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 <-- 0.687 --> Intermediate <-- 1.811 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1gzga_) through the intermediate protein (d1tx2a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1tx2a_ Dihydropteroate synthetaseDihydropteroate synthetase-​likeTIM beta/​alpha-​barrelα/β
Hit d1gzga_ 5-​aminolaevulinate dehydratase,​ ALAD (porphobilinogen synthase)AldolaseTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 0.687 --> Intermediate
DALI alignment (Z-score: 2.9 Raw score:483.20) query 1 ---------------SLQLRLALN----qidstvgdiagnAEAILRWTRHSAEQGAHLVA 41 ::::::::: :::::::::::::::::::: d1tx2a_ 1 kwdydlrcgeytlnlNEKTLIMGIlnvtpdsfsdggsyneVDAAVRHAKEMRDEGAHIID 60 query 42 fpemALTGypvedlalrSSFVEASRTALRELAARLAeEGFGeLPVLVGYldrsesaqpky 101 :::: ::::::::::::::::::: :::: ::::::: d1tx2a_ 61 ---iGGES-------faKVSVEEEIKRVVPMIQAVS-KEVK-LPISIDT----------- 97 query 102 gqpagaprnaaavlhrGRVALT-FAKHhlpnygvfdefryfvPGDT-mpivrlhgvdiaL 159 :::::: :::: :::: : d1tx2a_ 98 -----ykaevakqaieAGAHIInDIWG--------------aKAEPkiaevaahydvpiI 138 query 160 AICE---------dlwQDGGR----vpaarsagaglllsvnaspyerdkDDTRLELVRKR 206 :::: ::::: ::::::::::: d1tx2a_ 139 LMHNrdnmnyrnlmadMIADLydsikiakdagvrdeniildpgigfaktPEQNLEAMRNL 198 query 207 aQEAG---ctTAYLAmiggqdelvFDGD------------------sivVDRDGevvara 245 :::: ::::: :::: ::::: d1tx2a_ 199 -EQLNvlgypVLLGT-------srKSFIghvldlpveerlegtgatvclGIEKG------ 244 query 246 pqfsegCVVLdldlpaaeaepptgvvddglridrlviseeplpayeaeLAGGyadrldad 305 :::: :::: d1tx2a_ 245 cefvrvHDVK-----------------------------------emsRMAK-------- 261 query 306 eevysalvvglrayvakngfrsvliglsggidsalvaaiacdalgaqnvygvsmpskyss 365 d1tx2a_ 262 ------------------------------------------------------------ 262 query 366 dhskgdaaelarrtglnfrtvsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqe 425 d1tx2a_ 262 ------------------------------------------------------------ 262 query 426 ghivlapgnkselavgystlygdsvgaygpikdvyktsifrlaewrnraaaergqtppip 485 d1tx2a_ 262 ------------------------------------------------------------ 262 query 486 easitkpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgt 545 d1tx2a_ 262 ------------------------------------------------------------ 262 query 546 kisakgfgkdrrlpitnrwregh 568 d1tx2a_ 262 ---------------mmdamigk 269 FAST alignment (Normalized score: 1.23 Raw score:478.70) query 1 ----------------SLQLRLALNQIDSTVGD---IAGNAEAILRWTRHSAEQGAHLVA 41 ::::::::::::::::: :::::::::::::::::::::::: d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIID 60 query 42 FPEMALTGYPVEDLALRSSFVEASRTALRELAARLAEEGF-------------------- 81 :: d1tx2a_ 61 IG--------------------------------------GESFAKVSVEEEIKRVVPMI 82 query 82 ------GELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRVALTFAKHHLPNYGVF 135 ::::::: d1tx2a_ 83 QAVSKEVKLPISI----------------------------------------------- 95 query 136 DEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDK 195 d1tx2a_ 96 ------------------------------------------------------------ 96 query 196 DDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVL 255 d1tx2a_ 96 ------------------------------------------------------------ 96 query 256 DLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVG 315 d1tx2a_ 96 ------------------------------------------------------------ 96 query 316 LRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVS----------------- 358 d1tx2a_ 96 -------------------------------------------DTYKAEVAKQAIEAGAH 112 query 359 ----------------------------MPSKYSSDHSKGDAAELARRTGLNFRTVSIEP 390 :::: d1tx2a_ 113 IINDIWGAKAEPKIAEVAAHYDVPIILMHNRD---------------------------- 144 query 391 