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 <-- 2.423 --> Intermediate <-- 0.763 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1jw9b_) through the intermediate protein (d1gpma1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1gpma1 GMP synthetase,​ central domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1jw9b_ Molybdenum cofactor biosynthesis protein MoeBActivating enzymes of the ubiquitin-​like proteinsActivating enzymes of the ubiquitin-​like proteinsα/β

Supporting Alignments

Query <-- 2.423 --> Intermediate
DALI alignment (Z-score: 17.0 Raw score:1263.90) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1gpma1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1gpma1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1gpma1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1gpma1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1gpma1 1 ------------------------------------------------------------ 1 query 301 rlDADEEVYSALVVGLRAYVAkngFRSVLIGLSGGIDSALVAAIACDALGaQNVYGVSMP 360 ::::::::::::::::::: :::::::::::::::::::::::::: ::::::::: d1gpma1 1 --WTPAKIIDDAVARIREQVG---DDKVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVD 54 query 361 SKYSS-DHSKGDAAELARRTGLNFRTVSIEPMFDAYMAsLGLTGLAEENLQSRLRGTTLM 419 ::::: :::::::::::::::::::::::::::::::: ::::::::::::::::::::: d1gpma1 55 NGLLRlNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFD 113 query 420 AISNQE--GHIVLAPGNKSELAVGystlygdsvgAYGPIKDVYKTSIFRLAEWRNraaae 477 :::::: :::::::::::::::: ::::::::::::::::::::: d1gpma1 114 EEALKLedVKWLAQGTIYPDVIES-----aakmgLVEPLKELFKDEVRKIGLELG----- 163 query 478 rgqtppIPEASITKpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeyk 537 :::::::: d1gpma1 164 ------LPYDMLYR---------------------------------------------- 171 query 538 rrqyppgtkisakgfgkdrrlpitnrwregh 568 d1gpma1 172 ---------------------------hpfp 175 FAST alignment (Normalized score: 8.89 Raw score:2802.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1gpma1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1gpma1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1gpma1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1gpma1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1gpma1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF---RSVLIGLSGGIDSALVAAIACDALGAQNVYGV 357 ::::::::::::::::: ::::::::::::::::::::::: :::::::: d1gpma1 1 --WTPAKIIDDAVARIREQ------VGDDKVILGLSGGVDSSVTAMLLHRA-IGKNLTCV 51 query 358 SMPSKYSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGT 416 :::::::::::::::: :::::::::::::::::::::::::: :::::::::::::::: d1gpma1 52 FVDNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGE-NDPEAKRKIIGRVFVE 110 query 417 TLMAISNQEG----HIVLAPGNKSELAVGYSTLYGDSVG-------AYGPIKDVYKTSIF 465 :::::::: ::::::::::::: :::::::::::::: d1gpma1 111 VFDEEALK--LEDVKWLAQGTIYPDVI------------ESAAKMGLVEPLKELFKDEVR 156 query 466 RLAEWRNRAAAERGQTP-PIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELV 524 ::::: :::::::: d1gpma1 157 KIGLE------------LGLPYDMLY---------------------------------- 170 query 525 VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----- 568 d1gpma1 171 --------------------------------------------RHPFP 175 TMalign alignment (TM-score: 0.27 Raw score:151.12) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1gpma1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1gpma1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1gpma1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 : d1gpma1 1 --------------W--------------------------------------------- 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1gpma1 2 ------------------------------------------------------------ 2 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::::::::::::: :: :::::::::::::::::::::::: ::::::::: d1gpma1 2 ---TPAKIIDDAVARIREQVG--DD-KVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVD 54 query 361 SKYSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLM 419 ::::::::::::: :::::::::::::::::::::::: ::::::::::::::::::::: d1gpma1 55 NGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFD 113 query 420 AISNQEG-H-IVLAPGNKSELAVG---YSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRA 474 ::::::: : :::::::::::::: ::::::::::::::::::::::: d1gpma1 