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: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.848 --> Intermediate <-- 0.742 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1qasa3) through the intermediate protein (d1rvka1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1rvka1 Hypothetical protein Atu3453Enolase C-​terminal domain-​likeTIM beta/​alpha-​barrelα/β
Hit d1qasa3 Phospholipase C isozyme D1 (PLC-​D1)PLC-​like phosphodiesterasesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 0.848 --> Intermediate
DALI alignment (Z-score: 8.1 Raw score:836.10) query 1 mietpyylidkakltrnmeriahvreKSGAKALLALKC-----------fATWSVFDLMR 49 :::::::::::: :::::::::: d1rvka1 1 -------------------------yRDKVLAYGSIMCgdelegglatpeDYGRFAETLV 35 query 50 -DYMDGTTSS--------------SLFEVRLGRERFG--KETHAYSVA-----yGDNEID 87 ::::::::: ::::::::::::: ::::::::: :::::: d1rvka1 36 kRGYKGIKLHtwmppvswapdvkmDLKACAAVREAVGpdIRLMIDAFHwysrtdALALGR 95 query 88 EVVSH-ADKIIF--NSIS--QLERFADKaAGIARGLRLnpqrlGEWD-VPKVERVM--DR 139 ::::: :::::: :::: :::::::: ::::::::: :::: :::::::: :: d1rvka1 96 GLEKLgFDWIEEpmDEQSlsSYKWLSDN-LDIPVVGPE-----SAAGkHWHRAEWIkaGA 149 query 140 INGFMIHNNcenkdfglfdrMLGEIEeRFGALIA-RVDWVSLGGGIHftgddypvdafsa 198 ::::::::: :::::: ::::::: :::::::::::: d1rvka1 150 CDILRTGVN--------dvgGITPAL-KTMHLAEaFGMECEVHGNTA---------mnlh 191 query 199 rLRAFSdrygVQIYLEPGE----aSITKsttlevtvldtlynknlaivdssieahmldll 254 ::::: ::::::::: :::: d1rvka1 192 vVAATK----NCRWYERGLlhpflEYDD-------------------------------- 215 query 255 iyretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknw 314 d1rvka1 216 ------------------------------------------------------ghdylk 221 query 315 fngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1rvka1 222 slsdpmdrdgfvhvpdrpglgedidftfidnnrv 255 FAST alignment (Normalized score: 4.36 Raw score:1300.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREK--SGAKALLALKCFA----------------TW 42 :::::::: :: d1rvka1 1 ---------------------------YRDKVLAYGS-----IMCGDELEGGLATPEDYG 28 query 43 SVFDLMR-DYMDGTTSS---------------SLFEVRLGRERFG---KETHAY-SVAYG 82 ::::::: :::::::: :::::::::::: :::::: ::::: d1rvka1 29 RFAETLVKRGYKGIKL-HTWMPPVSWAPDVKMDLKACAAVREAV-GPDIRLMIDAFHWYS 86 query 83 DNEIDEVVS-----HADKIIFN-------SISQLERFADKAAGIARGLRLNPQRLGEW-- 128 ::::::::: ::::: ::::::::::: :::::: d1rvka1 87 RTDALALGRGLEKLGFDWI---EEPMDEQSLSSYKWLSDN-LDIPVV-----------GP 131 query 129 -----DVPKVERVM----DRINGFMIHNNCEN-----KDFGLFDRMLGEIEERFGALIAR 174 ::::::: :::::::: ::::::::::::::: d1rvka1 132 ESAAGKHWHRAE--WIKAGACDILRT------GVNDVGGITPALKTMHLAEA-------- 175 query 175 V--DWVSLGGGIHFTGDDYP--VDAFSARLRAFSDRYGVQ----IYLEPGEASITKSTTL 226 :::::: :::::::::: :::: d1rvka1 176 -FGMECEVH-----------GNTAMNLHVVAA--------TKNCRWYE------------ 203 query 227 EVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGE 286 d1rvka1 204 ------------------------------------------------------------ 204 query 287 FRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQS 346 