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 <-- 0.611 --> Intermediate <-- 0.668 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1tjya_) through the intermediate protein (d1vlja_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vlja_ NADH-​dependent butanol dehydrogenase A (TM0820)Dehydroquinate synthase-​likeDehydroquinate synthase-​likemulti
Hit d1tjya_ AI-​2 receptor LsrBPeriplasmic binding protein-​like IPeriplasmic binding protein-​like Iα/β

Supporting Alignments

Query <-- 0.611 --> Intermediate
DALI alignment (Z-score: 3.6 Raw score:436.20) query 1 ------------dadeeVYSALVVgLRAYVAKNGFRSVLIGLSGGID-saLVAAIACDAL 47 ::::::: :::::::::::::::::::::: :::::::::: d1vlja_ 1 hhhmenfvfhnptkivfGRGTIPK-IGEEIKNAGIRKVLFLYGGGSIkknGVYDQVVDSL 59 query 48 G--aqNVYGVSMpskyssdhskgdaaelarrtglnfrtvsiepmfdaymaslgltglaee 105 : ::::::: d1vlja_ 60 KkhgiEWVEVSG----------------------------------------------vk 73 query 106 nlQSRLRGTTLMAISNQEGH-IVLAPGNkselavgystlygDSVG--------------- 149 :::::::::::::::::: ::::::: :::: d1vlja_ 74 pnPVLSKVHEAVEVAKKEKVeAVLGVGG----------gsvVDSAkavaagalyegdiwd 123 query 150 -------------AYGPIkDVYKtsifrlaewrnraaaergqtppipeasitkpdypvld 196 ::::: :::: d1vlja_ 124 afigkyqiekalpIFDVL-TISA------------------------------------- 145 query 197 ailelyvdrdtgadaivaagydrelvvktlrmvdtaeYKRRQYP-PGTKIS--------- 246 ::::::: :::::: d1vlja_ 146 ---------------tgtemngnavitnektkekygvSSKALYPkVSIIDPsvqftlpke 190 query 247 ------------------------------------------------------------ 247 d1vlja_ 191 qtvygavdaishileyyfdgsspeisneiaegtirtimkmterliekpddyearanlaws 250 query 247 ------------------------------------------------------------ 247 d1vlja_ 251 atialngtmavgrrggewachriehslsalydiahgaglaivfpawmkyvyrknpaqfer 310 query 247 ------------------------------------------------------------ 247 d1vlja_ 311 fakkifgfegegeelilkgieafknwlkkvgapvslkdagipeedidkivdnvmllvekn 370 query 247 --------akgfgkdrrlpitnrwregh 266 d1vlja_ 371 lkpkgaslgrimvleredvreilklaak 398 FAST alignment (Normalized score: 2.06 Raw score:669.30) query 1 DADEEVYSALV----------------------VGLRAYVAKNGFRSVLIGLS------G 32 ::::::::::::::::::: : d1vlja_ 1 -----------HHHMENFVFHNPTKIVFGRGTIPKIGEEIKNAGIRKVLFLY-GGGSIKK 48 query 33 GIDSALVAAIACDALGAQ---NVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPM 89 ::::::::::::: ::::: d1vlja_ 49 NGVYDQVVDSLKK-----HGIEWVEV---------------------------------- 69 query 90 FDAYMASLGLTGLAEENLQ-------SRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYS 141 :::::::::::::::: ::::: d1vlja_ 70 -------------------SGVKPNPVLSKVHEAVEVAKKEKVEAVLG------------ 98 query 142 TLY-----GDSVG-----------------------------AYGPIKDVYKTSIFRLAE 167 :::: :::: d1vlja_ 99 ---VGGGSVVDS-AKAVAAGALYEGDIWDAFIGKYQIEKALPIFDV-------------- 140 query 168 