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: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.690 --> Intermediate <-- 1.570 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1rqga2) through the intermediate protein (d1jila_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jila_ Tyrosyl-​tRNA synthetase (TyrRS)Nucleotidylyl transferaseAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1rqga2 Methionyl-​tRNA synthetase (MetRS)Nucleotidylyl transferaseAdenine nucleotide alpha hydrolase-​likeα/β

Supporting Alignments

Query <-- 0.690 --> Intermediate
DALI alignment (Z-score: 6.1 Raw score:653.80) query 1 ---dadeeVYSAL-----vvglrayvAKNGFRSVLIGLS-----ggIDSALVAAIACDAL 47 ::::: ::::::::::::: :::::::::::::: d1jila_ 1 tnvliedlKWRGLiyqqtdeqgiedlLNKEQVTLYCGADptadslhIGHLLPFLTLRRFQ 60 query 48 G-aqNVYGVSMP--SKYS----------------SDHSKGDAAELARRTG-------LNF 81 : :::::::: :::: :::::::::::::::: ::: d1jila_ 61 EhghRPIVLIGGgtGMIGdpsgkseervlqteeqVDKNIEGISKQMHNIFefgtdhgAVL 120 query 82 RTVS--IEPMfdAYMASL----------------------gltGLAEENLQSRLRGTTLM 117 :::: :::: :::::: ::::::::::::::::: d1jila_ 121 VNNRdwLGQI--SLISFLrdygkhvgvnymlgkdsiqsrlehgISYTEFTYTILQAIDFG 178 query 118 AISNQEGH-IVLAPGNkselavgystlyGDSV--------------gAYGPiKDVY---- 158 :::::::: ::::::: :::: :::: :::: d1jila_ 179 HLNRELNCkIQVGGSD---------qwgNITSgielmrrmygqtdayGLTI-PLVTksdg 228 query 159 ----------------------------------ktsifrLAEW---------------- 168 :::: d1jila_ 229 kkfgksesgavwldaektspyefyqfwinqsdedvikflkYFTFlgkeeidrleqsknea 288 query 169 --------rnRAAAerGQTPpipeasitkpdypvldailelyvdrdtgadaivaagydre 220 :::: :::: d1jila_ 289 phlreaqktlAEEV--TKFI---------------------------------------- 306 query 221 lvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1jila_ 307 -----------------------------hgedalndairisqalf 323 FAST alignment (Normalized score: 2.35 Raw score:689.80) query 1 DADEEVYSA------------------LVVGLRAYVAKNGF--RSVLIGLSG-------- 32 ::::::::::: :::::: d1jila_ 1 ---------TNVLIEDLKWRGLIYQQTDEQGIEDLLNK---EQVTLYCG---ADPTADSL 45 query 33 ---GIDSALVAAIACDALGAQ-NVYGVSMPSKYS-------------------------- 62 ::::::::::::: :::::::: d1jila_ 46 HIGHLLPFLTLRRFQE-----HGHRPIVLI----GGGTGMIGDPSGKSEERVLQTEEQVD 96 query 63 --SDHSKGDAAELARRTGL-------NFRTVSIEPMFDAYMASLGLTG------------ 101 ::::::::::: ::::::::::::: d1jila_ 97 KNIEGISKQMHNI------FEFGTDHGAVLVNNRDWLGQ---------ISLISFLRDYGK 141 query 102 ---------------------LAEENLQSRLRGTTLMAISNQEGHIVLA---PGNKSELA 137 :::::::::::::::::::::::: :::: d1jila_ 