MFDAYMASLG----LTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLY 446 :::::::::::::::::::: d1tx2a_ 145 ----------NMNYRNLMADMIADLYDSIKIAKD-------------------------- 168 query 447 GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVD 506 d1tx2a_ 169 ------------------------------------------------------------ 169 query 507 RDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWRE 566 d1tx2a_ 169 ------------------------------------------------------------ 169 query 567 GH---------------------------------------------------------- 568 d1tx2a_ 169 --AGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPV 226 query 569 ------------------------------------------- 569 d1tx2a_ 227 EERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 269 TMalign alignment (TM-score: 0.25 Raw score:142.24) query 1 --SLQL------RLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPV 52 :::: ::: : :::: :::: ::: d1tx2a_ 1 KWDYDLRCGEYTLNL------------------------N-EKTL--IMGI--LNV---- 27 query 53 EDLALRSSFV--E-ASRTALRELAARLAEEGFGELPVLVGYLDR---SESAQPKYGQPAG 106 :: ::::: : :::::::::::::: ::: :::::::::: :: : : d1tx2a_ 28 --TP-DSFSDGGSYNEVDAAVRHAKEMR-DEG--AHIIDIGGESFAK---VS--V-E--- 72 query 107 APR-NAA-AV--LHRGRV-ALTFAKHHLPNYGVFDEFRYFVPGDTMPIV-RLHGVDIALA 160 ::: ::: :: :::::: ::::::::: :::::::: : ::::: d1tx2a_ 73 EEIKRVVPMIQAVSKEVKLPISIDTYKA-------------EVAKQAIEA-G---AHIIN 115 query 161 ICEDLWQDGGRVPAARSAGAGLLLSVNASP-YERD-K---DD-TRLELVRKRAQE--AGC 212 :::::::::::::::::: : ::::::::: :::: : :: :::::::::::: ::: d1tx2a_ 116 DIWGAKAEPKIAEVAAHY-D-VPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRD 173 query 213 T-TAYLAMIGG-QDELV-FD--GD--SIVVDRDGEVVARAPQFSE-GCVVLDLDLPAAEA 264 : ::::::::: ::: :: :: ::::: :::::::: ::: d1tx2a_ 174 ENIILDPGIGFA--KTPEQNLEAMRNLEQLN--VLGYPVLL-GTSR-------------- 214 query 265 EPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNG 324 :::::::: ::::: d1tx2a_ 215 ----------------------------------------------KSFIGHVL-DLPVE 227 query 325 FR----------------------------------------SVLIGLSGGIDSALVAAI 344 :: d1tx2a_ 228 ERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK------------------ 269 query 345 ACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGL 404 d1tx2a_ 270 ------------------------------------------------------------ 270 query 405 AEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSI 464 d1tx2a_ 270 ------------------------------------------------------------ 270 query 465 FRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELV 524 d1tx2a_ 270 ------------------------------------------------------------ 270 query 525 VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1tx2a_ 270 -------------------------------------------- 270 HHsearch alignment (Probability: 0.05 E-value:0.02) query 494 YPVLDAILELYVDRDTGADAIV---AAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAK 550 :::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: d1tx2a_ 156 IADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRK 215 query 551 GF 552 :: d1tx2a_ 216 SF 217
Intermediate <-- 1.811 --> Hit
DALI alignment (Z-score: 16.2 Raw score:1695.20) d1tx2a_ 1 ---------kwdydlrcgeytlnlNEKT--LIMGILNVTpdsfsdgGSYN---------- 39 :::: ::::::::: :::: d1gzga_ 1 nraypytrlrrnrrddfsrrlvreNVLTvdDLILPVFVL-------DGVNqresipsmpg 53 d1tx2a_ 40 ----EVDAAVRHAKEMRDEGAHIIDIGGESFAKVS---VEEEI---KRVVPMIQAVSKEV 89 ::::::::::::::::::::::::::::::: ::::: :::::::::::::: d1gzga_ 54 verlSIDQLLIEAEEWVALGIPALALFPVTPVEKKsldAAEAYnpeGIAQRATRALRERF 113 d1tx2a_ 90 -KLPISIDTY---------------------------KAEVAKQAIEAGAHIINDIWGAK 121 ::::::::: ::::::::::::::::::::::: d1gzga_ 114 pELGIITDVAldpftthgqngildddgyvlndvsidvLVRQALSHAEAGAQVVAPSDMMD 