WRNRAAAERGQTPPIPEASITKP------------------------------------- 190 d1vlja_ 141 -----------------------LTISATGTEMNGNAVITNEKTKEKYGVSSKALYPKVS 177 query 191 --------------------------------------------DYPVLDAILELYVDRD 206 :::::::::::::: d1vlja_ 178 IIDPSVQFTLPKEQTVYGAVDAISHILEYYFDGSSPEISNEIAEGTIRTIMKMTERLI-- 235 query 207 TGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1vlja_ 236 ------------------------------------------------------------ 236 query 267 ------------------------------------------------------------ 267 d1vlja_ 236 EKPDDYEARANLAWSATIALNGTMAVGRRGGEWACHRIEHSLSALYDIAHGAGLAIVFPA 295 query 267 ------------------------------------------------------------ 267 d1vlja_ 296 WMKYVYRKNPAQFERFAKKIFGFEGEGEELILKGIEAFKNWLKKVGAPVSLKDAGIPEED 355 query 267 ------------------------------------------- 267 d1vlja_ 356 IDKIVDNVMLLVEKNLKPKGASLGRIMVLEREDVREILKLAAK 398 TMalign alignment (TM-score: 0.39 Raw score:104.91) query 1 ---------------DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDS-ALVAAIAC 44 ::::::::::::: ::::::::::::::::::: :::::::: d1vlja_ 1 HHHMENFVFHNPTKI---VFGRGTIPKIGEE-IKNAGIRKVLFLYGGGSIKKNGVYDQVV 56 query 45 DALGA-QNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGL- 102 ::::: :::::::::: : : : d1vlja_ 57 DSLKKHGIEWVEVSGV--K---P-----------------------------------NP 76 query 103 AEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVG------------- 149 ::::::::::::::: : ::::::::: ::: : : :::::: d1vlja_ 77 --VLSKVHEAVEVAKKE-K--VEAVLGVGG-GSV---V-D-SAKAVAAGALYEGDIWDAF 125 query 150 ----------AYGPIKDVYKTS-------------------------------IFRLAEW 168 :::::::::::: ::::::: d1vlja_ 126 IGKYQIEKALPIFDVLTISATGTEMNGNAVITNEKTKEKYGVSSKALYPKVSIIDPSVQF 185 query 169 RNRAAAERGQTPPIPEASIT--K-PDYPVLDAILE----------------L-------- 201 : :: : ::::::::::: : d1vlja_ 186 ---------------T--LPKEQTVYGAVDAISHILEYYFDGSSPEISNEIAEGTIRTIM 228 query 202 -------------------------YV--DRD--T--GA--------------------- 209 :: ::: : :: d1vlja_ 229 KMTERLIEKPDDYEARANLAWSATIALNGTMAVGRRGGEWACHRIEHSLSALYDIAHGAG 288 query 210 ------------------DA-IVA--A----------------GYD--R------EL--- 221 :: ::: : ::: : : d1vlja_ 289 LAIVFPAWMKYVYRKNPAQFERFAKKIFGFEGEGEELILKGIEAFKNWLKKVGAP-VSLK 347 query 222 ---------------VVKTLRM--VDT---AEYK--RRQYPPGTKISAKGFGKDRRLPIT 259 : : : ::: d1vlja_ 348 DAGIPEEDIDKIVDN------VML--LVEK---NLK---------------------PKG 375 query 260 NRWREGH---------------- 266 ::::::: d1vlja_ 376 ASLGRIMVLEREDVREILKLAAK 398 HHsearch alignment (Probability: 0.06 E-value:0.07) query 14 LRAYVAKNGFRSVLIGLSGG-IDSALVAAIACDALGAQNVYGVS--MPSKYSSDHSKGDA 70 :::::::::::::::::::: ::::::::::::::::::::::: :::::::::::::: d1vlja_ 25 IGEEIKNAGIRKVLFLYGGGSIKKNGVYDQVVDSLKKHGIEWVEVSGVKPNPVLSKVHEA 84 query 71 AELARRTGLNFRT 83 ::::::::::::: d1vlja_ 85 VEVAKKEKVEAVL 97
