HorA Server Transitive Detail

Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets. J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity. Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu


Query: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.905 --> Intermediate <-- 0.834 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1m1nb_) through the intermediate protein (d1vl2a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vl2a1 Argininosuccinate synthetase,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1m1nb_ Nitrogenase iron-​molybdenum protein,​ beta chain​(​Helical backbone​(​ metal receptorChelatase-​likeα/β

Supporting Alignments

Query <-- 1.905 --> Intermediate
DALI alignment (Z-score: 12.5 Raw score:953.20) query 1 dadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1vl2a1 1 ----------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVANVG 36 query 61 ySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQSRL 111 :::: ::::::::::::: :::::::::::::: ::::: ::::::::::: d1vl2a1 37 -QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIARPL 94 query 112 RGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK----DV 157 :::::::::::::: :::::::: :::: :::: :::::: :: d1vl2a1 95 IAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpefLA 149 query 158 YK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaivaag 216 :: :::::::::: :::: d1vl2a1 150 KFkTDLINYAMEK----------GIPI--------------------------------- 166 query 217 ydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1vl2a1 167 -------------------------------------------------- 167 FAST alignment (Normalized score: 7.91 Raw score:1662.00) query 1 DADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPS 59 :::::::::::::::::::::: ::: ::::::::: d1vl2a1 1 -----------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVANV 35 query 60 KYSSDHSKGDAAELARRTG-LNFRTVSIEPMFD-AYMA---SLGLTGL-------AEENL 107 :::: ::::::::::::: ::::::::::::: :::: :::: ::::: d1vl2a1 36 -GQKD-DFVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRYLLGTAI 90 query 108 QSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG---------AY 151 ::::::::::::::::: :::::::::: :::: :: d1vl2a1 91 ARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALNPNLKVI 139 query 152 GPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILEL 201 :: :::::::::: d1vl2a1 140 SP-----WKDPEFLAKFKTDLINYAME--------------------------------- 161 query 202 YVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNR 261 d1vl2a1 162 ------------------------------------------------------------ 162 query 262 WREGH----- 266 d1vl2a1 162 -----KGIPI 166 TMalign alignment (TM-score: 0.47 Raw score:124.53) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1vl2a1 1 ----------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVANVG 36 query 61 YSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQSRL 111 :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::::: d1vl2a1 37 -QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPL 94 query 112 RGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D--VY 158 :::::::::::::: :::::::: : :::::::: :: :::::: : :: d1vl2a1 95 IAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEFLA 149 query 159 KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYD 218 :::::::::::: : : ::: d1vl2a1 150 -KFKTDLINYAME-K------G-IPI---------------------------------- 166 query 219 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1vl2a1 167 ------------------------------------------------ 167 HHsearch alignment (Probability: 0.97 E-value:0.00) query 24 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 82 ::::::::::::::::::::::: ::: ::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK-GFD-VIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 83 TVSIEPMFDAYMASLGLTGLA--------EENLQSRLRGTTLMAISNQEGHIVLAPG--- 131 ::::::::::::::::::::: :::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 132 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRNRAA 173 :::::::::::::::::: ::: :::::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPNLKV-ISPWKDPEFLAKFKTDLINYAMEKGIPI 166
Intermediate <-- 0.834 --> Hit
