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 <-- 0.926 --> Intermediate <-- 0.744 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1o5oa_) through the intermediate protein (d1vkfa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vkfa_ Glycerol uptake operon antiterminator-​related protein TM1436GlpP-​likeTIM beta/​alpha-​barrelα/β
Hit d1o5oa_ Uracil PRTase,​ UppPRTase-​likePRTase-​likeα/β

Supporting Alignments

Query <-- 0.926 --> Intermediate
DALI alignment (Z-score: 8.5 Raw score:752.00) query 1 mietpyylidkakltrnmeriahvreksgAKALLALKcfATWSvFDLMrdYMDGTTSSSL 60 :::::::: :::: :::: :::::::::: d1vkfa_ 1 ---------------------------mfKGIIAALW--DMDS-IGEI--EPDVVFLLKS 28 query 61 F--evrlgRERFG---KETHAYSV-----aYGDNEIDEVVS-HADKIIFNSISQLERFAD 109 : ::::: :::::::: ::::::::::: :::::::::::::::::: d1vkfa_ 29 DilnlkfhLKILKdrgKTVFVDMDfvnglgEGEEAILFVKKaGADGIITIKPKNYVVAKK 88 query 110 KAagIARGLRLNPQ--rlgeWDVPKVERVMdrINGFMIHNNcenkdfglfdrMLGEIEER 167 :: :::::::::: :::::::::: ::::::::: :::::::: d1vkfa_ 89 NG--IPAVLRFFALdskaveRGIEQIETLG--VDVVEVLPG----------aVAPKVARK 134 query 168 fgalIARVdWVSLGGGIHFTgddypvdafSARLRafsdrygvqIYLEPGeASITksttle 227 :::: ::::::::::: ::::: :::::: :::: d1vkfa_ 135 ----IPGR-TVIAAGLVETE------eeaREILK-------hvSAISTS-SRIL------ 169 query 228 vtvldtlynknlaivdssieahmldlliyretakvlpnegshsymicgksclagdvfgef 287 d1vkfa_ 170 ------------------------------------------------------------ 170 query 288 rfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvreftyadyeqsl 347 d1vkfa_ 170 ----------------------------------------------------------wk 171 query 348 s 348 d1vkfa_ 172 m 172 FAST alignment (Normalized score: 5.89 Raw score:1441.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGA---KALLALKCFATWSVFDLMRDYMDGTTS 57 ::::: ::: :::::: :::::::: d1vkfa_ 1 ------------------------------MFKGIIAA-LWD--MDSIGE--IEPDVVFL 25 query 58 S------SLFEVRLGRERFGKETHAYSVAY---------GDNEIDEVVS-HADKIIFNSI 101 : ::::::::: ::::::::: :::::::::: :::::::::: d1vkfa_ 26 LKSDILNLKFHLKILK-DRGKTVFVD----MDFVNGLGEGEEAILFVKKAGADGIITIKP 80 query 102 SQLERFADKAAGIARGLRLNPQRLGEW---------DVPKVERVMD-RINGFMIHNNCEN 151 :::::::: :::::::::: ::::::: :::::::: d1vkfa_ 81 KNYVVAKK--NGIPAVLRFF-------ALDSKAVERGIEQIET---LGVDVVEVL----- 123 query 152 KDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDA-FSARLRAFSDRYGVQ 210 ::::::::::: ::: ::::::::: ::::::::::: d1vkfa_ 124 --------PGAVAPKVARK-IPG-RTVIAAGLV-----------ETEEEAREILKH---- 158 query 211 -IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSH 269 :::::: d1vkfa_ 159 VSAISTS----------------------------------------------------- 165 query 270 SYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELD 329 d1vkfa_ 166 ------------------------------------------------------------ 166 query 330 GSVRTVREFTYADYEQSLS------- 348 d1vkfa_ 166 -------------------SRILWKM 172 TMalign alignment (TM-score: 0.33 Raw score:114.32) query 1 -MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSS 59 :: :::::::: d1vkfa_ 1 M-----------------------------FK--------------------GIIAALWD 11 query 60 LFEVRLGRERFGKETHAYSVAY-G-DNEIDEVVSH-ADKII-FN------SI-SQLERFA 108 ::: :: :::::::::::::: : :::::::::: ::::: :: :: ::::::: d1vkfa_ 12 MDS-IG--EIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDMDFVNGLGEGEEAILFVK 68 query 109 DKAAGIARGLRLNPQRLGEWDVPKVERVM-DRINGFMIHNNCENKDFGLFDRMLGEIEER 167 :::: : ::::: :: : :::::: ::::::::::: : : :::::::::: d1vkfa_ 69 KAGA-D-GIITI------KP-K-NYVVAKKNGIPAVLRFFA--L----D-SKAVERGIEQ 111 query 168 FGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITKS---- 223 :::: : :::::: ::::: :::::::::: ::::::: ::::::: d1vkfa_ 112 