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 <-- 1.450 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1qora2) 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 d1qora2 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 <-- 1.450 --> Hit
DALI alignment (Z-score: 6.2 Raw score:531.50) d1k92a1 1 -------------------ttiLKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYT 41 :::::::::::::::::::::::::::::::::::::: d1qora2 1 isfeqaaasflkgltvyyllrkTYEIKPDEQFLFHAAAGGVGLIACQWAKALGAKLIGTV 60 d1k92a1 42 AnlgqpdeedYDAIPRRAMEYGAENARLIDCrkqlvaegiaaiqcgafhnttggltyfnt 101 : ::::::::::::::::::::: d1qora2 61 G---------TAQKAQSALKAGAWQVINYRE----------------------------- 82 d1k92a1 102 tplgravtgtMLVAAMKEDG----VNIWGDGStykgndIERFYRYGLL-tNAELQIY--- 153 :::::::::: :::::::: :::::::::: ::::::: d1qora2 83 ---------eDLVERLKEITggkkVRVVYDSV------GRDTWERSLDclQRRGLMVsfg 127 d1k92a1 154 --------------------------------kpwldtdfIDELggrhemsEFMIACGfd 181 :::: ::::::: d1qora2 128 nssgavtgvnlgilnqkgslyvtrpslqgyittreelteaSNEL------fSLIASGV-- 179 d1k92a1 182 ykmsvek 188 d1qora2 180 ------- 180 FAST alignment (Normalized score: 6.13 Raw score:1124.00) d1k92a1 1 TTIL-----------------------KHLPVGQRIGIAF--SGGLDTSAALLWMRQKGA 35 ::::::::::: :::::::::::::::::: d1qora2 1 ----ISFEQAAASFLKGLTVYYLLRKTYEIKPDEQFLF--HAAAGGVGLIACQWAKALGA 54 d1k92a1 36 VPYAYTANLGQPDEED-YDAIPRRAMEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTG 94 :::::: ::::::::::::::::::: d1qora2 55 KLIGTV----------GTAQKAQSALKAGAWQVINY------------------------ 80 d1k92a1 95 GLTYFNTTPLGRAVTGT---MLVAAMKED-----GVNIWGDGSTYKGNDIERFYRYGLLT 146 :::::::: :::::::: :::::::::::: d1qora2 81 -----------------REEDLVERLKE-ITGGKKVRVVYDS------VGRDTWERSLDC 116 d1k92a1 147 -NAELQIYKPWLDTDFIDELG--------------------------------------- 166 ::::::: d1qora2 117 LQRRGLMV-------------SFGNSSGAVTGVNLGILNQKGSLYVTRPSLQGYITTREE 163 d1k92a1 167 ---GRHEMSEFMIACGFDYKMSVEK--- 188 :::::::::: d1qora2 164 LTEASNELFSLIA------------SGV 179 TMalign alignment (TM-score: 0.46 Raw score:86.01) d1k92a1 1 ----------------------TTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPY 38 ::::::::::::::::::::::::::::::::::: d1qora2 1 ISFEQAAASFLKGLTVYYLLRK---TYEIKPDEQFLFHAAAGGVGLIACQWAKALGAKLI 57 d1k92a1 39 AYTANLGQPDEEDYDAIPRRAMEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTY 98 ::: : :::::::::::::::::::::: d1qora2 58 GTV-G--------TAQKAQSALKAGAWQVINYREE------------------------- 83 d1k92a1 99 FNTTPLGRAVTGTMLVAAMKEDG---VNIWGDGSTYKGNDI-ERFYRYGLLTNAEL-QIY 153 :::::::::: ::::::::: :: :: :::: ::::: ::: d1qora2 84 -------------DLVERLKEITGGKKVRVVYDSV----GRD-TW-ERSL-DCLQRRGLM 123 d1k92a1 154 K-P-------------------------W---LDT----D--FIDELGGRHEMSEFMIAC 178 : : : ::: : ::::: :: :::::: d1qora2 124 VSFGNSSGAVTGVNLGILNQKGSLYVTRPSLQGYITTREELT-EASNE---LF-SLIASG 178 d1k92a1 179 GFDYKMSVEK 188 : d1qora2 179 V--------- 179 HHsearch alignment (Probability: 0.22 E-value:0.00) d1k92a1 6 HLPVGQRIGIAF-SGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRAMEYGA 64 :::::::::::: :::: ::::::::::::::::::::: : ::::::::::: d1qora2 25 EIKPDEQFLFHAAAGGV-GLIACQWAKALGAKLIGTVGT-----A----QKAQSALKAGA 74 d1k92a1 65 ENA 67 ::: d1qora2 75 WQV 77