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 <-- 1.239 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1gk8a1) 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 d1gk8a1 Ribulose 1,​5-​bisphosphate carboxylase-​oxygenaseRuBisCo,​ C-​terminal domainTIM 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 <-- 1.239 --> Hit
DALI alignment (Z-score: 14.3 Raw score:1556.80) d1tx2a_ 1 ---kwdYDLRcgeYTLNlNEKTLIMGILN-VTPDsfsdggsynEVDAAVRHAKEMRDEGA 56 :::: :::: ::::::::::: :::: ::::::::::::::::: d1gk8a1 1 gxphgiQVER--dKLNK-YGRGLLGCTIKpKLGL---------SAKNYGRAVYECLRGGL 48 d1tx2a_ 57 HIIDIG--GESFAKvsveeEIKRVVPMIQAVSKEVK------LPISIDTY------KAEV 102 :::::: :::::: ::::::::::::::::: :::::::: :::: d1gk8a1 49 DFTXDDenVNSQPF----mRWRDRFLFVAEAIYKAQaetgevKGHYLNATagtceeMMKR 104 d1tx2a_ 103 AKQAIEAGAHIINDIW--gaKAEP-KIAEVAAHYDVPIILMHNR-dNMNYRN-lmADMIA 157 :::::::::::::::: :::: ::::::::::::::::::: :::::: ::::: d1gk8a1 105 AVXAKELGVPIIMHDYltggFTANtSLAIYCRDNGLLLHIHRAMhaVIDRQRnhgIHFRV 164 d1tx2a_ 158 DLYDSIKIAkdagvrdenIILDPGIgfaktpeqNLEAmRNLEQ-LNVLG----------- 205 ::::::::: ::::::: :::: ::::: ::::: d1gk8a1 165 LAKALRMSG--------gDHLHSGT---vvgklEGER-EVTLGfVDLMRddyvekdrsrg 212 d1tx2a_ 206 ------------YPVLLGTSRksfighvldlpveerlegTGATVCLGIEKG--CEFVRVH 251 ::::::::: :::::::::::: ::::::: d1gk8a1 213 iyftqdwxsmpgVMPVASGGI------------------HVWHMPALVEIFgdDACLQFG 254 d1tx2a_ 252 ------------DVKEMSRMAKMMDAMIG------------------------------- 268 ::::::::::::::::: d1gk8a1 255 ggtlghpwgnapGAAANRVALEACTQARNegrdlareggdvirsackwspelaaacevwk 314 d1tx2a_ 269 -----------k 269 d1gk8a1 315 eikfefdtidkl 326 FAST alignment (Normalized score: 8.45 Raw score:2503.00) d1tx2a_ 1 KWDYDLRCG-----------EYTLNLNEKTLIMGILNVTPDSFSDGGSYN------EVDA 43 :::: :::::::::: :::: d1gk8a1 1 ---------GAPHGIQVERDKLNK--YGRGLLGCTI--------------KPKLGLSAKN 35 d1tx2a_ 44 AVRHAKEMRDEGAHIIDIGGESFA---------KVSVEEEIKRVVPMIQAVSKEVK--LP 92 ::::::::::::::::: ::::::::::::::::::::::: :: d1gk8a1 36 YGRAVYECLRGGLDFTA-------DDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKG 88 d1tx2a_ 93 ISIDTY-------KAEVAKQAIEAGAHIINDIWGAKA-----EPKIAEVAAHYDVPIILM 140 ::::: :::::::::::::::::: :::: :::::::::::::::::: d1gk8a1 89 HYLNA-TAGTCEEMMKRAVAAKELGVPIIMH--DYLTGGFTANTSLAIYCRDNGLLLHIH 145 d1tx2a_ 141 HNR-----DNMNYRNLMA----DMIADLYDSIKIAKDAGVRDEN---IILDPG---IGFA 185 : ::::: ::::::::::: :::::: :::: d1gk8a1 146 R--AMHAVIDRQR-----NHGIHFRVLAKALRM-----------SGGDHLHSGTVVGKLE 187 d1tx2a_ 186 KTPEQNLEAMRNLEQLNVL-----------------------GYPVLLGTSRKSFIGHVL 222 :::::::: ::::: ::::::: d1gk8a1 188 GEREVTLG---FVDLM---RDDYVEKDRSRGIYFTQDWASMPGVMPVAS----------- 230 d1tx2a_ 223 DLPVEERLEG---TGATVCLGIEKGC-----EFVRVH------------DVKEMSRMAKM 262 :::::::::: :::::: ::::::::::: d1gk8a1 231 ----------GGIHVWHMPALVE---IFGDDACLQFGGGTLGHPWGNAPGAAANRVALEA 277 d1tx2a_ 263 MDAMIGK--------------------------------------------- 269 :::: d1gk8a1 278 CTQA---RNEGRDLAREGGDVIRSACKWSPELAAACEVWKEIKFEFDTIDKL 326 TMalign alignment (TM-score: 0.65 Raw score:175.00) d1tx2a_ 1 -----KWDYDLRCGEYTLNLNEKTLIMGILNV--TPDSFSDGGSYNEVDAAVRHAKEMRD 53 ::::::: ::: :::::::::::: ::: :: ::::::::::: d1gk8a1 1 GAPHG-IQVERDK---LNK-YGRGLLGCTIKPKLGLS---------AK-NYGRAVYECLR 45 d1tx2a_ 54 EGAHIIDIGGESFAKVSVEEEIKRVVPMIQAVSKEVK------LPISIDTYK-----AE- 101 ::::::::::::::::: :::::::::::::::::: ::::::::: :: d1gk8a1 46 GGLDFTADDENVNSQPF--MRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMK 103 d1tx2a_ 102 VAKQAIEAGAHIINDIWG-AKA-EP-KIAEVAAHYDVPIILMHN-RDNMN-YRNL-MADM 155 :::::::::::::::::: ::: :: :::::::::::::::::: ::::: :::: ::: d1gk8a1 104 RAVAAKELGVPIIMHDYLTGGFTANTSLAIYCRDNGLLLHIHRAMHAVIDRQRNHG-IHF 162 d1tx2a_ 156 IADLYDSIKIAKDAGVRDENIILDPGIG--FAKTPEQNLEAMRNLEQ-LNVLG------- 205 ::::::::::: ::::::::: : :::: :::::: ::::: d1gk8a1 163 RVLAKALRMSG--------GDHLHSGTVVG----K-LEGE-REVTLGFVDLMRDDYVEKD 208 d1tx2a_ 206 ---------------Y-PVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKG--CEF 247 : :::::: : ::::::::::::: ::: d1gk8a1 209 RSRGIYFTQDWASMPGVMPVASG-G-----------------IHVWHMPALVEIFGDDAC 250 d1tx2a_ 248 VRVH--D----------VKEMSRMAKMMDAMIGK-------------------------- 269 :::: : ::::::::::::::::: d1gk8a1 251 LQFGGGTLGHPWGNAPGAAANRVALEACTQARNEGRDLAREGGDVIRSACKWSPELAAAC 310 d1tx2a_ 270 ---------------- 270 d1gk8a1 311 EVWKEIKFEFDTIDKL 326 HHsearch alignment (Probability: 0.90 E-value:0.00) d1tx2a_ 11 YTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIID--IGGESFAK 68 :::::::::::::::: :::::::::::::::::::::::::: ::::: :: d1gk8a1 11 DKLNKYGRGLLGCTIK--------PKLGLSAKNYGRAVYECLRGGLDFTXDDENVNS-QP 61 d1tx2a_ 69 VSV-EEEIKRVVPMIQAVSKEV--KLPISIDT--YKA----EVAKQAIEAGAHIIN---D 116 ::: :::::::::::::::::: :::::::: ::: ::::::::::::::: : d1gk8a1 62 FMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKELGVPIIMHDYL 121 d1tx2a_ 117 IWGAKAEPKIAEVAAHYDVPIILMHNRDNMNY-RNLMADMIADLYDSIKIAKDAGVRDEN 175 :::::::::::::::::::::::: ::::::: ::::::::::::::: :::::::: d1gk8a1 122 TGGFTANTSLAIYCRDNGLLLHIH-RAMHAVIDRQRNHGIHFRVLAKA--LRMSGGDH-- 176 d1tx2a_ 176 IILDPGIGFAKTPEQNLEAM 195 ::::::: ::::::::::: d1gk8a1 177 -LHSGTVV-GKLEGEREVTL 194