173 d1tx2a_ 122 AE-PKIAEVAA---HYDVPIILMHN----------------------------RDNMNyr 149 :: :::::::: ::::::::::: ::::: d1gzga_ 174 GRiGAIREALEsagHTNVRVMAYSAkyasayygpfrdavgsasnlgkgnkatyQMDPA-- 231 d1tx2a_ 150 nLMADMIADLYDSIKIAkdagvrdeNIILDPGIgfaktpeqnLEAMRNLEQLN-VLGYPV 208 :::::::::::::::: :::::::: ::::::::::: :::::: d1gzga_ 232 -NSDEALHEVAADLAEG--------ADMVMVKP--------gMPYLDIVRRVKdEFRAPT 274 d1tx2a_ 209 LLGTSrKSFIGHVLDLP--veerLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMmdam 266 ::::: ::::::::::: ::::::::::::::::::::::::::::::::: d1gzga_ 275 FVYQV-SGEYAMHMGAIqngwlaESVILESLTAFKRAGADGILTYFAKQAAEQLRR---- 329 d1tx2a_ 267 igk 269 d1gzga_ 330 --- 330 FAST alignment (Normalized score: 10.73 Raw score:3192.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKT------------------------------LIMGILNVTPD 30 ::::::::: d1gzga_ 1 -------------------NRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVL-- 39 d1tx2a_ 31 SFSDGGSYN------------------EVDAAVRHAKEMRDEGAHIIDIGGE--SFAK-- 68 ::::::::::::::::::::::: :::: d1gzga_ 40 ---------DGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALF--PVTPVEKK 88 d1tx2a_ 69 -VSVEEEI---KRVVPMIQAVSKEV-KLPISIDTY------------------------- 98 ::::::: :::::::::::::: :::::::: d1gzga_ 89 SLDAAEAYNPEGIAQRATRALRERFPELGIITDV-ALDPFTTHGQNGILDDDGYVLNDVS 147 d1tx2a_ 99 ---KAEVAKQAIEAGAHIINDIWGAKA----EPKIAEVAAHY---DVPIIL-MHNRDNMN 147 ::::::::::::::::::::: ::::::::::: :::::: :::: d1gzga_ 148 IDVLVRQALSHAEAGAQVVAPSDM---MDGRIGAIREALESAGHTNVRVMAYSAKY---- 200 d1tx2a_ 148 YRN-------------------------------LMADMIADLYDSIKIAKDAGVRDEN- 175 :::::::::::::: d1gzga_ 201 ---ASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLA-----------E 246 d1tx2a_ 176 --IILDPGIGFAKTPEQ--NLEAMRNLEQLN-VLGYPVLLGTSR---KSFIGHVLDLPVE 227 ::::: :::::::::::: ::::::::::: ::::::: d1gzga_ 247 GADMVMV----------KPGMPYLDIVRRVKDEFRAPTFVYQV-SGEYAMHMGA------ 289 d1tx2a_ 228 E------RLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK- 269 ::::::::::::::::::::::::::::::::: d1gzga_ 290 -IQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLR--------R 329 TMalign alignment (TM-score: 0.68 Raw score:182.16) d1tx2a_ 1 ---------------------------KWDYDLRCGEYTLNLNEKTLIMGILNVTPDS-- 31 ::::::::::::::: d1gzga_ 1 NRAYPYTRLRRNRRDDFSRRLVRENVL----------------TVDDLILPVFVLDGVNQ 44 d1tx2a_ 32 ------------FSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESFA-KVS--VEEE-I 75 ::::::::::::::::::::::::::::: ::: :::: : d1gzga_ 45 RESIPSMPGVER-------LSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYN 97 d1tx2a_ 76 --KRVVPMIQAVSKEVK-LPISIDTY---------------------------KAEVAKQ 105 ::::::::::::::: :::::::: ::::::: d1gzga_ 98 PEGIAQRATRALRERFPELGIITDVALDPFTTHGQNGILDDDGYVLNDVSIDVLVRQALS 157 d1tx2a_ 106 AIEAGAHIINDIWGAKAEP-KIAEVAAH--YD-VPIILM-HNR----------------- 143 ::::::::::::::::::: :::::::: :: :::::: ::: d1gzga_ 158 HAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRVMAYSAKYASAYYGPFRDAVGSASN 217 d1tx2a_ 144 -----DN--MNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMR 196 :: ::::::::::::::::::: : : ::::::::: :: ::: d1gzga_ 218 LGKGNKATYQMDPANSDEALHEVAADLA-E----G---ADMVMVKPG-------MP-YLD 261 d1tx2a_ 197 NLEQLN-VLGYPVLLGTSRKSFIGHVLDLPVEE--R-LEGTGATVCLGIEKGCEFVRVHD 252 :::::: ::::::::::::::::: ::::::: : ::::::::::::::::::::::: d1gzga_ 262 IVRRVKDEFRAPTFVYQVSGEYAM--HMGAIQNGWLAESVILESLTAFKRAGADGILTYF 319 d1tx2a_ 253 VKEMSRMAKMMDAMIGK 269 :::::::::: d1gzga_ 320 AKQAAEQLRR------- 329 HHsearch alignment (Probability: 0.86 E-value:0.00) d1tx2a_ 168 DAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLL 210 :::::: ::::::::: ::::::::: :::::::: d1gzga_ 245 AEGADM--VMVKPGMPY-------LDIVRRVKD--EFRAPTFV 276