d1rvka1 204 ------------------------------------------------------------ 204 query 347 LS---------------------------------------------------- 348 d1rvka1 204 --RGLLHPFLEYDDGHDYLKSLSDPMDRDGFVHVPDRPGLGEDIDFTFIDNNRV 255 TMalign alignment (TM-score: 0.40 Raw score:138.88) query 1 -MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKC-----FA----TW-SVFDLMR 49 ::::::::::::: :: :: ::::::: d1rvka1 1 Y-------------------------RDKVLAYGSIMCGDELEGGLATPEDYGRFAETLV 35 query 50 D-YM-DGTTSSS---------L-FEVRLGRERF--G---K-ETHAYSVAYGDNEIDEVV- 90 : :: ::::::: : :::::::::: : : :::::::::::::::::: d1rvka1 36 KRGYKGIKLHTWMPPVSWAPDVKMDLKACAAVREAVGPDIRLMIDAFHWYSRTDALALGR 95 query 91 SH----ADKIIF---N-SISQLERFADKAAGIARGLRLNPQRLGEW---DVPKVERVMDR 139 :: :::::: : :::::::::::: :::::::: :::: ::::::::: : d1rvka1 96 GLEKLGFDWIEEPMDEQSLSSYKWLSDNL-DIPVVGPE----SAAGKHWHRAEWIKAG-A 149 query 140 INGFMIHNNC-ENKDFGLFDRMLGEIEERFGALIA-RVDWVSLGGGIHFTGDDYPVDAFS 197 :::::::::: :::::::: :::::: ::::::::: ::: ::: d1rvka1 150 CDILRTGVNDV---------GGITPALK-TMHLAEAFGMECEVHG-NTA--------MNL 190 query 198 ARLRAFSDRYGVQIYLEPGEAS-ITKST-------------------------------- 224 ::::::: :::::::::::: ::::: d1rvka1 191 HVVAATK---NCRWYERGLLHPFLEYDDGHDYLKSLSDPMDRDGFVHVPDRPGLGEDIDF 247 query 225 --------TLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGK 276 d1rvka1 248 TFIDNNRV---------------------------------------------------- 255 query 277 SCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVR 336 d1rvka1 256 ------------------------------------------------------------ 256 query 337 EFTYADYEQSLS 348 d1rvka1 256 ------------ 256 HHsearch alignment (Probability: 0.03 E-value:0.31) query 130 VPKVERVMDRINGFMIHNNCENKDFGL-FDRMLGEIEERFGALIARV-DWVSLGGGIHFT 187 ::::::::::::::::::::::::::: ::::::::::::::::::: :::::::::: d1rvka1 29 RFAETLVKRGYKGIKLHTWMPPVSWAPDVKMDLKACAAVREAVGPDIRLMIDAFHWYS-- 86 query 188 GDDYPVDAFSARLRAFSDRYGVQIYLEP 215 :::::::::::::::::::::: d1rvka1 87 ------RTDALALGRGLEKLGFDWIEEP 108
Intermediate <-- 0.742 --> Hit
DALI alignment (Z-score: 7.1 Raw score:805.40) d1rvka1 1 -yrdkVLAYGSIMC-GDELE--gglATPEDYGRFAETLvkrgykgIKLHT---------- 46 ::::::::: ::::: ::::::::::::: ::::: d1qasa3 1 dqplsHYLVSSSHNtYLLEDqltgpSSTEAYIRALCKG------cRCLELdcwdgpnqep 54 d1rvka1 47 --WMPPVSWapdvkMDLKACAAVREAVG--pDIRLMIDAFHWYSRTDALALGRGLEKLG- 101 ::::::: :::::::::::::: :::::::::::::::::::::::::::: d1qasa3 55 iiYHGYTFT--skiLFCDVLRAIRDYAFkasPYPVILSLENHCSLEQQRVMARHLRAILg 112 d1rvka1 102 -----------------------fDWIEEpmdeqSLSSykwLSDNL-DIPV-VGPESAAG 136 ::::: :::: ::::: :::: :::::::: d1qasa3 113 pilldqpldgvttslpspeqlkgkILLKG---kkLGGK---LVPELsDMIIyCKSVHFGG 166 d1rvka1 137 K----hWHRAewikagacdILRTGVNdvGGITPalktmhlaeafgmECEVHG-------- 184 : :::: ::::::: ::::: :::::: d1qasa3 167 FsspgtSGQA--------fYEMASFSesRALRLlqesgngfvrhnvSCLSRIypagwrtd 218 d1rvka1 185 ----nTAMNLHVVaatkncrwYERGLLHPFL--EYDDghdylkslsdPMDRD----GFVH 234 :::::::: :::::::::: :::: ::::: :::: d1qasa3 219 ssnysPVEMWNGG-------cQIVALNFQTPgpEMDV-------ylgCFQDNggcgYVLK 