142 HVGVNYMLGKDSIQSRLEHGISYTEFTYTILQAIDFGHLNRELNC----KIQVGGS---- 193 query 138 VGYSTLY-GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLD 196 :::: d1jila_ 194 -------DQWGN------------------------------------------------ 198 query 197 AILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRL 256 d1jila_ 199 ------------------------------------------------------------ 199 query 257 PITNRWREGH-------------------------------------------------- 266 d1jila_ 199 ----------ITSGIELMRRMYGQTDAYGLTIPLVTKSDGKKFGKSESGAVWLDAEKTSP 248 query 267 ------------------------------------------------------------ 267 d1jila_ 249 YEFYQFWINQSDEDVIKFLKYFTFLGKEEIDRLEQSKNEAPHLREAQKTLAEEVTKFIHG 308 query 267 --------------- 267 d1jila_ 309 EDALNDAIRISQALF 323 TMalign alignment (TM-score: 0.46 Raw score:121.20) query 1 ------DADEEVYSALV--VG--L--RAYVAKNGFRSVLIGLSG----G-IDSALVAAIA 43 :::::::: : : :::::::::::::::::: : :::::::::: d1jila_ 1 TNVLIE---DLKWRGLIYQ-QTDEQGIEDLLNKEQVTLYCGADPTADSLHIGHLLPFLTL 56 query 44 CDALG-AQNVYGVSMPS--K------------YS----S-DHSKGDAAELARRTG----- 78 ::::: ::::::::::: : :: : ::::::::::::::: d1jila_ 57 RRFQEHGHRPIVLIGGGTGMIGDPSGKSEERVLQTEEQVDKNIEGISKQMHNIFEFGTDH 116 query 79 -LNFRTVS--IEPMFDAYMASL-----------------------GLTGLAEENLQSRLR 112 ::::::: :::: ::::::: ::::::::::::: d1jila_ 117 GAVLVNNRDWLGQI-SLISFLRDYGKHVGVNYMLGKDSIQSRLEH--GISYTEFTYTILQ 173 query 113 GTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDS-VG------------AYGPIKDVYK 159 :::::::::::::::::::: :: : : ::: :: ::::: ::: d1jila_ 174 AIDFGHLNRELNCKIQVGGS--DQ--W--G--NITSGIELMRRMYGQTDAYGLTI--PLV 223 query 160 TS-----IF-----------------------------R---LAEWRN------------ 170 :: :: : :::::: d1jila_ 224 TKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKEEIDRLEQ 283 query 171 -------------RAAAERGQTPP----------------IPEASITKPDYPVLDAILEL 201 ::::::::::: d1jila_ 284 SKNEAPHLREAQKTLAEEVTKFIHGEDALNDAIRISQALF-------------------- 323 query 202 YVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNR 261 d1jila_ 324 ------------------------------------------------------------ 324 query 262 WREGH 266 d1jila_ 324 ----- 324 HHsearch alignment (Probability: 0.02 E-value:0.47) query 163 FRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVA--AGYDRE 220 :::::::::::::::::::::::::::: ::::::::::::::::::::::: :::::: d1jila_ 203 IELMRRMYGQTDAYGLTIPLVTKSDGKK-FGKSESGAVWLDAEKTSPYEFYQFWINQSDE 261 query 221 LVVKTLRMV 229 ::::::::: d1jila_ 262 DVIKFLKYF 270
Intermediate <-- 1.570 --> Hit
