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 <-- 1.169 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1ui0a_) 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 d1ui0a_ Thermophilic uracil-​DNA glycosylaseDNA glycosylaseDNA glycosylaseα/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 <-- 1.169 --> Hit
DALI alignment (Z-score: 3.6 Raw score:390.30) d1vlja_ 1 hhhmenfvfhnptkivfgrgtipkigeeiknagirKVLFLYGGGS--------iKKNGVY 52 :::::::::: :::::: d1ui0a_ 1 --tlellqaqaqnctacrlmegrtrvvfgegnpdaKLMIVGEGPGeeedktgrpFVGKAG 58 d1vlja_ 53 DQVVDSLKKHGI---EWVEVSGV--------KPNP--VLSKVH-EAVEVAKKEKVEAVLG 98 :::::::::::: :::::::: :::: :::::: :::::::::::::::: d1ui0a_ 59 QLLNRILEAAGIpreEVYITNIVkcrppqnrAPLPdeAKICTDkWLLKQIELIAPQIIVP 118 d1vlja_ 99 VGgGSVVDSAKavaagalyegdiwdafigkyqiekALPIFDVLTisatgtemngnavitn 158 :: :::::::: ::::::::: d1ui0a_ 119 LG-AVAAEFFL-------gekvsitkvrgkwyewhGIKVFPMFH---------------- 154 d1vlja_ 159 ektkekygvsskalypkvsiIDPSvqftlpkeqtvygavdaishileyyfdgsspeisne 218 :::: d1ui0a_ 155 ------------------paYLLR------------------------------------ 160 d1vlja_ 219 iaegtirtimkmterliekpdDYEARAnlawsatialngtmavgrrggewachriehsls 278 :::::: d1ui0a_ 161 -------------------npSRAPGS--------------------------------- 168 d1vlja_ 279 alydiahgaglaivfpawmkyvyrknpaqferfakkifgfegegeelilkgieafknwlk 338 d1ui0a_ 169 ------------------------------------------------------------ 169 d1vlja_ 339 kvgapvslkdagipeedidkivdnvmllveknlkpkgaslgrimvleredvreilklaak 398 d1ui0a_ 169 ------------------------------------pkhltwldiqevkraldalppker 192 FAST alignment (Normalized score: 2.46 Raw score:678.70) d1vlja_ 1 HHHMENFVFHNPTKIVFGRGTIPKIGEEIKNAGIR------------------------- 35 d1ui0a_ 1 -----------------------------------TLELLQAQAQNCTACRLMEGRTRVV 25 d1vlja_ 36 --------KVLFLYGGGSIK------------KNGVYDQVVDSLKKHGI---EWVEVSGV 72 :::::::: ::::::::::::::::: ::::: d1ui0a_ 26 FGEGNPDAKLMIVGEG----PGEEEDKTGRPFVGKAGQLLNRILEAAGIPREEVYIT--- 78 d1vlja_ 73 KPNP-----------------VLSKV-HEAVEVAKKEKVEAVLGVGGGSVVDSAKAVAAG 114 ::::: :::::::::::::::::: :::::::: d1ui0a_ 79 ----NIVKCRPPQNRAPLPDEAKICTDKWLLKQIELIAPQIIVPL-GAVAAEFF------ 127 d1vlja_ 115 ALYEGDIWDAFIGKYQIEK------------------ALPIFDVLTISATGTEMNGNAVI 156 ::::::: d1ui0a_ 128 -------------------LGEKVSITKVRGKWYEWHGIKVFPM---------------- 152 d1vlja_ 157 TNEKTKEKYGVSSKALYPKVSIIDPSVQFTLPKEQTVYGAVDAISHILEYYFDGSSPEIS 216 d1ui0a_ 153 ------------------------------------------------------------ 