..  13  40......CGKGQCG-ACTVILDGKVVRACAENASVTTLEG--IGAPDCLHPLQHAWIQHGAAQCGCTPGFIVS-AKALLDENVAPSREDVRDWFQKHHN---CRC-TGYKPLVDA....... 148
61 -9.4602m74_A mol:protein length:136 Fibrillin-1  ali model follow..  20  36....NQCIVPICRHSCGDGFSRPNMCTCPSGQIAPSCGSRSIQHCNIRCMNGGSCSDD---HCLCQKGYIGTHCGQPVCESGCLNGGRC-------VAPNRCACTYGFT............ 131
62 -9.4001sij_A mol:protein length:907 Aldehyde oxidoreductase  ali model follow..  14  40......CEQGQCG-ACSVILDGKVVRACADGAQITTIEG--VGQPENLHPLQKAWVLHGGAQCGCSPGFIVS-AKGLLDTNADPSREDVRDWFQKHRN---CRC-TGYKPLVDA....... 148
63 -9.3501tpg_A mol:protein length:91 T-PLASMINOGEN ACTIVATOR F1-G  ali model follow..  23  1......................SYQVICRDEKTQMIYQQHQSWL-------RPVLRSNRVEYCWCNSGRA-VPVKSCSE-PRCFNGGTCQQ--ALYFSDFVCQCPEGFA............ 80
64 -9.2203h5c_B mol:protein length:317 Vitamin K-dependent protein Z  ali model follow..  18  4..GGSPCISQPCL------------------------HNGSCQD------------SIWGYTCTCSPGYEGSNCELAKNECHPERTDGCQHFCLPGQESYTCSCAQGYRLGEDHKQC.... 82
65 -9.1003me2_R mol:protein length:216 Tumor necrosis factor receptor superfamily me  ali model follow..  19  36........LGRCCSRCEPGKYLSSKCTCGPDYLDTWNEEDKCLLHKVCDA-VDPGNHTAPRRCACTAGYHWNSDECCRRNTECAPGFGAQHPLQLNKDTVCTPCLLGFFSDVFSST..... 159

FFAS is supported by the NIH grant R01-GM087218-01
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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.

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.

Li W, Godzik A. cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006 May 26;