DALI alignment (Z-score: 9.4 Raw score:1159.10) d1jila_ 1 tnvliedlkwrgliyqqtdeqgiedllnKEQVTLYC-GADPTAdSLHIGHLL-PFLTLRR 58 :::::::: :::::: :::::::: ::::::: d1rqga2 1 ----------------------------MVRYMVTSaLPYANG-PIHAGHLAgAYLPADI 31 d1jila_ 59 FQEHG------HRPIVLIGggtGMIGdpsgkseeRVLQ------TEEQVDKNIEGISKQM 106 ::::: :::::::: :::: :::: :::::::::::::::: d1rqga2 32 FVRYLrlkgedVVFICGTD---EHGT------piSFRAlkegrsPREIVDEFHEQIKITF 82 d1jila_ 107 HN-IFEFgtdhgAVLVNNRD-WLGQIslisflrDYGKHV--------------------- 143 :: :::: :::::::: ::::: :::::: d1rqga2 83 QRaKISF-----DFFGRTELpIHYKL-----sqEFFLKAyenghlvkkvtkqaycehdkm 132 d1jila_ 144 ---------------------GVNY----------------------------------- 147 :::: d1rqga2 133 flpdrfaicgrpisfrdsahyYIKMqdfaerlkrwiekqpwkpnvknmvlswieegleer 192 d1jila_ 148 -----mlgkdsiqsrlehgiSYTEfTYTILQAIDFGH-------------lnRELN---- 185 :::: :::::::::::: :::: d1rqga2 193 aitrdlnwgipvpldeedmkGKVL-YVWFEAPIGYISitiehfkrigkpnewKKYWlnid 251 d1jila_ 186 ---cKIQVGGSDQWGNIT-SGIELMRRMYG--------QTDAY--GLTIPLVTksdgKKF 231 :::::::::::::: ::::::::::: ::::: :::::::: ::: d1rqga2 252 gqtrVIHFIGKDNIPFHAiFWPAFLMAYGKykdeeveaEWNLPydIPANEYLT--leGKK 309 d1jila_ 232 GK-sESGAVWLDAeKTSPY----------------efyqFWINQsdedvikflkyftflg 274 :: ::::::::: ::::: ::::: d1rqga2 310 FStsRNWAIWVHE-FLDVFpadylryylttimpetrdsdFSFSD---------------- 352 d1jila_ 275 keeidrleqskneaphlreaQKTLaeevtkfihgedalndairisqalf 323 :::: d1rqga2 353 -------------------fKVRI---------------------neel 361 FAST alignment (Normalized score: 5.46 Raw score:1864.00) d1jila_ 1 TNVLIEDLKWRGLIYQQTDEQGIEDLLNKEQVTLY-CGADPTADSLHIGHL-LPFLTLRR 58 ::::::: :::::: :::::::: :::::::: d1rqga2 1 ----------------------------MVRYMVTSALPYAN-GPIHAGHLAGAYLPADI 31 d1jila_ 59 FQE------HGHRPIVLIGGGTGMIGDPSGKSEERVLQ---------------TEEQVDK 97 ::: ::::::::::: ::::::: d1rqga2 32 FVRYLRLKGEDVVFICGTDE------------------HGTPISFRALKEGRSPREIVDE 73 d1jila_ 98 NIEGISKQMHNIFEFGTDHG-----AVLVNN-RDWLGQISLISFLR----DYGKHVGVNY 147 ::::::::::: :::::: ::::: ::::: d1rqga2 74 FHEQIKITFQR---------AKISFDFFGRTELPIHY---------KLSQEFFLK----- 110 d1jila_ 148 MLGKDS------------------------------------------------------ 153 d1rqga2 111 ------AYENGHLVKKVTKQAYCEHDKMFLPDRFAICGRPISFRDSAHYYIKMQDFAERL 164 d1jila_ 154 ----------------IQSRLEHGISYTEF--------------------------TYTI 171 :::::::::: :::: d1rqga2 165 KRWIEKQPWKPNVKNMVLSWIEEGLE----ERAITRDLNWGIPVPLDEEDMKGKVLYVWF 220 d1jila_ 172 LQAIDFGHLNRELNC-----------------------KIQVGGSDQWGNI-TSGIELMR 207 :::::::::::: ::::::::::::: :::::::: d1rqga2 