114 EEALKLEDVKWLAQGTIYPDVIESAAK--------MGLVEPLKELFKDEVRKIGLELG-- 163 query 475 AAERGQTPPIPEASITKPDY--PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVD 532 :::::::: :: d1gpma1 164 ---------LPYDMLYR-HPFP-------------------------------------- 175 query 533 TAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1gpma1 176 ------------------------------------ 176 HHsearch alignment (Probability: 1.00 E-value:0.00) query 306 EEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSS 365 ::::::::::::::::: :::::::::::::::::::::::::::::::::::::::: d1gpma1 4 AKIIDDAVARIREQVGD---DKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRL 60 query 366 DHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQE 425 ::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::: d1gpma1 61 NEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGEN-DPEAKRKIIGRVFVEVFDEEALKL 119 query 426 GHI-VLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPI 484 ::: :::::::::::::::::::: ::::::::::::::::::: :::::::::::: d1gpma1 120 EDVKWLAQGTIYPDVIESAAKMGL----VEPLKELFKDEVRKIGLEL-GLPYDMLYRHPF 174 query 485 P 485 : d1gpma1 175 P 175
Intermediate <-- 0.763 --> Hit
DALI alignment (Z-score: 3.1 Raw score:366.90) d1gpma1 1 ----------wtpakiiddavariREQVGDDKVILGLsGGVDSSVTAMLLHRAIGKNLTC 50 ::::::::::::: :::::::::::::::::::::: d1jw9b_ 1 aelsdqemlrynrqiilrgfdfdgQEALKDSRVLIVG-LGGLGCAASQYLASAGVGNLTL 59 d1gpma1 51 VFVD------------ngllRLNEAeqVLDMFGDHFG-------LNIVHVPaedrflsal 91 :::: ::::: :::::::::: ::::::: d1jw9b_ 60 LDFDtvslsnlqrqtlhsdaTVGQP--KVESARDALTrinphiaITPVNAL--------- 108 d1gpma1 92 agendpeakrkiigrvFVEVFDEEALKledVKWLAQG------tiypdviesaaKMGLVE 145 ::::::::::: ::::::: :::::: d1jw9b_ 109 ---------------lDDAELAALIAE---HDLVLDCtdnvavrnqlnagcfaaKVPLVS 150 d1gpma1 146 PL-----------------------------kelFKDEVRKIG----------------- 159 :: ::::::::: d1jw9b_ 151 GAairmegqitvftyqdgepcyrclsrlfgeagvMAPLIGVIGslqameaikmlagygkp 210 d1gpma1 160 --------------lelglpydmlyrhpfp 175 d1jw9b_ 211 asgkivmydamtcqfremklmrnpgcevcg 240 FAST alignment (Normalized score: 3.13 Raw score:642.30) d1gpma1 1 WTPAKIIDDAVARIREQ---------------------------VGDDKVILGLSGGVDS 33 :::::::: ::::::: d1jw9b_ 1 -----------------AELSDQEMLRYNRQIILRGFDFDGQEALKDSRVLI-VGLGGLG 42 d1gpma1 34 SVTAMLLHRAI--GKNLTCVFVDNGLLRL-----------------------NEAEQVLD 68 ::::::::: ::::::: :::::::: d1jw9b_ 43 CAASQYLAS--AGVGNLTLL---------DFDTVSLSNLQRQTLHSDATVGQPKVESARD 91 d1gpma1 69 MFGDH---FGLNIVHVPAEDRFLSALAGENDPEAKRKIIGRV----FVEVFDEEALKLED 121 ::: :::::::: ::::::::::: d1jw9b_ 92 ALT--RINPHIAITPV--------------------------NALLDDAELAALIAE--- 120 d1gpma1 122 VKWLAQGTIYPDVIESA----------------AKMGLVEPLKELFKDEVRKIGLELGLP 165 ::::::: ::::::: d1jw9b_ 121 HDLVLDC----------TDNVAVRNQLNAGCFAAKVPLVS-------------------- 150 d1gpma1 166 YDMLYRHPFP-------------------------------------------------- 175 d1jw9b_ 151 ----------GAAIRMEGQITVFTYQDGEPCYRCLSRLFGEAGVMAPLIGVIGSLQAMEA 200 d1gpma1 176 ---------------------------------------- 176 d1jw9b_ 201 IKMLAGYGKPASGKIVMYDAMTCQFREMKLMRNPGCEVCG 240 TMalign alignment (TM-score: 0.42 Raw score:73.39) d1gpma1 1 ------------WTPAKIIDD-AVARIREQVG-DD--KVILGL-SGGVDSSVTAMLLHRA 43 :: ::::::::: :: :::::: :::::::::::::::: d1jw9b_ 1 AELSDQEMLRYN-------RQI-ILRGFDFDGQEALKDSRVLIVGLGGLGCAASQYLASA 52 d1gpma1 44 IGKNLTCVFVDNGLLR-----------------LN-EAEQVLDMFGDHFG--LNIVHVPA 83 : :::::::: ::: :: :::::::::: ::: ::::::: d1jw9b_ 53 -G-VGNLTLLD--FDTVSLSNLQRQTLHSDATVGQPKVESARDALT-RINPHIAITPVN- 106 d1gpma1 84 EDRFLSALAGENDPEAKRKIIGRVFVEVFDEEALKLEDVKWLAQ---------------- 127 : : :::::::::::: : :::: d1jw9b_ 107 A--L---------------LDDAELAALIAE-H-------DLVLDCTDNVAVRNQLNAGC 141 d1gpma1 128 -------GTI------YPDVI---------E-SA--A-----------------KMGLVE 145 ::: ::::: : :: : :: d1jw9b_ 142 FAAKVPLVSGAAIRMEGQITVFTYQDGEPCYRCLSRLFGEAGVMAPLIGVIGSL----QA 197 d1gpma1 146 PL-----------K----ELFKD--------------------EVRKIGLELGLPYDMLY 170 :: : ::::: d1jw9b_ 198 MEAIKMLAGYGKPASGKIVMYDAMTCQFREMKLMRNPGCEVCG----------------- 240 d1gpma1 171 RHPFP 175 d1jw9b_ 241 ----- 241 HHsearch alignment (Probability: 0.05 E-value:0.07) d1gpma1 15 REQVGDDKVILGLSGGVDSSVTAMLLH 41 ::::::::::::::::::::::::::: d1jw9b_ 25 QEALKDSRVLIVGLGGLGCAASQYLAS 51