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 <-- 0.843 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1knwa2) 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 d1knwa2 Diaminopimelate decarboxylase LysAPLP-​binding barrelTIM 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 <-- 0.843 --> Hit
DALI alignment (Z-score: 9.4 Raw score:998.80) d1tx2a_ 1 kwdydlrcgeytlnlnektlimgilnvtpdsfsdggsynEVDAAVRHAKEMrDEGAH-II 59 :::::::::::: ::::: :: d1knwa2 1 ---------------------------------------DAQIIRRQIAAL-KQFDVvRF 20 d1tx2a_ 60 DIGGEsfakvsveeeikRVVPMiQAVSKEvKLPISIDTykAEVAKQAIEAGA-------- 111 ::::: ::::: :::::: :::::::: :::::::::::: d1knwa2 21 AQKAC-----------sNIHIL-RLMREQ-GVKVDSVS--LGEIERALAAGYnpqthpdd 65 d1tx2a_ 112 HIINdIWGAkaEPKIAEVAAHYDVPIILMhnrdnmnyrnlmadmiadLYDSIKIAKDAGv 171 :::: :::: :::::::::::::::::: :::::::::::: d1knwa2 66 IVFT-ADVI--DQATLERVSELQIPVNAG------------------SVDMLDQLGQVS- 103 d1tx2a_ 172 RDENIILDPG------------IGFAKtpeqnleamrnLEQLNVLG----------yPVL 209 :::::::::: ::::: :::::::: ::: d1knwa2 104 PGHRVWLRVNpgfghghsqktnTGGEN-----skhgiwYTDLPAALdviqrhhlqlvGIH 158 d1tx2a_ 210 LGTSRksfighvldlpvEERLEGTGATVCLGIEKG--------cEFVRVHD--------- 252 ::::: :::::::::::::::::: ::::::: d1knwa2 159 MHIGS------------GVDYAHLEQVCGAMVRQViefgqdlqaISAGGGLsvpyqqgee 206 d1tx2a_ 253 ------VKEMSRMAKMMDAMIGK------------------ 269 ::::::::::::::::: d1knwa2 207 avdtehYYGLWNAAREQIARHLGhpvkleiepgrflvaqsg 247 FAST alignment (Normalized score: 6.75 Raw score:1739.00) d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNE-VDAAVRHAKEMRD-EGAHI 58 :::::::::: ::::: d1knwa2 1 ----------------------------------------DAQIIRRQIAA---LKQFDV 17 d1tx2a_ 59 IDIGGESFAKVSVEEEIKR---VVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGA---- 111 :::::: :::::::::: ::::::: :::::::::::::: d1knwa2 18 VRFAQK-------------ACSNIHILRLMRE-QGVKVDS--VSLGEIERALAAGYNPQT 61 d1tx2a_ 112 ----HIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIAD-LYDSIKIA 166 ::::::: :::::::::::::::::: :::::::: d1knwa2 62 HPDDIVFTADV---IDQATLERVSELQIPVNA-------------------GSVDMLDQL 99 d1tx2a_ 167 KDAGVRDE-----NIILDPGIGFAKTPEQNLE----------------------AMRNLE 199 :: ::::::: :::::: d1knwa2 100 GQ------VSPGHRVWLRVN------------PGFGHGHSQKTNTGGENSKHGIWYTDLP 141 d1tx2a_ 200 QLNVL--------GYPVLLGTSRKSFIGHVLDLPVEE----RLEGTGATVCLGIE----- 242 :::: :::::::: :::::::::::::: d1knwa2 142 AALD-VIQRHHLQLVGIHMHI----------------GSGVDYAHLEQVCGAMVRQVIEF 184 d1tx2a_ 243 -KGCEFVRVH---------------------DVKEMSRMAKMMDAMIGK----------- 269 :::::: :::::::::::::::: d1knwa2 185 GQDLQAI---SAGGGLSVPYQQGEEAVDTEHYYGLWNAAREQIARHL--GHPVKLEIEPG 239 d1tx2a_ 270 -------- 270 d1knwa2 240 RFLVAQSG 247 TMalign alignment (TM-score: 0.54 Raw score:144.82) d1tx2a_ 1 -------------KWDYDLRCGEYTLNLNEKTLIMGILNV--TPDSFSDGGSYNEVDAAV 45 ::::::::: :: :::::: d1knwa2 1 DAQIIRRQIAALK------------------QFDVVRFAQKACS----------NIHILR 32 d1tx2a_ 46 RHAKEMRDEGAHIIDIGGESFAKVSVEEEIKRVVPMIQ-AVSKEVKLP-ISIDTY-KAE- 101 ::::::: ::::: :::::::::: ::::::::: :::::: ::: d1knwa2 33 LMREQGV------KVDSV----------SLGEIERALAAGYNPQTHPDDIVFTADVIDQA 76 d1tx2a_ 102 VAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHN-R---------D-NMNY-- 148 ::::::: ::::::: :::::::::::::: ::::::::: : : :::: d1knwa2 77 TLERVSE-LQIPVNA-GSVDMLDQLGQVSP--GHRVWLRVNPGFGHGHSQKTNTGGENSK 132 d1tx2a_ 149 ---RNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGF---AKTPEQNLEAMRNLEQ-L 201 :: :::::::::::: ::: :::::::::: :::::::::::::: : d1knwa2 133 HGI-----WY-TDLPAALDVIQR-HHL--QLVGIHMHIGSGV--DYAHLEQVCGAMVRQV 181 d1tx2a_ 202 NV-LGYP-VLLGTSRKSFIG---HVLDLPVEERLEGTGATVCLGIEKGC------EFVRV 250 :: :::: ::::::::: :: ::: ::::::::::::::::::: ::::: d1knwa2 182 IEFGQDLQAISAGGGLS-VPYQQ---GEE-AVDTEHYYGLWNAAREQIARHLGHPVKLEI 236 d1tx2a_ 251 HD---------VKEMSRMAKMMDAMIGK 269 :: d1knwa2 237 EPGRFLVAQSG----------------- 247 HHsearch alignment (Probability: 0.66 E-value:0.00) d1tx2a_ 124 PKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIG 183 :::::::::::::::::::::::::::: ::::::::::::::::::::: ::::::: d1knwa2 141 PAALDVIQRHHLQLVGIHMHIGSGVDYA--HLEQVCGAMVRQVIEFGQDLQ--AISAGGG 196 d1tx2a_ 184 FAKT 187 :::: d1knwa2 197 LSVP 200