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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.669 --> Intermediate <-- 0.743 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1db3a_) 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 d1db3a_ GDP-​mannose 4,​6-​dehydrataseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.669 --> Intermediate
DALI alignment (Z-score: 12.4 Raw score:948.50) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK---- 457 :::::::::::::::: :::::::: :::: :::: :::::: d1vl2a1 93 PLIAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpef 147 query 458 DVYK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaiva 516 :::: :::::::::: :::: d1vl2a1 148 LAKFkTDLINYAMEK----------GIPI------------------------------- 166 query 517 agydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1vl2a1 167 ---------------------------------------------------- 167 FAST alignment (Normalized score: 5.35 Raw score:1644.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSM 359 :::::::::::::::::::::: ::: ::::::: d1vl2a1 1 -------------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVA 33 query 360 PS-KYS-SDHSKGDAAELARRTG---LNFRTVSIEPMFD-AYMA---SLGLTGL------ 404 :: ::: :::::::::: ::::::::::::: :::: :::: d1vl2a1 34 NVGQKDDFVAIKEKALK------TGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRY 84 query 405 -AEENLQSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG----- 451 :::::::::::::::::::::: :::::::::: :::: d1vl2a1 85 LLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALN 133 query 452 ----AYGPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVL 497 :::: :::::::::: d1vl2a1 134 PNLKVISP-----WKDPEFLAKFKTDLINYAME--------------------------- 161 query 498 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR 557 d1vl2a1 162 ------------------------------------------------------------ 162 query 558 LPITNRWREGH----- 568 d1vl2a1 162 -----------KGIPI 166 TMalign alignment (TM-score: 0.23 Raw score:131.95) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKYSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D-- 458 :::::::::::::::: :::::::: : :::::::: :: :::::: : d1vl2a1 93 PLIAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEF 147 query 459 VYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAG 518 :: :::::::::::: : : ::: d1vl2a1 148 LA-KFKTDLINYAME-K------G-IPI-------------------------------- 166 query 519 YDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1vl2a1 167 -------------------------------------------------- 167 HHsearch alignment (Probability: 0.96 E-value:0.00) query 326 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 384 ::::::::::::::::::::::: :::::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK--GFDVIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 385 TVSIEPMFDAYM--------ASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPG--- 433 :::::::::::: ::::::::::::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 434 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRN 472 ::::::::::::::: :::::: ::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPN-LKVISPWKDPEFLAKFKTDLINYAMEKG 163
Intermediate <-- 0.743 --> Hit