153 d1vlja_ 217 NEIAEGTIRTIMKMTERLIEKPDDYEARANLAWSATIALNGTMAVGRRGGEWACHRIEHS 276 d1ui0a_ 153 ------------------------------------------------------------ 153 d1vlja_ 277 LSALYDIAHGAGLAIVFPAWMKYVYRKNPAQFERFAKKIFGFEGEGEELILKGIEAFKNW 336 d1ui0a_ 153 ------------------------------------------------------------ 153 d1vlja_ 337 LKKVGAPVSLKDAGIPEEDIDKIVDNVMLLVEKNLKPKGASLGRIMVLEREDVREILKLA 396 d1ui0a_ 153 ------------------------------------------------------------ 153 d1vlja_ 397 AK---------------------------------------- 398 d1ui0a_ 153 --FHPAYLLRNPSRAPGSPKHLTWLDIQEVKRALDALPPKER 192 TMalign alignment (TM-score: 0.20 Raw score:79.42) d1vlja_ 1 ------------------HHHMENFVFHNPTKIVFGRGTIPKIGEEIKNAGIRKVLFLYG 42 :::: : : d1ui0a_ 1 TLELLQAQAQNCTACRLM-------EGRT-R-V--------------------------- 24 d1vlja_ 43 GGSIKKNGVYDQVVDSLKKHGIEWVEVSGVKPNPVLSKVHEAVEVAKKEKVEAVLGVGGG 102 : d1ui0a_ 25 -----------------------------------------------------------V 25 d1vlja_ 103 SVVDSAKAVAAGALYEGDIWDAFIGKYQIEKALPIFDVLTISAT-------------G-- 147 ::: : d1ui0a_ 26 -----------------------------------------FGEGNPDAKLMIVGEGPGE 44 d1vlja_ 148 -TEMNGNAV-ITNEKTKEKYGV----------------SSKALYPKVSIIDPSVQFTLPK 189 :::::: :::: d1ui0a_ 45 E--EDKTGRP--------FVGKAGQLLNRILEAAGIPR---------------------- 72 d1vlja_ 190 EQTVYGAVDAISHILEY--YFDGSSPEISNEIAEGTIRTIMKMTERLIEKPDDYEARANL 247 :::: ::::::::: : ::: ::::::::::::::::::::: d1ui0a_ 73 -EEVY---ITNIVKCRPPQ--N-RAP--LPDEAKICTDKWLLKQIELIA----------- 112 d1vlja_ 248 AWSATIALNGTMAVGRRGGEWACHRIEHSLSALYDIAHGAGLAIVFPAWMKYVYRKNPAQ 307 :: ::: :: : : : d1ui0a_ 113 --------------------------------------PQ-IIV-PL--G---A-----V 122 d1vlja_ 308 FERFAKKIFGFEGEGE--ELILK-GIEAFKNWLKKVGAPVS---LKDAGIPEEDIDKIVD 361 : :: ::::: ::: ::: ::: :::::: : :: d1ui0a_ 123 A--AE--FFLGE-KVSIT--KVRG-KWY--EWHGIK-V-FPMFH---------------- 154 d1vlja_ 362 NVMLLVEKNLKPKGASLGRIMVLERE----DVREILKLAAK------------- 398 :::::::::: ::::::::::: d1ui0a_ 155 ----------------PAYLLRNPSRAPGSPKHLTWLDIQEVKRALDALPPKER 192 HHsearch alignment (Probability: 0.53 E-value:0.01) d1vlja_ 11 NPTKIVFGRGTIPKIGEEIKNAGIRKVLFLYGGGSIKK--NG------VYDQVVDSLKKH 62 ::::::::::::: :::::::::::::: :: :::::::::::: d1ui0a_ 20 GRTRVVFGEGNPD-----------AKLMIVGEGPGEEEDKTGRPFVGKAGQLLNRILEAA 68 d1vlja_ 63 GIE---WVEVSGV------KPNPVLSKVHEAV-----EVAKKEKVEAVLGVGGG 102 ::: ::::::: ::::::::::::: ::::::::::::::::: d1ui0a_ 69 GIPREEVYITNIVKCRPPQNRAPLPDEAKICTDKWLLKQIELIAPQIIVPLGAV 122