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 <-- 2.454 --> Intermediate <-- 1.736 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1zfja1) through the intermediate protein (d1bd0a2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1bd0a2 Alanine racemasePLP-​binding barrelTIM beta/​alpha-​barrelα/β
Hit d1zfja1 Inosine monophosphate dehydrogenase (IMPDH)Inosine monophosphate dehydrogenase (IMPDH)TIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 2.454 --> Intermediate
DALI alignment (Z-score: 14.1 Raw score:1260.00) query 1 mietpyylidkAKLTRNMERIAHVReKSGAKALLALKCFA---TWSV-FDLMRD-YMDGT 55 :::::::::::::: :::::::::::::: :::: :::::: ::::: d1bd0a2 1 --------vdlDAIYDNVENLRRLL-PDDTHIMAVVKANAyghGDVQvARTALEaGASRL 51 query 56 TSSSLFEVRLGRE-RFGKETHAYSVAYGDnEIDEVVSHADKIIFNSISQLERFAD---ka 111 ::::::::::::: ::::::::::::::: ::::::::::::::::::::::::: d1bd0a2 52 AVAFLDEALALREkGIEAPILVLGASRPA-DAALAAQQRIALTVFRSDWLEEASAlysgp 110 query 112 aGIARGLRLNPQ--RLGEWDVPKVER-VMDR-------INGFMIHNNceNKDFGL--FDR 159 ::::::::::: :::::::::::: :::: ::::::::: :::::: ::: d1bd0a2 111 fPIHFHLKMDTGmgRLGVKDEEETKRiVALIerhphfvLEGLYTHFA-tADEVNTdyFSY 169 query 160 MLGEIEERFGALiARVDWVSLGG-GIHFtgddypvdaFSARLrafsdrygvQIYLEPGEA 218 :::::::::::: :::::::::: :::: ::::: ::::::::: d1bd0a2 170 QYTRFLHMLEWLpSRPPLVHCANsAASL--------rFPDRT---------FNMVRFGIA 212 query 219 SITKsttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsymicgksc 278 :::: d1bd0a2 213 MYGL-------------------------------------------------------- 216 query 279 lagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvref 338 d1bd0a2 217 -----------------------------------------------------apspgik 223 query 339 tyadyeqsls 348 d1bd0a2 224 pllpyplkea 233 FAST alignment (Normalized score: 7.91 Raw score:2253.00) query 1 MIETPYYLIDKA-KLTRNMERIAHVREK--SGAKALLALKCFA---------TWSVFDLM 48 ::::::::::::::: :::::::: :::::::: d1bd0a2 1 ------------VDLDAIYDNVENLRRLLPDDTHIMAV-----VKANAYGHGDVQVARTA 43 query 49 RD-YMDGTTSSSLFEVRLGRE-RFGKETHAYSVAYGDNEIDEVVSHA--DKIIFNSISQL 104 :: :::::::::::::::::: :::::::: :::::::::::::: ::::::::::: d1bd0a2 44 LEAGASRLAVAFLDEALALREKGIEAPILV-LGASRPADAALAAQ--QRIALTVFRSDWL 100 query 105 ERFADKAA----GIARGLRLNP--QRLGEWDVPKVERVMD--------RINGFMIHNNCE 150 ::::::: :::::::::: :::::::::::::::: ::::::: :::: d1bd0a2 101 EEASALY-SGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYT-HFAT 158 query 151 N--KDFGLFDRMLGEIEERFGALIA---RVDWVSLGGGIHFTGDDYPVDA---------F 196 : ::::::::::::::: :::: :::::: : d1bd0a2 159 ADEVNTDYFSYQYTRFLH-MLEW--LPSRPPLVH----------------CANSAASLRF 199 query 197 SARLRAFSDRYGVQ--IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLL 254 ::: ::::::::: d1bd0a2 200 PDR-----------TFNMVRFGIAM----------------------------------- 213 query 255 IYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNW 314 d1bd0a2 214 ------------------------------------------------------------ 214 query 315 FNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS-------------------- 348 d1bd0a2 214 ----------------------------------YGLAPSPGIKPLLPYPLKEA 233 TMalign alignment (TM-score: 0.49 Raw score:170.45) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKC-F--AT-WSVFDLMRD-YMDGT 55 ::::::::::::::::: :::::::::::: : :: ::::::::: ::::: d1bd0a2 1 --------VDLDAIYDNVENLRRLL-PDDTHIMAVVKANAYGHGDVQVARTALEAGASRL 51 query 56 TSSSLFEVRLGRE-RFGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFA-DKAA- 112 ::::::::::::: ::::::::::::::: :::::::::::::::::::::::: :::: d1bd0a2 52 AVAFLDEALALREKGIEAPILVLGASRPA-DAALAAQQRIALTVFRSDWLEEASALYSGP 110 query 113 -GIARGLRLNPQ--RLGEWDVPKVERVMD-RI------N-GFMIHNNCENKDFGL-FDRM 160 ::::::::::: ::::::::::::::: :: : ::::::::::::::: :::: d1bd0a2 111 FPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQ 170 query 161 LGEIEERFGALIARVD-WVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEAS 219 :::::: ::::::::: :::::: :::: :: ::::: : ::::::::: d1bd0a2 171 YTRFLH-MLEWLPSRPPLVHCAN-SAAS---LR---FPDRT---F------NMVRFGIAM 213 query 220 ITKS-------------TTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNE 266 :::: d1bd0a2 214 YGLAPSPGIKPLLPYPL------------------------------------------- 230 query 267 GSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIR 326 :: : d1bd0a2 231 -----------------------------------KE-A--------------------- 233 query 327 ELDGSVRTVREFTYADYEQSLS 348 d1bd0a2 234 ---------------------- 234 HHsearch alignment (Probability: 0.97 E-value:0.00) query 9 IDKAKLTRNMERIAHVREKSGAKALLALKCFA----TWSVFDLMRDYM-DGTTSSSLFEV 63 :::::::::::::::::: ::::::::::::: :::::::::::: ::::::::::: d1bd0a2 1 VDLDAIYDNVENLRRLLP-DDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEA 59 query 64 RLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAG---IARGLRL 120 :::::::::::::::::::::::::::::::::::::::::::::::::: ::::::: d1bd0a2 60 LALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKM 119 query 121 NPQ--RLGEWDVPKVERVMDRIN--------GFMIHNNCEN-KDFGLFDRMLGEIEERFG 169 ::: :::::::::::::::::: :::::::::: :::::::::::::::::: d1bd0a2 120 DTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLE 179 query 170 ALIARVDWVSLG 181 :::::::::::: d1bd0a2 180 WLPSRPPLVHCA 191
Intermediate <-- 1.736 --> Hit
DALI alignment (Z-score: 7.2 Raw score:834.30) d1bd0a2 1 ------------------------------------------------------------ 1 d1zfja1 1 snwdtkflkkgytfddvllipaeshvlpnevdlktkladnltlnipiitaamdtvtgskm 60 d1bd0a2 1 ----------------vDLDAIYDNVENLRRLLPDdTHIMAVVKANaygHGDVQVARTAL 44 :::::::::::::::::: :::::::::: ::::::::::: d1zfja1 61 aiaiaragglgvihknmSITEQAEEVRKVKRSEGR-LLVAAAVGVT---SDTFERAEALF 116 d1bd0a2 45 EAGASRLAVAF--------LDEALALREKGIEAPILVLgASRP-ADAALAAQQRI-ALTV 94 ::::::::::: ::::::::::::::::::: :::: ::::::::::: :::: d1zfja1 117 EAGADAIVIDTahghsagvLRKIAEIRAHFPNRTLIAG-NIATaEGARALYDAGVdVVKV 175 d1bd0a2 95 ------------------fRSDWLEEASAlysgPFPIHFHLKmdtgmgrLGVKDEEETKR 136 :::::::::: ::::::::: ::::::::::: d1zfja1 176 gigpgsicttrvvagvgvpQVTAIYDAAA-varEYGKTIIAD-------GGIKYSGDIVK 227 d1bd0a2 137 IVALIerhphfvLEGLYTH--FATA----DEVN--------------------------- 163 ::::: ::::::: :::: :::: d1zfja1 228 ALAAG-------GNAVMLGsmFAGTdeapGETEiyqgrkyktyrgmgsiaamkknklvpe 280 d1bd0a2 164 -----tDYFSYQYTRFLHMLEWLPsrpplvhcansaaslrfpdrtfnmvrfgiamyglap 218 :::::::::::::::::: d1zfja1 281 giegrvAYKGAASDIVFQMLGGIR-----sgmgyvgagdiqelhenaqfvemsgaglies 335 d1bd0a2 219 spgikpllpyplkea 233 d1zfja1 336 hphdvqitneapnys 350 FAST alignment (Normalized score: 5.20 Raw score:1484.00) d1bd0a2 1 V----------------------------------------------------------- 1 d1zfja1 1 -SNWDTKFLKKGYTFDDVLLIPAESHVLPNEVDLKTKLADNLTLNIPIITAAMDTVTGSK 59 d1bd0a2 2 ------------------DLDAIYDNVENLRRLLPD--DTHIMAVVKANAYGHGDVQVAR 41 ::::::::::::::: ::::::::: ::: ::::::: d1zfja1 60 MAIAIARAGGLGVIHKNMSITEQAEEVRKVKRS---EGRLLVAAAVG--VTS-DTFERAE 113 d1bd0a2 42 TALEAGASRLAVA---------FLDEALALREKG--IEAPILVLGA--SRPADAALAAQQ 88 :::::::::::: :::::::::: :::::::: :::::::::::: d1zfja1 114 ALFEAGADAIVI-DTAHGHSAGVLRKIAEIRA--HFPNRTLIAG--NIATAEGARALYDA 168 d1bd0a2 89 R-IALTVF-------------------RSDWLEEASALYSGPFPIHFHLKMDTGMGRL-G 127 : ::::: :::::::::::: :::::::::: : d1zfja1 169 GVDVVKV-GIGPGSICTTRVVAGVGVPQVTAIYDAAAVA-REYGKTIIAD--------GG 218 d1bd0a2 128 VKDEEETKRIVALIERHPHF-VLEGLYTHFATADEVN----------------------- 163 :::::::::::: ::::::: d1zfja1 219 IKYSGDIVKALA--------AGGNAVML---------GSMFAGTDEAPGETEIYQGRKYK 261 d1bd0a2 164 -------------------------------TDYFSYQYTRFLHMLEWLPSRPPLVHCAN 192 ::::::::::::::: d1zfja1 262 TYRGMGSIAAMKKNKLVPEGIEGRVAYKGAASDIVFQMLGGIRSGM-------------- 307 d1bd0a2 193 SAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEA------------------- 233 d1zfja1 308 -----------------------------------------GYVGAGDIQELHENAQFVE 326 d1bd0a2 234 ------------------------ 234 d1zfja1 327 MSGAGLIESHPHDVQITNEAPNYS 350 TMalign alignment (TM-score: 0.57 Raw score:133.32) d1bd0a2 1 ----------------------------VDLDAIYDNVENLRR-LLPDD----------T 21 : :::: : d1zfja1 1 SNWDTKFLKKGYTFDDVLLIPAESHVLP--------------NE-VDLKTKLADNLTLNI 45 d1bd0a2 22 HIMAVVKANAYGHGDVQVARTALEAGASRLAVAF-L-D-EALALREKGI-----EAPILV 73 ::::::::::: :::::::::: ::::::::: : : :::::::::: :::::: d1zfja1 46 PIITAAMDTVT---GSKMAIAIAR-AGGLGVIHKNMSITEQAEEVRKVKRSEGRLLVAAA 101 d1bd0a2 74 LGASR--PAD-AALAAQQ-R-IALTV---F----RSDWLEEASALYSGPFPIHFHLKMDT 121 :::: ::: ::::::: : ::::: : ::::::::: ::: ::::::::::: d1zfja1 102 -VGVTSDTFERAEALFEAGADAIVIDTAHGHSAGVLRKIAEIR--AHF-PNRTLIAGNIA 157 d1bd0a2 122 GMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADE--------VNTDYFSYQYTR 173 ::: ::::::::: ::::::::::::: :::::::: d1zfja1 158 -------TAE-GARALYDAG-------VDVVKVGIGPGSICTTRVVAG----VGVPQVTA 198 d1bd0a2 174 FLHMLEWL-PSRPPLVHCANSAASLRFPDRTF----NMVRFGIAM-YG------------ 215 :::::::: ::::: ::::::::::::::::: ::::::::: :: d1zfja1 199 IYDAAAVAREYGKT-IIADGGIKYSGDIVKALAAGGNAVMLGSMFAGTDEAPGETEIYQG 257 d1bd0a2 216 ----------------------------LA------------------------------ 217 :: d1zfja1 258 RKYKTYRGMGSIAAMKKNKLVPEGIEGRVAYKGAASDIVFQMLGGIRSGMGYVGAGDIQE 317 d1bd0a2 218 ------------------PSPGIKPL-------LPYPLKEA 233 :: :::::: d1zfja1 318 LHENAQFVEMSGAGLIES------HPHDVQITNEAPNYS-- 350 HHsearch alignment (Probability: 0.06 E-value:0.21) d1bd0a2 146 HFVLEGLYTHFATADEVNTDYFSYQ 170 ::::::::::::::::::::::::: d1zfja1 232 GGNAVMLGSMFAGTDEAPGETEIYQ 256