IETL-G-VDVVEV-LPGAV---------APKVARKIPG---RTVIAAG-LVETEEEAREI 155 query 224 ---------TTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMIC 274 d1vkfa_ 156 LKHVSAIST--------------------------------------------------- 164 query 275 GKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMV-----KKNWFNGVKMPAIAIRELD 329 : :: d1vkfa_ 165 --------------------------------S-SRILWKM------------------- 172 query 330 GSVRTVREFTYADYEQSLS 348 d1vkfa_ 173 ------------------- 173 HHsearch alignment (Probability: 0.01 E-value:0.17) query 6 YYLIDKAKLTRNMERIAHVREK 27 :::::::::::::::::::::: d1vkfa_ 97 FFALDSKAVERGIEQIETLGVD 118
Intermediate <-- 0.744 --> Hit
DALI alignment (Z-score: 3.1 Raw score:278.20) d1vkfa_ 1 -----------------------------------------------MFKG--------- 4 :::: d1o5oa_ 1 hmknlvvvdhplikhkltimrdkntgpkefrellreitlllayeatrHLKCeevevetpi 60 d1vkfa_ 5 -----------IIAALWD-------------------------------------mdSIG 16 ::::::: ::: d1o5oa_ 61 tktigyrindkDIVVVPIlraglvmadgilellpnasvghigiyrdpetlqaveyyaKLP 120 d1vkfa_ 17 EIE-PDVVFLLK---sdILNLKFHLKILKDRG-KTVFVDMDfvnglgEGEEAILFVKKAG 71 ::: :::::::: ::::::::::::::: :::::::: ::::::::::::: d1o5oa_ 121 PLNdDKEVFLLDpmlatGVSSIKAIEILKENGaKKITLVAL-----iAAPEGVEAVEKKY 175 d1vkfa_ 72 -aDGIITIKPKnyvvakkngipavlrffaldskavergieqietlgvdvvevlpgavapk 130 ::::::::: d1o5oa_ 176 edVKIYVAALD------------------------------------------------- 186 d1vkfa_ 131 varkipgrtviaaglveteeeareilkhvsaistssrilwkm 172 d1o5oa_ 187 ------------------erlndhgyiipglgdagdrlfrtk 210 FAST alignment (Normalized score: 2.56 Raw score:487.10) d1vkfa_ 1 MFK---GIIAALWDMDSIGEIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDMDFVNGL 57 :::::: d1o5oa_ 1 ---HMKNLVVVD------------------------------------------------ 9 d1vkfa_ 58 GEGEEAILFVKK------------------------------------------------ 69 d1o5oa_ 10 ------------HPLIKHKLTIMRDKNTGPKEFRELLREITLLLAYEATRHLKCEEVEVE 57 d1vkfa_ 70 --------AGADGIITIKPKNYVVAKKNGI-PAVLRFFA--------------------- 99 :::: ::::::: d1o5oa_ 58 TPITKTIGYRIN------------------DKDIVVVP-ILRAGLVMADGILELLPNASV 98 d1vkfa_ 100 -------------LDSKAVERGIEQIE--TLGV---DVVEVLP-------GAVAPKVARK 134 ::::: :::: ::::: :::::::::: d1o5oa_ 99 GHIGIYRDPETLQAVEYY---------AKLPPLNDDKEVFL--LDPMLATGVSSIKAIEI 147 d1vkfa_ 135 IPG------RTVIAAGLV--ETEEEAREILKHV---SAISTSSRILWKM----------- 172 ::::::: :::::::::::: ::::: d1o5oa_ 148 ---LKENGAKKITLVA--LIAAPEGVEAVEKK-YEDVKIYV--------AALDERLNDHG 193 d1vkfa_ 173 ----------------- 173 d1o5oa_ 194 YIIPGLGDAGDRLFRTK 210 TMalign alignment (TM-score: 0.41 Raw score:69.98) d1vkfa_ 1 --MFKGIIAALWDMDSI---------------------GEIEPDVVFLLKS--DILNLKF 35 ::::::::::::: :::: d1o5oa_ 1 HM--KNLVVVDHPLIKHKLTIMRDKNTGPKEFRELLRE---------ITLLLA------- 42 d1vkfa_ 36 HLKILKDRGKTVFVDMDFVNGLGEGEEAILFVKKAGADGI---------------ITIKP 80 :::: :::: d1o5oa_ 43 ----------YEAT----------------------RHLKCEEVEVETPITKTIG----- 65 d1vkfa_ 81 KNYVVAKKNGIPA--VLRFF-----------------------ALD----------SKAV 105 ::::: ::::: ::: :::: d1o5oa_ 66 --------YRINDKDIVVVPILRAGLVMADGILELLPNASVGHIGIYRDPETLQAVEYYA 117 d1vkfa_ 106 ERGIEQIETLGVDVVEVLP--G----AV--APKVARKIPGRTVIAAGLVETEEEAREIL- 156 :: :::: ::::::::: : :: ::::::::::::::::::::::::::::: d1o5oa_ 118 -KL--PPLN-DDKEVFLLDPMLATGVSSIKAIEILKENGAKKITLVALIAAPEGVEAVEK 173 d1vkfa_ 157 KH-VSAISTSSRIL-----------------------WKM 172 :: ::::::::::: d1o5oa_ 174 KYEDVKIYVAALDERLNDHGYIIPGLGDAGDRLFRTK--- 210 HHsearch alignment (Probability: 0.03 E-value:0.03) d1vkfa_ 91 IPAVLRFFALDSK-----AVERGIEQIETLGVDVVEVL------PGAVAPKVARKIPGRT 139 ::::::::::::: :::::::::::::::::::: :: :::::::::::: d1o5oa_ 122 LNDDKEVFLLDPMLATGVSSIKAIEILKENGAKKITLVALIAAPEG--VEAVEKKYEDVK 179 d1vkfa_ 140 VIAAG 144 ::::: d1o5oa_ 180 IYVAA 184