Intermediate <-- 0.668 --> Hit
DALI alignment (Z-score: 8.9 Raw score:727.50) d1vlja_ 1 ------------------------------------------------------------ 1 d1tjya_ 1 gsaeriafipklvgvgfftsggngaqeagkalgidvtydgptepsvsgqvqlvnnfvnqg 60 d1vlja_ 1 -------------------------------hhhmenfvfhnptkivfgrGTIPKIGEEI 29 :::::::::: d1tjya_ 61 ydaiivsavspdglcpalkramqrgvkiltwdsdtkpecrsyyinqgtpkQLGSMLVEMA 120 d1vlja_ 30 KNAG---iRKVLFLYGGG---SIKKngVYDQVVDSLKKH--GIEW-VEVSgVKPNPVlSK 80 :::: :::::::::: :::: :::::::::::: :::: :::: :::::: :: d1tjya_ 121 AHQVdkekAKVAFFYSSPtvtDQNQ--WVKEAKAKISQEhpGWEIvTTQF-GYNDAT-KS 176 d1vlja_ 81 VHEAVEVAKKEK-VEAVLGVGGgSVVDSAKAVAAGALYegdiwdafigkyqieKALPIFD 139 :::::::::::: ::::::::: ::::::::::::::: ::::::: d1tjya_ 177 LQTAEGIIKAYPdLDAIIAPDA-NALPAAAQAAENLKR---------------NNLAIVG 220 d1vlja_ 140 VLtisATGTeMNGNavitnektkekygvsSKALyPKVSIIDPsvqftlpkeqtvygavda 199 :: :::: :::: :::: :::::::: d1tjya_ 221 FS---TPNV-MRPY--------------vQRGT-VKEFGLWD------------------ 243 d1vlja_ 200 ishileyyfdgsspeisneiaegtirtimkMTERLIEK---------------------- 237 :::::::: d1tjya_ 244 ---------------------------vvqQGKISVYVanallknmpmnvgdsldipgig 276 d1vlja_ 238 --------------------pDDYEaranlawsaTIALngtmavgrrggewachriehsl 277 :::: :::: d1tjya_ 277 kvtvspnseqgyhyeakgngiVLLPervifnkdnIDKY---------------------- 314 d1vlja_ 278 salydiahgaglaivfpawmkyvyrknpaqferfakkifgfegegeelilkgieafknwl 337 d1tjya_ 315 ------------------------------------------------------------ 315 d1vlja_ 338 kkvgapvslkdagipeedidkivdnvmllveknlkpkgaslgrimvleredvreilklaa 397 d1tjya_ 315 -----------------------------------------------------------d 315 d1vlja_ 398 k 398 d1tjya_ 316 f 316 FAST alignment (Normalized score: 2.27 Raw score:806.50) d1vlja_ 1 HHHMENFVFHNPTKIVFGRGTIPKIGEEIKNAGI---RKVLFLYGGGSIKK------NGV 51 ::::::::: ::: d1tjya_ 1 ----------------------------------GSAERIAFIPKL-----VGVGFFTSG 21 d1vlja_ 52 YDQVVDSLKKHGIEWVEVSGVKP---NPVLSKVHEAVEVAKKEKVEAVLGVGGGSVV--- 105 :::::::::::::::::: :::::::::::::::::::::::: d1tjya_ 22 GNGAQEAGKALGIDVTYD-----GPTEPSVSGQVQLVNNFVNQGYDAIIV-------SAV 69 d1vlja_ 106 --DSAKAVAAGALYEGDIWDAFIGKYQIEK---ALPIFDVLTISATGTEMNGNAVITNEK 160 :::::::::: :::::: d1tjya_ 70 SPDGLCPALKRA------------------MQRGVKILT--------------------- 90 d1vlja_ 161 TKEKYGVSSKAL--------YPKVSIIDPSVQFTLPKEQTVYGAVDAISHILEYYFDGSS 212 ::::::: d1tjya_ 91 ------------WDSDTKPECRSYYIN--------------------------------- 105 d1vlja_ 213 PEISNEIAEG--TIRTIMKMTERLIEKPDDYEARANLAWSATIALNGTMAVGRRGGEWAC 270 ::::::::::::: d1tjya_ 106 ----------QGTPKQLGSMLVEMA----------------------------------- 120 d1vlja_ 271 HRIEHSLSALYDIA---------------------------------------------- 284 d1tjya_ 121 --------------AHQVDKEKAKVAFFYSSPTVTDQNQWVKEAKAKISQEHPGWEIVTT 166 d1vlja_ 285 -----HGAGLAIVFPAWMKYVYRKNPAQFERFAKKIFGFEGEGEELILKGIEAFKNWLKK 339 ::::::::::::::::: d1tjya_ 167 QFGYNDATKSLQTAEGIIKAYP-------------------------------------- 188 d1vlja_ 340 VGAPVSLKDAGIPEEDIDKIVDNVMLLVEKNLKPKGASLGRIMVLEREDVREILKLAAK- 398 d1tjya_ 189 -----------------------------------------------------------D 189 d1vlja_ 399 ------------------------------------------------------------ 399 d1tjya_ 190 LDAIIAPDANALPAAAQAAENLKRNNLAIVGFSTPNVMRPYVQRGTVKEFGLWDVVQQGK 249 d1vlja_ 399 ------------------------------------------------------------ 399 d1tjya_ 250 ISVYVANALLKNMPMNVGDSLDIPGIGKVTVSPNSEQGYHYEAKGNGIVLLPERVIFNKD 309 d1vlja_ 399 ------- 399 d1tjya_ 310 NIDKYDF 316 TMalign alignment (TM-score: 0.33 Raw score:132.32) d1vlja_ 1 ------------------------------------------------------------ 1 d1tjya_ 1 GSAERIAFIPKLVGVGFFTSGGNGAQEAGKALGIDVTYDGPTEPSVSGQVQLVNNFVNQG 60 d1vlja_ 1 ---------------------------------------------HHHMENFVFHNPTKI 15 d1tjya_ 61 YDAIIVSAVSPDGLCPALKRAMQRGVKILTWDSDTKPECRSYYIN--------------- 105 d1vlja_ 16 VFGR-GT-IPKIGEEIKNA-GI--RKVLFLYGGG-SIKKNGVYDQVVDSLKK-HG-IEWV 67 ::: :: ::::::::::: :: :::::::::: ::::::::::::::::: :: :::: d1tjya_ 106 -QGTPKQLGSMLVEMAAHQVDKEKAKVAFFYSSPTVTDQNQWVKEAKAKISQEHPGWEIV 164 d1vlja_ 68 EVSGVKPNPVLSKVHEAVEVAKKE-KVEAVLGVGGGSVVDSAKAVAAGALYEGDIWDAFI 126 :::::::::: ::::::::::::: ::::::::: :::::::::::::::: d1tjya_ 165 TTQFGYNDAT-KSLQTAEGIIKAYPDLDAIIAPD-ANALPAAAQAAENLKR--------- 213 d1vlja_ 127 GKYQIEKALPIFDVLTISATGTEMNGNAVITNEKTKEKYGVSSKALYPKVSIIDPSVQFT 186 ::::::: : : :::: :::: :::::::: ::: : d1tjya_ 214 ------NNLAIVG-F--S-TPNV-MRPY-------------VQRGTVKE-FGL-W----- 242 d1vlja_ 187 LPKEQTVYGAVDAISHILEYYFDGSSPEISNEIAEGTIRTIMKMTERLIE-K-------- 237 : :: ::::::::::: : d1tjya_ 243 -----D--VV-----------------------------QQGKISVYVANALLKNMPMNV 266 d1vlja_ 238 -----------------------------PDDYEARANLAWSATI-ALNGTMAVGRRGGE 267 :::: ::: :::::: :::::: d1tjya_ 267 GDSLDIPGIGKVTVSPNSEQGYHYEAKGNGIVL--LPE-RVIFNKD-NIDKYD------- 315 d1vlja_ 268 WACHRIEHSLSALYDIAHGAGLAIVFPAWMKYVYRKNPAQFERFAKKIFGFEGEGEELIL 327 : d1tjya_ 316 ------------------F----------------------------------------- 316 d1vlja_ 328 KGIEAFKNWLKKVGAPVSLKDAGIPEEDIDKIVDNVMLLVEKNLKPKGASLGRIMVLERE 387 d1tjya_ 317 ------------------------------------------------------------ 317 d1vlja_ 388 DVREILKLAAK 398 d1tjya_ 317 ----------- 317 HHsearch alignment (Probability: 0.82 E-value:0.00) d1vlja_ 34 IRKVLFLYGG-GSIKKNGVYDQVVDSLKKHGIEWVEVSGVKPNPVLSKVHEAVEVAKKEK 92 :::::::::: :::::::::::::::::::::::::::: ::::::::::::::::::: d1tjya_ 3 AERIAFIPKLVGVGFFTSGGNGAQEAGKALGIDVTYDGP--TEPSVSGQVQLVNNFVNQG 60 d1vlja_ 93 VEAVLGVGG--GSVVDSAKAVAAGALYEGDIWDAFIGKYQIEKALPIFDVLTISATGT 148 ::::::::: :::::::::: :::::::::::::::::: d1tjya_ 61 YDAIIVSAVSPDGLCPALKRA-------------------MQRGVKILTWDSDTKPEC 99