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 <-- 1.735 --> Intermediate <-- 1.067 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1iz0a2) through the intermediate protein (d1k92a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1k92a1 Argininosuccinate synthetase,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1iz0a2 Quinone oxidoreductaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.735 --> Intermediate
DALI alignment (Z-score: 11.0 Raw score:898.40) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1k92a1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1k92a1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1k92a1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1k92a1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1k92a1 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvGLRAyvakngfRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMP 360 :::: ::::::::::::::::::::::::: :::::::: d1k92a1 1 ---------ttilkHLPV------gQRIGIAFSGGLDTSAALLWMRQKGA--VPYAYTAN 43 query 361 SKY-SSDHsKGDAAELARRTGL-NFRTVSIEPMFDAYMASLG-----------ltGLAEE 407 ::: :::: ::::::::::::: ::::::::::::::::::: ::::: d1k92a1 44 LGQpDEED-YDAIPRRAMEYGAeNARLIDCRKQLVAEGIAAIqcgafhnttggltYFNTT 102 query 408 NLQSRLRGTTLMAISNQEGH-IVLAPGnkselaVGYST-lyGDSV--------gAYGPIK 457 :::::::::::::::::::: :::::: ::::: :::: :::::: d1k92a1 103 PLGRAVTGTMLVAAMKEDGVnIWGDGS-----tYKGNDierFYRYglltnaelqIYKPWL 157 query 458 -------dVYKTSIFRLAEWRNRaaaergqtppipeasITKPDypvldailelyvdrdtg 510 ::::::::::::::: ::::: d1k92a1 158 dtdfidelGGRHEMSEFMIACGF-------------dyKMSVE----------------- 187 query 511 adaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1k92a1 188 ---------------------------------------------------------k 188 FAST alignment (Normalized score: 4.46 Raw score:1458.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1k92a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1k92a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1k92a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1k92a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1k92a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF----------RSVLIGLSGGIDSALVAAIACDALG 350 :::::::::::::::::::::: d1k92a1 1 -------------------------TTILKHLPVGQRIGIAFSGGLDTSAALLWMRQ--- 32 query 351 AQ---NVYGVSMPSKYSSDH------SKGDAAELARRTGL-NFRTVSIEPMFDAYMASLG 400 ::::::::: :::::::::::::: ::::::::::::::::: d1k92a1 33 --KGAVPYAYTANL------GQPDEEDYDAIPRRAMEYGAENARLIDCRKQLVAEGIA-- 82 query 401 LTG----------------LAEENLQSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYS 443 ::::::::::::::::::::::: :::::::::: d1k92a1 83 ---AIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKEDGVNIWGDGSTYK------- 132 query 444 TLY------GDSVG---------AYGPIKDVYKTS-----------IFRLAEWRNRAAAE 477 :::: :::: ::::::::::: d1k92a1 133 ---GNDIERFYRY-GLLTNAELQIYKP--------WLDTDFIDELGGRHEMSEFMIA--- 177 query 478 RGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYK 537 d1k92a1 178 ------------------------------------------------------------ 178 query 538 RRQYPPGTKISAKGFGKDRRLPITNRWREGH----------- 568 d1k92a1 178 -------------------------------CGFDYKMSVEK 188 TMalign alignment (TM-score: 0.25 Raw score:141.19) query 1 ---SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLAL 57 d1k92a1 1 TTI--------------------------------------------------------- 3 query 58 RSSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHR 117 d1k92a1 4 ------------------------------------------------------------ 4 query 118 GRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARS 177 d1k92a1 4 ------------------------------------------------------------ 4 query 178 AGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDR 237 :: d1k92a1 4 ----------------------------------------------LK------------ 5 query 238 DGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGG 297 d1k92a1 6 ------------------------------------------------------------ 6 query 298 YADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGV 357 :: ::: ::::::::::::::::::::::::: ::::: d1k92a1 6 -----------------HL--PVG----QRIGIAFSGGLDTSAALLWMRQKGA--VPYAY 40 query 358 SMPSKYSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAYMASLG---LT--------GLA 405 :::::::::::::::::::::::: ::::::::::::::::::: :: ::: d1k92a1 41 TANLGQPDEEDYDAIPRRAMEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFN 100 query 406 EENLQSRLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTL-YGDS--V-------GAYG 454 :::::::::::::::::::::: :::::: :: ::::: ::: : :::: d1k92a1 101 TTPLGRAVTGTMLVAAMKEDGVNIWGDGS---TY--KGNDIE-RFYRYGLLTNAELQIYK 154 query 455 PIKD---VY-KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTG 510 :::: :: ::::::::::::::: : ::: ::: :: d1k92a1 155 PWLDTDFIDE-LGGRHEMSEFMIACG-----F-DYK--MSV-EK---------------- 188 query 511 ADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1k92a1 189 ---------------------------------------------------------- 189 HHsearch alignment (Probability: 0.96 E-value:0.00) query 326 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 384 ::::::::::::::::::::::: ::::::::::::::::::::::::::::::: ::: d1k92a1 11 QRIGIAFSGGLDTSAALLWMRQK--GAVPYAYTANLGQPDEEDYDAIPRRAMEYGAENAR 68 query 385 TVSIEPMFDAYMASLGLTGLAEENLQSR-----------LRGTTLMAISNQEGHIVLAPG 433 :::::::::::::::::::::::::::: ::::::::::::::::::::: d1k92a1 69 LIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKEDGVNIWGDG 128 query 434 ------NKSELAVGYSTLYGDSVGAYGPIKDVY-------KTSIFRLAEWRN 472 ::::::::::::::: ::::::::::: :::::::::::: d1k92a1 129 STYKGNDIERFYRYGLLTNAE-LQIYKPWLDTDFIDELGGRHEMSEFMIACG 179
Intermediate <-- 1.067 --> Hit
DALI alignment (Z-score: 7.0 Raw score:542.40) d1k92a1 1 ------------------ttiLKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTA 42 ::::::::::::::::::::::::::::::::::::::: d1iz0a2 1 lspeeaaafpvsfltaylalkRAQARPGEKVLVQAAAGALGTAAVQVARAMGLRVLAAAS 60 d1k92a1 43 nlgqpdeedYDAIPRRAMEYGAENARLIDcrkqlvaegiaaiqcgafhnttggltyfntt 102 :::::::::::::::::::: d1iz0a2 61 ---------RPEKLALPLALGAEEAATYA------------------------------- 80 d1k92a1 103 plgravtgtMLVAAMKED-GVNIWGDGStykgndIERFyRYGLL-tnAELQIYK------ 154 ::::::::: ::::::::: :::: ::::: ::::::: d1iz0a2 81 ---------EVPERAKAWgGLDLVLEVR------GKEV-EESLGllaHGGRLVYiapipp 124 d1k92a1 155 --------------------pwldtdfIDELggrhemsEFMIACgfdykmsvek 188 :::: :::::: d1iz0a2 125 lrlmrrnlavlgfwltpllregalveeALGF-----llPRLGRE---------l 164 FAST alignment (Normalized score: 5.94 Raw score:1043.00) d1k92a1 1 TTIL----------------------KHLPVGQRIGIAF--SGGLDTSAALLWMRQKGAV 36 ::::::::::: ::::::::::::::::::: d1iz0a2 1 ----LSPEEAAAFPVSFLTAYLALKRAQARPGEKVLV--QAAAGALGTAAVQVARAMGLR 54 d1k92a1 37 PYAYTANLGQPDEED-YDAIPRRAMEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGG 95 ::::: :::::::::::::::::: d1iz0a2 55 VLAAA----------SRPEKLALPLALGAEEAAT-------------------------- 78 d1k92a1 96 LTYFNTTPLGRAVTGTMLVAAMKED-GVNIWGDGSTYKGNDIER---FYRYGLLT-NAEL 150 ::::::::::: :::::::: :::::::: :::: d1iz0a2 79 --------------YAEVPERAKAWGGLDLVLEV----------RGKEVEESLGLLAHGG 114 d1k92a1 151 QIYKPWLDTDFIDELG------------------------------GRHEMSEFMIACGF 180 ::: ::::::::::: d1iz0a2 115 RLV-------------YIAPIPPLRLMRRNLAVLGFWLTPLLREGALVEEALGFLLP--- 158 d1k92a1 181 DYKMSVEK------ 188 d1iz0a2 159 --------RLGREL 164 TMalign alignment (TM-score: 0.39 Raw score:72.73) d1k92a1 1 ----------TTILKHLPVGQRIGIAFSGGLDTSAALLW-MRQKGAVPYAYTANLGQPDE 49 :::::::::::: :: ::::::::::::: : d1iz0a2 1 LSPEEAAAFP-----------------VSFLTAYLALKRAQA--RPGEKVLVQAAAG--A 39 d1k92a1 50 EDYDAIPRRAMEYGAENARLIDCRKQL-------------VAEGIAAIQCGAFHNTTGGL 96 ::::::::::: :::::::::::::: d1iz0a2 40 -LGTAAVQVARA-MGLRVLAAASRPEKLALPLALGAEEAA-------------------- 77 d1k92a1 97 TYFNTTPLGRAVTGTMLVAAMKEDGVNIWGDGSTYKGNDIERFYRYGLLTNAEL------ 150 :: ::::::::::::::::::: :: :::: ::: ::::: d1iz0a2 78 -----------TY-AEVPERAKAWGGLDLVLEV----RG-KEVE-ESL-GLLAHGGRLVY 118 d1k92a1 151 -----------Q-IYKPWLDTDF-IDELGGRHEMSEFMIAC-GFDY-------KMSVEK 188 : ::::: : :::::::::::::: :::: d1iz0a2 119 IAPIPPLRLMRRNLAVLG----FW---LTPLLREGALVEEALGFLLPRLGREL------ 164 HHsearch alignment (Probability: 0.35 E-value:0.00) d1k92a1 5 KHLPVGQRIGI-AFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRAMEYG 63 ::::::::::: :::::::: :::::::::::::::::::::: :::::::: d1iz0a2 23 AQARPGEKVLVQAAAGALGT-AAVQVARAMGLRVLAAASRPEK---------LALPLALG 72 d1k92a1 64 AENARL 69 :::::: d1iz0a2 73 AEEAAT 78