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 <-- 0.701 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1jv1a_) 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 d1jv1a_ UDP-​N-​acetylglucosamine pyrophosphorylaseNucleotide-​diphospho-​sugar transferasesNucleotide-​diphospho-​sugar transferasesα/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 <-- 0.701 --> Hit
DALI alignment (Z-score: 3.1 Raw score:423.60) d1gpma1 1 ------------------------------------------------------------ 1 d1jv1a_ 1 mnindlkltlskagqehllrfwneleeaqqvelyaelqamnfeelnfffqkaiegfrmep 60 d1gpma1 1 ---------wtpakiidDAVARIREQVGDDKVILGLS----------------------- 28 :::::::::::::::::::: d1jv1a_ 61 vprevlgsatrdqdqlqAWESEGLFQISQNKVAVLLLaggqgtrlgvaypkgmydvglps 120 d1gpma1 29 ggvdssVTAMLLHRAI---------gkNLTCVFVDNGLLrlNEAEQVLDMfgDHFGL--- 76 :::::::::: :::::::::::: ::::::::: ::::: d1jv1a_ 121 rktlfqIQAERILKLQqvaekyygnkcIIPWYIMTSGRT-mESTKEFFTK-hKYFGLkke 178 d1gpma1 77 NIVHVPaeDR---------------------FLsalagendpeakrkiIGRVFVEVFD-- 113 :::::: :: :: :::::::::: d1jv1a_ 179 NVIFFQ-qGMlpamsfdgkiileeknkvsmaPD---------------GNGGLYRALAaq 222 d1gpma1 114 EEALKL--EDVKWLAQ--------------------------gTIYP-------dviESA 138 :::::: :::::::: :::: ::: d1jv1a_ 223 NIVEDMeqRGIWSIHVycvdnilvkvadprfigfciqkgadcgAKVVektnptepvgVVC 282 d1gpma1 139 A----------------------------------------------------------- 139 : d1jv1a_ 283 Rvdgvyqvveyseislataqkrssdgrllfnagnianhfftvpflrdvvnvyepqlqhhv 342 d1gpma1 140 ---------------------------------kmglveplKELFKDEVRkiglelglpy 166 ::::::::: d1jv1a_ 343 aqkkipyvdtqgqlikpdkpngikmekfvfdifqfakkfvvYEVLREDEF---------- 392 d1gpma1 167 dmlYRHP----------------------------------------------------- 173 :::: d1jv1a_ 393 --sPLKNadsqngkdnpttarhalmslhhcwvlnagghfidengsrlpaiprlkdandvp 450 d1gpma1 174 --------------------------------------fp 175 d1jv1a_ 451 iqceisplisyageglesyvadkefhapliidengvhelv 490 FAST alignment (Normalized score: 1.95 Raw score:569.90) d1gpma1 1 WT---------------------------------------------------------- 2 d1jv1a_ 1 --MNINDLKLTLSKAGQEHLLRFWNELEEAQQVELYAELQAMNFEELNFFFQKAIEGFRM 58 d1gpma1 3 -------------PAKIIDDAVARIREQVGDD--KVILGLSG------------------ 29 ::::::::::::::::: :::::: d1jv1a_ 59 EPVPREVLGSATRDQDQLQAWESEGLFQIS--QNKVAVLL--LAGGQGTRLGVAYPKGMY 114 d1gpma1 30 ----------GVDSSVTAMLLHRAIGK---------NLTCVFVDNGLL--RLNEAEQVLD 68 :::::::::::::: :::::::::: :::::::::: d1jv1a_ 115 DVGLPSRKTLFQIQAERILKLQQV---AEKYYGNKCIIPWYIMTSG--RTMESTKEFFTK 169 d1gpma1 69 MFGDHFGL---------NIVHVPAEDRFLSALAGENDPEAKRKI---------------- 103 :::::: d1jv1a_ 170 --------HKYFGLKKENVIFFQ---------------------QGMLPAMSFDGKIILE 200 d1gpma1 104 ----------IGRVFVE-----VFDEEALKLEDVKWLAQGTIYPDVIESAAKMGLVEPLK 148 ::::::: :::::::: ::::::: d1jv1a_ 201 EKNKVSMAPDGNGGLYRALAAQNIVEDMEQ-RGIWSIH---------------------- 237 d1gpma1 149 ELFKDEVRKIGLELGLPYDMLYRHPFP--------------------------------- 175 d1jv1a_ 238 ---------------------------VYCVDNILVKVADPRFIGFCIQKGADCGAKVVE 270 d1gpma1 176 ------------------------------------------------------------ 176 d1jv1a_ 271 KTNPTEPVGVVCRVDGVYQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTVPFLRDV 330 d1gpma1 176 ------------------------------------------------------------ 176 d1jv1a_ 331 VNVYEPQLQHHVAQKKIPYVDTQGQLIKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLRED 390 d1gpma1 176 ------------------------------------------------------------ 176 d1jv1a_ 391 EFSPLKNADSQNGKDNPTTARHALMSLHHCWVLNAGGHFIDENGSRLPAIPRLKDANDVP 450 d1gpma1 176 ---------------------------------------- 176 d1jv1a_ 451 IQCEISPLISYAGEGLESYVADKEFHAPLIIDENGVHELV 490 TMalign alignment (TM-score: 0.54 Raw score:93.82) d1gpma1 1 ------------------------------------------------------------ 1 d1jv1a_ 1 MNINDLKLTLSKAGQEHLLRFWNELEEAQQVELYAELQAMNFEELNFFFQKAIEGFRMEP 60 d1gpma1 1 ----------------WTPAKIIDD--AVAR-IREQVGDDKVILGL-S------------ 28 : :: :::::::::::::: : d1jv1a_ 61 VPREVLGSATRDQDQL--------QAW--ESEGLFQISQNKVAVLLLAGGQGTRLGVAYP 110 d1gpma1 29 GG-----------VDSSVTAMLLHRAIG---------KNLTCVFVDNGLLRLNEAEQVLD 68 :: : ::::::::::::: ::::::::::::::::::::::: d1jv1a_ 111 KGMYDVGLPSRKTL-FQIQAERILKLQQVAEKYYGNKCIIPWYIMTSGRTMESTKEFFTK 169 d1gpma1 69 MFGDHFGL--NIVHVPAEDRFLSALAGENDP-------------EAKRKIIGRVFVEVFD 113 ::: :::: ::::: : ::: : ::::: :::::::::::::: d1jv1a_ 170 HKY-FGLKKENVIFF-Q--QGM--L-PAMSFDGKIILEEKNKVS--MAPDGNGGLYRALA 220 d1gpma1 114 --EEALKL-E-DVKWLAQGT-----IY-------------------PDVIE--------- 136 :::::: : ::::::::: :: ::::: d1jv1a_ 221 AQNIVEDMEQRGIWSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVEKTNPTEPVGV 280 d1gpma1 137 S------------------------------AA--------KMG---------------- 142 : :: ::: d1jv1a_ 281 VCRVDGVYQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTVPFLRDVVNVYEPQLQH 340 d1gpma1 143 ----------------------------------------L---VEPLKE--LF-K---- 152 : ::: :: : d1jv1a_ 341 HVAQKKIPYVDTQGQLIKPDKPNGIKMEKFVFDIFQFAKKFVVY---EVLREDEFSPLKN 397 d1gpma1 153 ---------------DEVRKI-----------------------------------GLEL 162 :::::: :::: d1jv1a_ 398 ADSQNGKDNPTTARHALMSLHHCWVLNAGGHFIDENGSRLPAIPRLKDANDVPIQCEISP 457 d1gpma1 163 G--------------------------------LPYDMLYRHPFP 175 : d1jv1a_ 458 LISYAGEGLESYVADKEFHAPLIIDENGVHELV------------ 490 HHsearch alignment (Probability: 0.01 E-value:0.52) d1gpma1 17 QVG-DDKVILGLSGGVDS 33 ::: :::::::::::::: d1jv1a_ 86 QISQNKVAVLLLAGGQGT 103