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 <-- 1.691 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1ccwb_) 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 d1ccwb_ Glutamate mutase,​ large subunitCobalamin (vitamin B12)-​dependent enzymesTIM 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 <-- 1.691 --> Hit
DALI alignment (Z-score: 17.6 Raw score:1986.10) d1tx2a_ 1 ---------------------------------kwdydlrcGEYT-------LNLN--EK 18 :::: :::: :: d1ccwb_ 1 melknkkwtdeefhkqreevlqqwptgkevdlqeavdylkkIPAEknfaeklVLAKkkGI 60 d1tx2a_ 19 TLIMGILNVTpdsfsdggsynEVDAAVRHAKEMRD-EGAHIIDIGGESfakvSVEE---- 73 :::::::::: :::::::::::::: :::::::::::: :::: d1ccwb_ 61 TMAQPRAGVA-----------LLDEHIELLRYLQDeGGADFLPSTIDA-ytrQNRYdece 108 d1tx2a_ 74 ------------------EIKRVVPMIQAVSKEVKLPISIDTY---KAEVAKQAIEAGAH 112 ::::::::::::::::::::::::: :::::::::::::: d1ccwb_ 109 ngikesekagrsllngfpGVNFGVKGCRKVLEAVNLPLQARHGtpdSRLLAEIIHAGGWT 168 d1tx2a_ 113 IINDiwGAKA-----------------EPKIAEVAAHY-----DVPIILMHNRDnmnyrn 150 :::: :::: ::::::::::: ::::::::::: d1ccwb_ 169 SNEG--GGISynvpyaknvtiekslldWQYCDRLVGFYeeqgvHINREPFGPLT--gtlv 224 d1tx2a_ 151 LMADMIADLYDSIKIAKDAGVRdeNIILDPGIGfaktpeqNLEAMRN-LEQL-NVLG--- 205 :::::::::::::::::::::: ::::::::: ::::::: :::: :::: d1ccwb_ 225 PPSMSNAVGITEALLAAEQGVK--NITVGYGEC------gNMIQDIAaLRCLeEQTNeyl 276 d1tx2a_ 206 ---------YPVLLGTSrKSFIGhvldLPVEERLEGTGATVCLGIEKGCEFVRVH----- 251 :::::::: ::::: :::::::::::::::::::::::::::: d1ccwb_ 277 kaygyndvfVTTVFHQW-MGGFP----QDESKAFGVIVTATTIAALAGATKVIVKtphea 331 d1tx2a_ 252 -----------DVKEMSRMAKMMDAMI--------------------------------- 267 :::::::::::::::: d1ccwb_ 332 igiptkeanaaGIKATKMALNMLEGQRmpmskeletemavikaetkcildkmfelgkgdl 391 d1tx2a_ 268 ------------------------------------------------------------ 268 d1ccwb_ 392 aigtvkafetgvmdipfgpskynagkmmpvrdnlgcvrylefgnvpfteeiknynrerlq 451 d1tx2a_ 268 ------------------------------gk 269 d1ccwb_ 452 erakfegrdvsfqmviddifavgkgrligrpe 483 FAST alignment (Normalized score: 8.60 Raw score:3098.00) d1tx2a_ 1 KWDYDLR--------------------------------------CGEYTLNLN------ 16 :::: d1ccwb_ 1 -------MELKNKKWTDEEFHKQREEVLQQWPTGKEVDLQEAVDYLKKI-----PAEKNF 48 d1tx2a_ 17 ----------EKTLIMGILNVTPDSFSDGGSYN----EVDAAVRHAKEMR-DEGAHIIDI 61 :::::::: ::::::::::::: ::::::::: d1ccwb_ 49 AEKLVLAKKKGITMAQPR---------------AGVALLDEHIELLRYLQDEGGADFLPS 93 d1tx2a_ 62 GGESFAKVSVEEEIKR----------------------------------VVPMIQAVSK 87 ::: :::::::::: d1ccwb_ 94 TID-------------AYTRQNRYDECENGIKESEKAGRSLLNGFPGVNFGVKGCRKVLE 140 d1tx2a_ 88 EVKLPISIDTY---KAEVAKQAIEAGAHIINDIWGAKA---------------------- 122 ::::::::::: :::::::::::::::: d1ccwb_ 141 AVNLPLQARHGTPDSRLLAEIIHAGGWTSN--------EGGGISYNVPYAKNVTIEKSLL 192 d1tx2a_ 123 -EPKIAEVAAH-----YDVPIILMHNRDNMNYRN-----LMADMIADLYDSIKIAKDAGV 171 :::::::::: ::::::::::: ::::::::::::::::::::: d1ccwb_ 193 DWQYCDRLVGFYEEQGVHINREPFGPL-------TGTLVPPSMSNAVGITEALLAAEQGV 245 d1tx2a_ 172 RDE-NIILDPGIGFAKTPEQN-----LEAMRNLEQLNVLG----------------YPVL 209 ::::::: ::::::::::: :::: d1ccwb_ 246 ---KNITVGYG----------ECGNMIQDIAALRCLE---EQTNEYLKAYGYNDVFVTTV 289 d1tx2a_ 210 LGTSRKSFIGHVLDL---------PVEERLEGTGATVCLGIEKGCEFVRVH--------- 