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 <-- 0.999 --> Intermediate <-- 0.991 --> Hit

HHsearch
probability
HHsearch
probability

The query (T542_A.pdb A) is transitively linked to the hit (d1jgta1) through the intermediate protein (d1gpma1) by significant HHsearch probability (>0.9).

  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 d1jgta1 beta-​Lactam synthetaseAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β

Supporting Alignments

Query <-- 0.999 --> 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 <-- 0.991 --> Hit
DALI alignment (Z-score: 10.2 Raw score:934.40) d1gpma1 1 -----------WTPAKIIDDAVARIREQVGD-DKVILGLSGGVDSSVTAMLLHRAIGKnL 48 :::::::::::::::::::: :::::::::::::::::::::::::: : d1jgta1 1 pglsrrilpegEAVAAVRAALEKAVAQRVTPgDTPLVVLSGGIDSSGVAACAHRAAGE-L 59 d1gpma1 49 TCVFVDNGLLrlnEAEQVLdMFGDHFGLNIVHVPAED-RFLSAL---agendpEAKRKII 104 :::::::::: :::::: ::::::::::::::::: :::::: ::::::: d1jgta1 60 DTVSMGTDTS--nEFREAR-AVVDHLRTRHREITIPTtELLAQLpyavwasesVDPDIIE 116 d1gpma1 105 GRVFVEVFDEEAlKLEDVkWLAQG-TIYPD-----------------viESAA------- 139 :::::::::::: ::::: ::::: ::::: :::: d1jgta1 117 YLLPLTALYRAL-DGPER-RILTGyGADIPlggmhredrlpaldtvlahDMATfdglnem 174 d1gpma1 140 --------KMGLVEPLK-------------------elfKDEVRKIGLELgLPYDMLYRH 172 ::::::::: ::::::::::: ::::::::: d1jgta1 175 spvlstlaGHWTTHPYWdrevldllvsleaglkrrhgrdKWVLRAAMADA-LPAETVNRP 233 d1gpma1 173 PF------------------------------------------------------p 175 :: d1jgta1 234 KLssfsrllldhgvaedrvheakrqvvrelfdltvgggrhpsevdtddvvrsvadrt 290 FAST alignment (Normalized score: 8.09 Raw score:1822.00) d1gpma1 1 -----------WTPAKIIDDAVARIREQ-VGDDKVILGLSGGVDSSVTAMLLHRAIGKNL 48 ::::::::::::::::: :::::::::::::::::::::::::::: :: d1jgta1 1 PGLSRRILPEGEAVAAVRAALEKAVAQRVTPGDTPLVVLSGGIDSSGVAACAHRAAG-EL 59 d1gpma1 49 TCVFVDNGLLRL--NEAEQVLDMFGDHFGLNIVHVP-AEDRFLSALAGENDPE------- 98 :::::::: :::::: ::::::::::::::: :::::::: d1jgta1 60 DTVSMGTD----TSNEFREA-RAVVDHLRTRHREITIPTTELLAQ--------LPYAVWA 106 d1gpma1 99 ----AKRKIIGRVFVEVFDEEALKLEDVKWLAQGTIYPDVIESA---------------- 138 ::::::::::::::::: ::::: :::::: d1jgta1 107 SESVDPDIIEYLLPLTALYRA-LDGPE-RRILTG----------YGADIPLGGMHREDRL 154 d1gpma1 139 ---------------------------AKMGLVEPLKELF-------------------- 151 ::::::::: d1jgta1 155 PALDTVLAHDMATFDGLNEMSPVLSTLAGHWTTHPY----WDREVLDLLVSLEAGLKRRH 210 d1gpma1 152 ---KDEVRKIGLELGLPYDMLYRHPFP--------------------------------- 175 :::::::::: ::::::::: d1jgta1 211 GRDKWVLRAAMAD-ALPAETVNR----PKLSSFSRLLLDHGVAEDRVHEAKRQVVRELFD 265 d1gpma1 176 ------------------------- 176 d1jgta1 266 LTVGGGRHPSEVDTDDVVRSVADRT 290 TMalign alignment (TM-score: 0.66 Raw score:115.18) d1gpma1 1 -----------WTPAKIIDDAVARIREQVGD-DKVILGLSGGVDSSVTAMLLHRAIGKNL 48 :::::::::::::::::::: :::::::::::::::::::::::::: : d1jgta1 1 PGLSRRILPEGEAVAAVRAALEKAVAQRVTPGDTPLVVLSGGIDSSGVAACAHRAAGE-L 59 d1gpma1 49 TCVFVDNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA--------------GE 94 ::::::::::: :::::: ::::::::::::::: :: :::: d1jgta1 60 DTVSMGTDTSN--EFREAR-AVVDHLRTRHREITI--PT-TELLAQLPYAVWASESVD-- 111 d1gpma1 95 NDPEA-KRKIIGRVFVEVFDEEALKLEDVKWLAQGTI--YPD--------------VI-E 136 : ::::::::::::::: ::::::::::::: ::: :: : d1jgta1 112 ----PD-IIEYLLPLTALYRAL--DGPERRILTGYGADIPLGGMHREDRLPALDTVLAHD 164 d1gpma1 137 SAA------------K----MGLVEP----LK-EL-------F------KDEVRKIGLEL 162 ::: : :::::: :: :: : ::::::::::: d1jgta1 165 MATFDGLNEMSPVLSTLAGHWTTHPYWDREVLDLLVSLEAGLKRRHGRDKWVLRAAMADA 224 d1gpma1 163 GLPYDMLYRHP------------------------------------------------- 173 ::::::::::: d1jgta1 225 LPAETVNRPKLSSFSRLLLDHGVAEDRVHEAKRQVVRELFDLTVGGGRHPSEVDTDDVVR 284 d1gpma1 174 ------FP 175 d1jgta1 285 SVADRT-- 290 HHsearch alignment (Probability: 0.99 E-value:0.00) d1gpma1 7 IDDAVARIREQV-GDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRLNEAEQ 65 :::::::::::: ::::::::::::::::::::::::: ::::::::::::: ::::: d1jgta1 18 RAALEKAVAQRVTPGDTPLVVLSGGIDSSGVAACAHRA-AGELDTVSMGTDT---SNEFR 73 d1gpma1 66 VLDMFGDHFGLNIVHVPAEDRFL-SALAGENDPEAK-RKIIGRVFVEVFDEEALKLEDVK 123 ::::::::::::::::::::::: :::::::::::: ::::::::::::::::::::::: d1jgta1 74 EARAVVDHLRTRHREITIPTTELLAQLPYAVWASESVDPDIIEYLLPLTALYRALDGPER 133 d1gpma1 124 WLAQGTIYPDVIESAAKMGLVEPLKELFKDE 154 ::::::::::::::::::::::::::::::: d1jgta1 134 RILTGYGADIPLGGMHREDRLPALDTVLAHD 164