DALI alignment (Z-score: 4.5 Raw score:485.90) d1vl2a1 1 KEKVVLAYSGGLDTSVILKWLCEKGFDVIAYVanvgqkddfvaikekalktgASKVYVEd 60 :::::::::::::::::::::::::::::::: ::::::: d1db3a_ 1 SKVALITGVTGQDGSYLAEFLLEKGYEVHGIK------------------rpKFHLHYG- 41 d1vl2a1 61 lrrefvtdyiftallgnamyegryllgtaiARPLIAKRQVEIAEkegAQYVAHGA----- 115 :::::::::::::: :::::::: d1db3a_ 42 ----------------------------dlSDTSNLTRILREVQ---PDEVYNLGamshv 70 d1vl2a1 116 -----------tgkGNDQVRFELTYAA-LNPN-LKVISP--------------------- 141 ::::::::::::: :::: :::::: d1db3a_ 71 avsfespeytadvdAMGTLRLLEAIRFlGLEKkTRFYQAstselyglvqeipqkettpfy 130 d1vl2a1 142 ---------------------------wKDPEflaKFKT--------------------- 153 :::: :::: d1db3a_ 131 prspyavaklyaywitvnyresygmyacNGIL---FNHEsprrgetfvtrkitraiania 187 d1vl2a1 154 -------------------DLINY------------------------------------ 158 ::::: d1db3a_ 188 qglesclylgnmdslrdwgHAKDYvkmqwmmlqqeqpedfviatgvqysvrqfvemaaaq 247 d1vl2a1 159 ------------------------------------------------------------ 159 d1db3a_ 248 lgiklrfegtgveekgivvsvtghdapgvkpgdviiavdpryfrpaeetllgdptkahek 307 d1vl2a1 159 --------------------amekgipi 166 d1db3a_ 308 lgwkpeitlremvsemvandleaakkhs 335 FAST alignment (Normalized score: 3.42 Raw score:805.80) d1vl2a1 1 KEKVVLAY--SGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGA----S 54 :::::: ::::::::::::::::::::::: : d1db3a_ 1 SKVALI--TGVTGQDGSYLAEFLLEKGYEVHGI----------------------KRPKF 36 d1vl2a1 55 KVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLI------AKRQVEIAEKEGA 108 ::: ::::::::::::: d1db3a_ 37 HLH--------------------------------------YGDLSDTSNLTRILREVQP 58 d1vl2a1 109 QYVAHGATG-------------KGNDQVRFELTYAALN-------PNLKVISPWKDPEFL 148 :::::::: ::::::::::::::: ::::::: d1db3a_ 59 DEVYNLGA-MSHVAVSFESPEYTADVDAMGTLRLLEA-IRFLGLEKKTRFYQ-------- 108 d1vl2a1 149 AKFKTDLINYAMEKGIPI------------------------------------------ 166 d1db3a_ 109 ------------------ASTSELYGLVQEIPQKETTPFYPRSPYAVAKLYAYWITVNYR 150 d1vl2a1 167 ------------------------------------------------------------ 167 d1db3a_ 151 ESYGMYACNGILFNHESPRRGETFVTRKITRAIANIAQGLESCLYLGNMDSLRDWGHAKD 210 d1vl2a1 167 ------------------------------------------------------------ 167 d1db3a_ 211 YVKMQWMMLQQEQPEDFVIATGVQYSVRQFVEMAAAQLGIKLRFEGTGVEEKGIVVSVTG 270 d1vl2a1 167 ------------------------------------------------------------ 167 d1db3a_ 271 HDAPGVKPGDVIIAVDPRYFRPAEETLLGDPTKAHEKLGWKPEITLREMVSEMVANDLEA 330 d1vl2a1 167 ----- 167 d1db3a_ 331 AKKHS 335 TMalign alignment (TM-score: 0.46 Raw score:76.29) d1vl2a1 1 KEKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGASKVYVED 60 ::::::::::::::::::::::::::::::::: : ::::::::: d1db3a_ 1 SKVALITGVTGQDGSYLAEFLLEKGYEVHGIKR---------------P--KFHLHYGDL 43 d1vl2a1 61 LRR-----------------------------EFVTDYIFTALLGNAMYEGRYLLG-TAI 90 ::: ::: ::: d1db3a_ 44 SDTSNLTRILREVQPDEVYNLGAMSHVAVSFE---------------------SPEYTAD 82 d1vl2a1 91 ARPLIAKRQVEIAE-KEG--AQYVAHGATGKGN---------------------D--QVR 124 :::::::::::::: ::: ::::::::: ::: : ::: d1db3a_ 83 VDAMGTLRLLEAIRFLGLEKKTRFYQAST-SELYGLVQEIPQKETTPFYPRSPYAVAKLY 141 d1vl2a1 125 FELTYAALN---PNLKVIS----------------------------------------- 140 ::::::::: ::::::: d1db3a_ 142 AYWITVNYRESYGMYACNGILFNHESPRRGETFVTRKITRAIANIAQGLESCLYLGNMDS 201 d1vl2a1 141 ----------P--W-------------K-------------------------------- 143 : : : d1db3a_ 202 LRDWGHAKDYVKMQWMMLQQEQPEDFVIATGVQYSVRQFVEMAAAQLGIKLRFEGTGVEE 261 d1vl2a1 144 ------------------------------------------D-----PEFLAKFK-TDL 155 : :: ::::: ::: d1db3a_ 262 KGIVVSVTGHDAPGVKPGDVIIAVDPRYFRPAEETLLGDPTKAHEKLGWK-PEITLREMV 320 d1vl2a1 156 INY--AM---------EKGIPI 166 ::: : d1db3a_ 321 SEMVA-NDLEAAKKHS------ 335 HHsearch alignment (Probability: 0.20 E-value:0.01) d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEKGFDVIAYVAN-----VGQKDDFVAIKEKALKT 51 ::::::::::::::::::::::::::::::::: ::::::::::::::::: d1db3a_ 2 KVALITGVTGQDGSYLAEFLLEKGYEVHGIKRPKFHLHYGDLSDTSNLTRILREV 56