251 : :::::::::::::::::::::::::: d1ccwb_ 290 F--------------HQWMGGFPQDESKAFGVIVTATTIAALAGATKVIV-KTPHEAIGI 334 d1tx2a_ 252 ----DVKEMSRMAKMMDAMIGK-------------------------------------- 269 ::::::::::::::: d1ccwb_ 335 PTKEANAAGIKATKMALNM---LEGQRMPMSKELETEMAVIKAETKCILDKMFELGKGDL 391 d1tx2a_ 270 ------------------------------------------------------------ 270 d1ccwb_ 392 AIGTVKAFETGVMDIPFGPSKYNAGKMMPVRDNLGCVRYLEFGNVPFTEEIKNYNRERLQ 451 d1tx2a_ 270 -------------------------------- 270 d1ccwb_ 452 ERAKFEGRDVSFQMVIDDIFAVGKGRLIGRPE 483 TMalign alignment (TM-score: 0.73 Raw score:197.39) d1tx2a_ 1 ---------------------------------------KWDYDLRCGEY-----TL--N 14 ::::: :: : d1ccwb_ 1 MELKNKKWTDEEFHKQREEVLQQWPTGKEVDLQEAVDYL------KKIPAEKNFAEKLVL 54 d1tx2a_ 15 -LNE-KTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRD-EGAHIIDIGGESFAKVSV 71 ::: :::::::: ::: :::::::::::::: :::::::::::::::::: d1ccwb_ 55 AKKKGITMAQPRA-GVA----------LLDEHIELLRYLQDEGGADFLPSTIDAYTRQNR 103 d1tx2a_ 72 E--E------------------E-IKRVVPMIQAVSKEVKLPISIDT-Y--KAEVAKQAI 107 : : : ::::::::::::::::::::::: : ::::::::: d1ccwb_ 104 YDECENGIKESEKAGRSLLNGFPGVNFGVKGCRKVLEAVNLPLQARHGTPDSRLLAEIIH 163 d1tx2a_ 108 EAGAHIINDI-WGAK-----------A--EP-KIAEVAAHYD-----VPIILMHNRDNMN 147 :::::::::: :::: : :: :::::::::: ::::::::::::: d1ccwb_ 164 AGGWTSNEGGGISYNVPYAKNVTIEKSLLDWQYCDRLVGFYEEQGVHINREPFGPLTGTL 223 d1tx2a_ 148 YRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLE--AMRNL-EQLNV- 203 : :::::::::::::::::::::: :::::::: ::: ::::: ::::: d1ccwb_ 224 V--PPSMSNAVGITEALLAAEQGVK--NITVGYGE--------CGNMIQDIAALRCLEEQ 271 d1tx2a_ 204 LG------------YPVLLGTSRKSFIGHVLDLPVEE-RLEGTGATVCLGIEKGCEFVRV 250 :: :::::::: ::: : ::::: :::::::::::::::::::::: d1ccwb_ 272 TNEYLKAYGYNDVFVTTVFHQW-MGG-F----PQDESKAFGVIVTATTIAALAGATKVIV 325 d1tx2a_ 251 --------------H--DVKEMSRMAKMMDAMIG-------------------------- 268 : ::::::::::::::::: d1ccwb_ 326 KTPHEAIGIPTKEANAAGIKATKMALNMLEGQRMPMSKELETEMAVIKAETKCILDKMFE 385 d1tx2a_ 269 ------------------------------------------------------------ 269 d1ccwb_ 386 LGKGDLAIGTVKAFETGVMDIPFGPSKYNAGKMMPVRDNLGCVRYLEFGNVPFTEEIKNY 445 d1tx2a_ 269 --------------------------------------K 269 d1ccwb_ 446 NRERLQERAKFEGRDVSFQMVIDDIFAVGKGRLIGRPE- 483 HHsearch alignment (Probability: 0.78 E-value:0.00) d1tx2a_ 69 VSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEV----AKQA----------IEAGAHII 114 ::::::::::::::::::: :::::::::::::: :::: :::::::: d1ccwb_ 70 ALLDEHIELLRYLQDEGGA-DFLPSTIDAYTRQNRYDECENGIKESEKAGRSLLNGFPGV 128 d1tx2a_ 115 NDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDE 174 : : :::::::::::::::::::: :::::: :: :::::::::::: d1ccwb_ 129 N-F----GVKGCRKVLEAVNLPLQARH--GTPDSR-LL----------AEIIHAGGWTSN 170 d1tx2a_ 175 N-----IILDPGIGFAKTPEQNLE----AMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLP 225 : ::::::::: ::::::: :::::::::::::::: : :::::: d1ccwb_ 171 EGGGISYNVPYAKNV--TIEKSLLDWQYCDRLVGFYEEQGVHIN----R-----EPFGPL 219 d1tx2a_ 226 VEERLEGTGATV------CLGIEKGCEFVRV---------HDVKEMSRMAKMMDAMIGK 269 :::::::::::: ::::::::::::: ::::::::::::::::::: d1ccwb_ 220 TGTLVPPSMSNAVGITEALLAAEQGVKNITVGYGECGNMIQDIAALRCLEEQTNEYLKA 278