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 <-- 1.026 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1im8a_) 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 d1im8a_ Hypothetical protein HI0319 (YecO)S-​adenosyl-​L-​methionine-​dependent methyltransferasesS-​adenosyl-​L-​methionine-​dependent methyltransferasesα/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 <-- 1.026 --> Hit
DALI alignment (Z-score: 3.0 Raw score:373.80) d1gpma1 1 -------------------wTPAKIIDDAVARIREQVGD-DKVIL-GLSGgvdsSVTAML 39 ::::::::::::::::::: ::::: :::: :::::: d1im8a_ 1 fifdenvaevfpdmiqrsvpGYSNIITAIGMLAERFVTAdSNVYDlGCSR----GAATLS 56 d1gpma1 40 LHRAI---gkNLTCVFVdngllrlneAEQVLDMFGDHFG-------LNIVHVpaedrfls 89 ::::: ::::::: ::::::::::::: :::::: d1im8a_ 57 ARRNInqpnvKIIGIDN---------SQPMVERCRQHIAayhseipVEILCN-------- 99 d1gpma1 90 alagendpeakrkiigrvfveVFDEEalKLEDVKWLAQGT-------------iypdvie 136 ::::: :::::::::::: d1im8a_ 100 ---------------------DIRHV--EIKNASMVILNFtlqflppedrialltkiyeg 136 d1gpma1 137 saakMGLVE--------------------------------------------------- 145 ::::: d1im8a_ 137 lnpnGVLVLsekfrfedtkinhllidlhhqfkrangyselevsqkrtalenvmrtdsiet 196 d1gpma1 146 -------------plKELFKDEvrkiglelglpydmlyrhpfp 175 ::::::: d1im8a_ 197 hkvrlknvgfsqvelWFQCFNF--------------gsmiavk 225 FAST alignment (Normalized score: 2.18 Raw score:432.70) d1gpma1 1 WTPAK--------------------IIDDAVARIREQV------GDDKVILGLSGGVDS- 33 :::::::::::: ::::::: d1im8a_ 1 -----FIFDENVAEVFPDMIQRSVPGYSNIITAIGML-AERFVTADSNVYD--------L 46 d1gpma1 34 ----SVTAMLLHRAIGK-----NLTCVFVDNGLLRL---NEAEQVLDMFGDHF--GLNIV 79 ::::::::: :::::::: ::::::::: :::: ::::: d1im8a_ 47 GCSRGAATLSARR----NINQPNVKIIGID------NSQPMVERCRQH-IAAYHSEIPVE 95 d1gpma1 80 HVPAEDRFLSALAGENDPEAKRKI------------------------IGRVFVEVFDEE 115 :: :::::::::::: d1im8a_ 96 IL----------------------CNDIRHVEIKNASMVILNFTLQFLPPEDRIALLTKI 133 d1gpma1 116 ALKLEDV---KWLAQGTIYPDVIESAAKMGLVEPLKELFKDEVRKIGLELGLPYDMLYRH 172 :::: :::::::: d1im8a_ 134 YEGL---NPNGVLVLSEK------------------------------------------ 148 d1gpma1 173 PFP--------------------------------------------------------- 175 d1im8a_ 149 ---FRFEDTKINHLLIDLHHQFKRANGYSELEVSQKRTALENVMRTDSIETHKVRLKNVG 205 d1gpma1 176 -------------------- 176 d1im8a_ 206 FSQVELWFQCFNFGSMIAVK 225 TMalign alignment (TM-score: 0.42 Raw score:74.04) d1gpma1 1 --------------------W-TPA-KIIDDAVARIREQVGDDKVILGLSGGVDSSVTAM 38 : :: :: ::::::::::::::::::::::: ::::: d1im8a_ 1 FIFDENVAEVFPDMIQRSVPGY-SNI-IT-AIGMLAERFVTADSNVYDLGCSR--GAATL 55 d1gpma1 39 LLHRAIG-K-NLTCVFVDNGLLRLNEAEQVLDMFGDHFG--LNIVHVPAEDRFLSALAGE 94 ::::::: : ::::::: : :: :::::::::: :::: :::::::: d1im8a_ 56 SARRNINQPNVKIIGID-N--SQ-PMVERCRQHI-AAYHSEIPVEILCN----------- 99 d1gpma1 95 NDPEAKRKIIGRVFVEVFDEEALKLEDVKWLAQ-G------------------------- 128 : ::: :: :: :::::: : d1im8a_ 100 ----------D--IRH-VE--IK----NASMVILNFTLQFLPPEDRIALLTKIYEGLNPN 140 d1gpma1 129 ----TIYPDVI-----------------------------------------ESAA---- 139 ::::::: :::: d1im8a_ 141 GVLVLSEKFRFEDTKINHLLIDLHHQFKRANGYSELEVSQKRTALENVMRTDSIETHKVR 200 d1gpma1 140 -----KMGL-VE-PLKELFKDEV------RKIGLELGLPYDMLYRHPFP 175 :: : ::::::::: d1im8a_ 201 LKNVG--FSQ-VE-LWFQCFNFGSMIAVK-------------------- 225 HHsearch alignment (Probability: 0.24 E-value:0.16) d1gpma1 7 IDDAVARIREQVGDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRLNEAEQV 66 :::::::::::::::::::::::::::::: :::::::::::::::::::: ::::: d1im8a_ 26 ITAIGMLAERFVTADSNVYDLGCSRGAATL-SARRNINQPNVKIIGIDNSQ----PMVER 80 d1gpma1 67 LDMFGDHFG----LNIVHVPAED 85 ::::::::: :::::::::: d1im8a_ 81 CRQHIAAYHSEIPVEILCNDIRH 103