264 d1rvka1 235 VPD------rPGLGedidftfidnnrv 255 ::: :::: d1qasa3 265 PAFlrdpnttFNSR------altqgpw 285 FAST alignment (Normalized score: 3.78 Raw score:1019.00) d1rvka1 1 Y----RDKVLAYGSIMC--------GDELEGGLATPED--YGRFAETLVKRGYKGIKLH- 45 :::::::: :::: ::::::::::::::::::: d1qasa3 1 -DQPLSHYLVSSS----HNTYLLEDQLTG---------PSSTEAYIRALCKGCRCLELDC 46 d1rvka1 46 ---------TWMPPVSWAPDVK-----MDLKACAAVREAVGP-------DIRLMIDAFHW 84 :::::: :::::::::::: ::::::: :: d1qasa3 47 WDGPNQEPIIYHGYT-------FTSKILFCDVLRAIRDY---AFKASPYPVILSLE--NH 94 d1rvka1 85 YSRTDALALGRGLEKLGFDWIEEPMDEQSLSSYKWLSDNLDI------------------ 126 ::::::::::::::: d1qasa3 95 CSLEQQRVMARHLRA---------------------------ILGPILLDQPLDGVTTSL 127 d1rvka1 127 -------------------------------PVVGPESAAGKHWHRAEWIKAGAC----- 150 :::: d1qasa3 128 PSPEQLKGKILLKGKKLGGKLVPELSDMIIYCKSV--------------------HFGGF 167 d1rvka1 151 -----------DILRTGVNDVGGITPALKTMHLAEAF-----------GMECEVHGN--- 185 ::::: :::::::::: :::::: d1qasa3 168 SSPGTSGQAFYEMASF------SESRALRLLQ-----ESGNGFVRHNVSCLSRI---YPA 213 d1rvka1 186 ----------TAMNLHVVAATK-NCRWYERGLLHPFLEYDDGHDYLKSLSDPMD------ 228 :::::: :::::: d1qasa3 214 GWRTDSSNYSPVEMWN------GGCQIVA-------------------------LNFQTP 242 d1rvka1 229 ---------------RDGFVHVPDRPGLGEDIDFTFIDNNRV------------------ 255 :::::::: d1qasa3 243 GPEMDVYLGCFQDNGGCGYVLKP-------------------AFLRDPNTTFNSRALTQG 283 d1rvka1 256 -- 256 d1qasa3 284 PW 285 TMalign alignment (TM-score: 0.55 Raw score:140.64) d1rvka1 1 -YRDKVLAYGSIMC-GDELE---GGLATPEDYGRFAETLVKRGYKGIKLHT--------- 46 ::::::::::::: ::::: :::::::::::::: : : :::::: d1qasa3 1 DQPLSHYLVSSSHNTYLLEDQLT-GPSSTEAYIRALCK-G---C-RCLELDCWDGPNQEP 54 d1rvka1 47 --WMPPVSWAPDVKMDLKACAAVREAVGP--DIRLMIDAFHWYSRTDALALGRGLE-KL- 100 :::::::: : :::::::::::::::: ::::::::::::::::::::::::: :: d1qasa3 55 IIYHGYTFTS-K-ILFCDVLRAIRDYAFKASPYPVILSLENHCSLEQQRVMARHLRAILG 112 d1rvka1 101 -GF---------------------DWIEEPMDEQSLSSYKWLSDNLDIPVVGPESAAGKH 138 :: :::::: : ::::: :: :::::: d1qasa3 113 PILLDQPLDGVTTSLPSPEQLKGKILLKGK--K-LGGKL--VP-ELSDMI---------- 156 d1rvka1 139 WHRAEWIKAGACDILRTGVNDVGGITPA-LKTMHLAEAFGMECEVHGN----T---A--- 187 :::::: :::::::: :::: : ::::::: : : d1qasa3 157 ------------IYCKSV--HFGGFSSPGTSGQ--A-----FYEMASFSESRALRLLQES 195 d1rvka1 188 --MNLHVVAATKNCRW----------------------YERGLLHP-F-L-EYDDG--HD 218 ::::::: : :::: :::::::: : : ::::: d1qasa3 196 GNGFVRHNV-S-CLSRIYPAGWRTDSSNYSPVEMWNGGCQIVALNFQTPGPEMDVYLG-- 251 d1rvka1 219 YLKSLSDPMDRD----GFVHVPDR----PGLGEDID-----FTFIDNNRV 255 ::::: :::::::: :::::::: d1qasa3 252 -------CFQDNGGCGYVLKPAFLRDPNTTFNSRALTQGPW--------- 285 HHsearch alignment (Probability: 0.09 E-value:0.23) d1rvka1 28 GRFAETLVKRGYKGIKLHTWMPPVS------W-----APDVKMDLKACAAVREAV--GPD 74 ::::::::::::::::::::::::: : ::::: :::::::::: ::: d1qasa3 28 TEAYIRALCKGCRCLELDCWDGPNQEPIIYHGYTFTSKILFC---DVLRAIRDYAFKASP 84 d1rvka1 75 IRLMIDAFHWYSRTDALALGRGLEK-LGFDWIEEPMD 110 ::::::::::::::::::::::::: ::::::::::: d1qasa3 85 YPVILSLENHCSLEQQRVMARHLRAILGPILLDQPLD 121