221 EAPIGYISITIE---HFKRIGKPNEWKKYWLNIDGQTRVIHFIGKDNIPFHAIFWPAFLM 277 d1jila_ 208 RMYGQTD----------------AYGLTIPLVTKSDGKKFGKSES--------GAVWLDA 243 : ::::::::::::: ::::: d1rqga2 278 A------YGKYKDEEVEAEWNLPYDIPANEYLTLEG---------KKFSTSRNWAIWV-- 320 d1jila_ 244 EKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKEEIDRLEQSKNEAPHLREAQKTLAEEVT 303 d1rqga2 321 ------------------------------------------------------------ 321 d1jila_ 304 KFIHGEDALNDAIRISQALF---------------------------------------- 323 d1rqga2 321 --------------------HEFLDVFPADYLRYYLTTIMPETRDSDFSFSDFKVRINEE 360 d1jila_ 324 - 324 d1rqga2 361 L 361 TMalign alignment (TM-score: 0.52 Raw score:167.59) d1jila_ 1 TNVLIEDLKWRGLIYQQTDEQGIEDLLNKEQVTLYC-GADPTADSLHIGHLL-PFLTLRR 58 :::::::: :::::: :::::::: ::::::: d1rqga2 1 ----------------------------MVRYMVTSALPYANG-PIHAGHLAGAYLPADI 31 d1jila_ 59 FQ-EHG---H-RPIVLIGGGTGMIGDPSGKSEERVLQ------TEEQVDKNIEGISKQMH 107 :: ::: : ::::::: :::::: ::::: ::::::::::::::::: d1rqga2 32 FVRYLRLKGEDVVFICGT--DEHGTP------ISFRALKEGRSPREIVDEFHEQIKITFQ 83 d1jila_ 108 NIFEFGTDHGAVLVNNRD-WLGQISLISFLRDYGKH-VG--------------------- 144 ::::: ::::::::: ::::::: ::::::::: :: d1rqga2 84 RAKIS----FDFFGRTELPIHYKLSQ-EFFLKAYENGHLVKKVTKQAYCEHDKMFLPDRF 138 d1jila_ 145 ----------------VNYML-G-------------------K--D-----SIQSRL--E 159 ::::: : : : : d1rqga2 139 AICGRPISFRDSAHYYIKMQDFAERLKRWIEKQPWKPNVKNMVLSWIEEGL-----EER- 192 d1jila_ 160 HGISYTE-----------------FTYTILQAIDFGH-LN-----------RELNC---- 186 :::::: ::::::::::::: :: ::::: d1rqga2 193 -AITRDLNWGIPVPLDEEDMKGKVLYVWFEAPIGYISITIEHFKRIGKPNEWKKYWLNID 251 d1jila_ 187 ----KIQVGGSDQWGNIT-SGIELMRRM-Y--------GQTDAYGLTIPLVTKSDGKKFG 232 :::::::::::::: ::::::::: : :::::::::::::::::::::: d1rqga2 252 GQTRVIHFIGKDNIPFHAIFWPAFLMAYGKYKDEEVEAEWNLPYDIPANEYLTLEGKKFS 311 d1jila_ 233 KSESGAVWLDAEKTSPY-EFYQFW-INQSDEDVIKFLKYF---------TFLGKEEIDRL 281 ::::::::::: ::::: ::: : :::::::: d1rqga2 312 TSRNWAIWVHE-FLDVFP-ADY-LR-------YYLTTIMPETRDSDFSF----------- 350 d1jila_ 282 EQSKNEAPHLREAQKTLAEE-VTKFIHGEDALNDAIRISQALF 323 : :::::::: : d1rqga2 351 ----------S-DFKVRINEE--L------------------- 361 HHsearch alignment (Probability: 0.98 E-value:0.00) d1jila_ 34 LYCGADPT--ADSLHIGHLL-PFL----TLRRFQEHGHRPIVLIGGGTGMIGDP-SGKSE 85 :::::::: :: ::::::: ::: ::::::::::::::::::::: ::: ::::: d1rqga2 5 MVTSALPYANGP-IHAGHLAGAYLPADIFVRYLRLKGEDVVFICGTDEH--GTPISFRAL 61 d1jila_ 86 ERVLQTEEQVDKNIEGISKQMHNIFEF 112 ::::::::::::::::::::::::::: d1rqga2 62 KEGRSPREIVDEFHEQIKITFQRAKIS 88