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 <-- 1.885 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1p4ca_) 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 d1p4ca_ Membrane-​associated (S)-​mandelate dehydrogenaseFMN-​linked oxidoreductasesTIM 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 <-- 1.885 --> Hit
DALI alignment (Z-score: 6.1 Raw score:757.60) d1bd0a2 1 ------------------------------------------------------------ 1 d1p4ca_ 1 nlfnvedyrklaqkrlpkmvydyleggaedeygvkhnrdvfqqwrfkpkrlvdvsrrslq 60 d1bd0a2 1 ------------------------------------------vdldaiyDNVENLRRLLP 18 ::::::::::: d1p4ca_ 61 aevlgkrqsmplligptglngalwpkgdlalaraatkagipfvlstasnMSIEDLARQCD 120 d1bd0a2 19 ddTHIMAVVKanaYGHG--DVQVARTALEAGASRLAVAF--------------------- 55 :::::::: :::: :::::::::::::::::::: d1p4ca_ 121 --GDLWFQLY---VIHReiAQGMVLKALHTGYTTLVLTTdvavngyrerdlhnrfkippf 175 d1bd0a2 56 -----------------------------------lDEALALREkGIEAPILVLGASRPA 80 :::::::: ::::::::::::::: d1p4ca_ 176 ltlknfegidlgkmdkanlemqaalmsrqmdasfnwEALRWLRD-LWPHKLLVKGLLSAE 234 d1bd0a2 81 DAALAAQ-QRIALTV------------fRSDWLEEASALYsgpfPIHFHLKmdtgmgrLG 127 ::::::: ::::::: :::::::::::: ::::::: :: d1p4ca_ 235 DADRCIAeGADGVILsnhggrqldcaisPMEVLAQSVAKT----GKPVLID-------SG 283 d1bd0a2 128 VKDEEETKRIVALIerhphfvLEGLYTH--FATA-DEVNTDYFSYQYTRFLHMLE----- 179 :::::::::::::: ::::::: :::: :::::::::::::::::::: d1p4ca_ 284 FRRGSDIVKALALG-------AEAVLLGraTLYGlAARGETGVDEVLTLLKADIDrtlaq 336 d1bd0a2 180 ---wLPSRpplvhcansaaslrfpdrtfnmvrfgiamyglapspgikpllpyplkea 233 :::: d1p4ca_ 337 igcpDITS----------------------------------------lspdylqne 353 FAST alignment (Normalized score: 4.75 Raw score:1361.00) d1bd0a2 1 VDLDAIYDNVENLRRLLPDDT--------------------------------------- 21 d1p4ca_ 1 ---------------------NLFNVEDYRKLAQKRLPKMVYDYLEGGAEDEYGVKHNRD 39 d1bd0a2 22 -------------------------------HIMAVVKANAYGH------------GDVQ 38 :::: :::: d1p4ca_ 40 VFQQWRFKPKRLVDVSRRSLQAEVLGKRQSMPLLI---------GPTGLNGALWPKGDLA 90 d1bd0a2 39 VARTALEAGASRLAVAFLD------EALALREKGIEAPILVLGAS--------RPADAAL 84 ::::::::: ::::: ::::::: ::::::::: ::::::: d1p4ca_ 91 LARAATKAG-IPFVL----STASNMSIEDLAR-QCDGDLWFQ---LYVIHREIAQGMVLK 141 d1bd0a2 85 AAQQR-IALTVF------------------------------------------------ 95 ::::: ::::: d1p4ca_ 142 ALHTGYTTLVL-TTDVAVNGYRERDLHNRFKIPPFLTLKNFEGIDLGKMDKANLEMQAAL 200 d1bd0a2 96 ---------RSDWLEEASALYSGPFPIHFHLKMDTGMGRL-GVKDEEETKRIVALIERHP 145 :::::::::::: :::::: ::::::::::::: d1p4ca_ 201 MSRQMDASFNWEALRWLRDLW----PHKLLV---------KGLLSAEDADRCIA------ 241 d1bd0a2 146 HF-VLEGLYTHFATADEVNTDYFS------------YQYTRFLHMLEWLPSRPPLVHCAN 192 ::::::: :::::::::::::: :::::: d1p4ca_ 242 --EGADGVIL--------------SNHGGRQLDCAISPMEVLAQSVAKTG---KPVLID- 281 d1bd0a2 193 SAASLR----FPDRT--------FNMVRFGIAMYGLAPSPGIKPLLPYPLKEA------- 233 :::: :::::::::: d1p4ca_ 282 ------SGFRRGSD-IVKALALGAEAVLLGRAT--------------------LYGLAAR 314 d1bd0a2 234 --------------------------------------- 234 d1p4ca_ 315 GETGVDEVLTLLKADIDRTLAQIGCPDITSLSPDYLQNE 353 TMalign alignment (TM-score: 0.48 Raw score:111.28) d1bd0a2 1 VDLDAI---------------------------------------YDNVENL-RR----- 15 ::: :: :: : d1p4ca_ 1 NLF-NVEDYRKLAQKRLPKMVYDYLEGGAEDEYGVKHNRDVFQQW-----RFK-PKRLVD 53 d1bd0a2 16 -----LLPDDTH----IMAVVKANAYGHGDVQVARTALEAGASRLAVAF-L-----DEAL 60 ::::: :: ::::::::: : :::: d1p4ca_ 54 VSRRS--LQAEVLGKR---------------------QS-MPLLIGPTGLNGALWPKGDL 89 d1bd0a2 61 ALREKGIE-A-PILVLGASR-PADAALAAQ-Q-R-IALTVFR--SDWLEEASALYSGPFP 112 :::::::: : :::: :::: :::::::: : : ::::::: ::::::::::::: :: d1p4ca_ 90 ALARAATKAGIPFVL-STASN-MSIEDLARQCDGDLWFQLYVIHREIAQGMVLKALH-TG 146 d1bd0a2 113 IHFHLKMDTGMGR---------------------------------------------LG 127 ::::::::::::: :: d1p4ca_ 147 YTTLVLTTDVAVNGYRERDLHNRFKIPPFLTLKNFEGIDLGKMDKANLEMQAALMSRQMD 206 d1bd0a2 128 V-KDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRP- 185 : :::::::::::::: :: :::::: : :::::::::::: ::: d1p4ca_ 207 ASFNWEALRWLRDLWP-----HK-LLVKGL----------L--SAEDADRCIAEG-ADGV 247 d1bd0a2 186 ----------------------------PLVHCANSA----AS-LRFPDRTFNMVRFGIA 212 ::::::::: :: ::::::: :::::::: d1p4ca_ 248 ILSNHGGRQLDCAISPMEVLAQSVAKTGKPVLIDSGFRRGSDIVKALALGA-EAVLLGRA 306 d1bd0a2 213 M--------------Y--G------------------------LAPSPGIKPLLPY--PL 230 : : : :: d1p4ca_ 307 TLYGLAARGETGVDEVLTLLKADIDRTLAQIGCPDITSLSPDY-----------LQNE-- 353 d1bd0a2 231 KEA 233 d1p4ca_ 354 --- 354 HHsearch alignment (Probability: 0.03 E-value:0.22) d1bd0a2 55 FLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTV-------------FRSDWLE 101 ::::::::::: :::::::::::::::::::::::::::: ::::::: d1p4ca_ 210 NWEALRWLRDL-WPHKLLVKGLLSAEDADRCIAEGADGVILSNHGGRQLDCAISPMEVLA 268 d1bd0a2 102 EASALYSGPFPIHFHLKMDTGMGRLGV 128 :: :::::::::::::: :::: d1p4ca_ 269 QS------VAKTGKPVLIDSGF-RRGS 288