DALI alignment (Z-score: 6.9 Raw score:528.50) d1vl2a1 1 ------------------------------------------------------------ 1 d1m1nb_ 1 sqqvdkikasyplfldqdykdmlakkrdgfeekypqdkidevfqwtttkeyqelnfqrea 60 d1vl2a1 1 ------------------------------------------------------------ 1 d1m1nb_ 61 ltvnpakacqplgavlcalgfektmpyvhgsqgcvayfrsyfnrhfrepvscvsdsmted 120 d1vl2a1 1 ------------------------------------------------------------ 1 d1m1nb_ 121 aavfggqqnmkdglqnckatykpdmiavsttcmaevigddlnafinnskkegfipdefpv 180 d1vl2a1 1 ------------------------------------------------------------ 1 d1m1nb_ 181 pfahtpsfvgshvtgwdnmfegiaryftlksmddkvvgsnkkinivpgfetylgnfrvik 240 d1vl2a1 1 ------------------------------------------------------------ 1 d1m1nb_ 241 rmlsemgvgysllsdpeevldtpadgqfrmyaggttqeemkdapnalntvllqpwhlekt 300 d1vl2a1 1 ------------------------------------------------------------ 1 d1m1nb_ 301 kkfvegtwkhevpklnipmgldwtdeflmkvseisgqpipasltkergrlvdmmtdshtw 360 d1vl2a1 1 --KEKVVLAYSGGlDTSVILKWLCEKGFDV-IAYVANvgqkddFVAIKEKALKTG----- 52 ::::::::::: :::::::::::::::: :::::: :::::::::::: d1m1nb_ 361 lhGKRFALWGDPD-FVMGLVKFLLELGCEPvHILCHN-----gNKRWKKAVDAILaaspy 414 d1vl2a1 53 --aSKVYVEdlrrefvtdyiftallgnamyegryllgtaiarplIAKRQVEIAEKEGAQY 110 :::::: :::::::::::::::: d1m1nb_ 415 gknATVYIG----------------------------------kDLWHLRSLVFTDKPDF 440 d1vl2a1 111 VAHgatgkgndQVRFElTYAALNP------NLKVISP---------wkdPEFL--AKFK- 152 ::: ::::: ::::::: ::::::: :::: :::: d1m1nb_ 441 MIG--------NSYGK-FIQRDTLhkgkefEVPLIRIgfpifdrhhlhrSTTLgyEGAMq 491 d1vl2a1 153 -----------------tdlinyamekgipi 166 d1m1nb_ 492 ilttlvnsilerldeetrgmqatdynhdlvr 522 FAST alignment (Normalized score: 2.21 Raw score:651.20) d1vl2a1 1 KEKVVLAYSGG------------------------------------------------- 11 d1m1nb_ 1 -----------SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTK 49 d1vl2a1 12 -------------------LDTSVILKWLCEKGFDVIAYVANVGQKD-----DFVAIKEK 47 ::::::::::::: ::::::: :::::::: d1m1nb_ 50 EYQELNFQREALTVNPAKACQPLGAVLCALGF-EKTMPYV-------HGSQGCVAYFRSY 101 d1vl2a1 48 ALKTGA-----SKVYVEDLRREFVTDYIFTALLGNAMYEGRYLL-GTAIARPLIAKRQVE 101 ::: :::::::::::::: :::::::::::: d1m1nb_ 102 FNR---HFREPVSCVSDSMTEDAAV-------------------FGGQQNMKDGLQN--- 136 d1vl2a1 102 IAEKEGAQYVAHGATGKG-----------NDQVRFELTYAA---LNPNLKVISPWKDPEF 147 :::::::::::: ::::::::::: ::::::::: d1m1nb_ 137 CKATYKPDMIAV------STTCMAEVIGDDLNAFINNSKK-EGFIPDEFPVPF------- 182 d1vl2a1 148 LAKFKTDLINYAMEKGIPI----------------------------------------- 166 d1m1nb_ 183 -------------------AHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKI 223 d1vl2a1 167 ------------------------------------------------------------ 167 d1m1nb_ 224 NIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDA 283 d1vl2a1 167 ------------------------------------------------------------ 167 d1m1nb_ 284 PNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASL 343 d1vl2a1 167 ------------------------------------------------------------ 167 d1m1nb_ 344 TKERGRLVDMMTDSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKK 403 d1vl2a1 167 ------------------------------------------------------------ 167 d1m1nb_ 404 AVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEV 463 d1vl2a1 167 ----------------------------------------------------------- 167 d1m1nb_ 464 PLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR 522 TMalign alignment (TM-score: 0.47 Raw score:77.77) d1vl2a1 1 ------------------------------------------------------------ 1 d1m1nb_ 1 SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREA 60 d1vl2a1 1 ------------------------------------------------------------ 1 d1m1nb_ 61 LTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTED 120 d1vl2a1 1 ------------------------------------------------------------ 1 d1m1nb_ 121 AAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPV 180 d1vl2a1 1 ------------------------------------------------------------ 1 d1m1nb_ 181 PFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIK 240 d1vl2a1 1 ------------------------------------------------------------ 1 d1m1nb_ 241 RMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKT 300 d1vl2a1 1 ------------------------------------------------------------ 1 d1m1nb_ 301 KKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTW 360 d1vl2a1 1 -KEKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDD--FVAIKEKALKTGASK-V 56 ::::::::::::::::::::::: ::::::::::: :::: ::::::::::::::: : d1m1nb_ 361 LHGKRFALWGDPDFVMGLVKFLLE-LGCEPVHILCH-NGNKRWKKAVDAILAASPYGKNA 418 d1vl2a1 57 YVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGAT 116 :::::: ::::::::::::: : :::::: d1m1nb_ 419 TVYIGK----------------------------DLWHLRSLVFTDK----P-DFMIGN- 444 d1vl2a1 117 GKGNDQVRFELTYAALNPN-LKVISPW---K--DP--EFLAKFKTDLINYAMEK------ 162 : ::::::::::::::: ::::::: : : :: :: ::::::::: d1m1nb_ 445 --S-YGKFIQRDTLHKGKEFEVPLIRIGFPIFD-RHH--LH-RS-TTLGYEGAMQILTTL 496 d1vl2a1 163 --------------------------GIPI 166 d1m1nb_ 497 VNSILERLDEETRGMQATDYNHDLVR---- 522 HHsearch alignment (Probability: 0.86 E-value:0.00) d1vl2a1 20 WLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAM 79 ::::::::::::::::::::::::::::::::::::: :::::::::::::::::::: d1m1nb_ 304 VEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIP---ASLTKERGRLVDMMTDSHTW 360 d1vl2a1 80 YEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGAT 116 :::::::: ::::::::::::::::::::::::::: d1m1nb_ 361 LHGKRFAL--WGDPDFVMGLVKFLLELGCEPVHILCH 395