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 <-- 1.326 --> Intermediate <-- 1.440 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1qhoa4) through the intermediate protein (d1kfwa1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1kfwa1 Psychrophilic chitinase B(Trans)glycosidasesTIM beta/​alpha-​barrelα/β
Hit d1qhoa4 Cyclodextrin glycosyltransferase(Trans)glycosidasesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 1.326 --> Intermediate
DALI alignment (Z-score: 6.4 Raw score:778.60) query 1 ------------------------------------------------------------ 1 d1kfwa1 1 pltstvngyrnvgyfaqwgvygrafqakqldvsgtaknlthinysfgninnqtltcfman 60 query 1 -----mietpyylidkAKLT----------------------RNMERIAHVREKSG-AKA 32 :::: :::::::::::::: ::: d1kfwa1 61 kaqgtgpngsdgagdaWADFgmgyaadksvsgkadtwdqplaGSFNQLKQLKAKNPkLKV 120 query 33 LLALK------------------cfATWSVFDLMR-----------------DYMDGTTS 57 ::::: :::::::::: :::::::: d1kfwa1 121 MISLGgwtwsknfskaaateasrqkLVSSCIDLYIkgnlpnfegrggagaaaGIFDGIDI 180 query 58 SS-----------------------LFEVRLGRERFG---------KETHAYSVA----Y 81 :: :::::::::::: ::::::::: : d1kfwa1 181 DWewpgtnsglagngvdtvndranfKALLAEFRKQLDaygstnnkkYVLSAFLPAnpadI 240 query 82 GDNEI--DEVVSHADKIIFN----------------------------------SISQLE 105 ::::: ::::::::::::: :::::: d1kfwa1 241 DAGGWddPANFKSLDFGSIQgydlhgawnptltghqanlyddpadprapskkfsADKAVK 300 query 106 RFA-DKAAgIARGLRLNPQrlgeWDVPKVERVM-DRINGFMIHNNCenkdfglFDRMlGE 163 ::: :::: :::::::::: :::::::::: :::::::::::: :::: :: d1kfwa1 301 KYLaAGIDpKQLGLGLAAD-niaTTKQKTDYIVsKGLGGGMWWELS------gDRNG-EL 352 query 164 IEeRFGALIA---RVDWvslgggihftgddypvdafsarlrafsdrygvqiylepgeasi 220 :: ::::::: :::: d1kfwa1 353 VG-AMSDKFRaaaPGPV------------------------------------------- 368 query 221 tksttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsymicgkscla 280 d1kfwa1 369 ------------------------------------------------------------ 369 query 281 gdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvrefty 340 d1kfwa1 369 ------------------------------------------------------------ 369 query 341 adyeqsls 348 d1kfwa1 369 --teaapp 374 FAST alignment (Normalized score: 3.56 Raw score:1283.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREK------SGAKALLALKCFA-----------TWS 43 :::::::: ::: d1kfwa1 1 ---------------------------PLTSTVNGYRNVGY-----FAQWGVYGRAFQAK 28 query 44 VFD--LMRDYMDGTTSS------------------------------------------- 58 ::: :::::::::::: d1kfwa1 29 QLDVSGTAKNLTHINYSFGNINNQTLTCFMANKAQGTGPNGSDGAGDAWADFGMGYAADK 88 query 59 ---------------SLFEVRLGRERFG-KETHAYSVAY--------------------- 81 ::::::::::::: :::::: d1kfwa1 89 SVSGKADTWDQPLAGSFNQLKQLKAKNPKLKVMIS----LGGWTWSKNFSKAAATEASRQ 144 query 82 --GDNEIDEVV-----------------SHADKIIFN----------------------- 99 ::::::::: :::::::: d1kfwa1 145 KLVSSCIDLYIKGNLPNFEGRGGAGAAAGIFDGIDI-DWEWPGTNSGLAGNGVDTVNDRA 203 query 100 -SISQLERFADKAA----------GIARGLRLNPQRLGEWDVPK------------VERV 136 ::::::::::: ::::::::: :::: d1kfwa1 204 NFKALLAEFRKQ--LDAYGSTNNKKYVLSAFLP-----------ANPADIDAGGWDDPAN 250 query 137 MDRINGFMIHNNCENKDFG------------------------------LFDRMLGEIEE 166 ::::::::: :::: ::::::::::: d1kfwa1 251 FKSLDFGSI-QGYD-----LHGAWNPTLTGHQANLYDDPADPRAPSKKFSADKAVKKYLA 304 query 167 RFGALIARVD------WVSLGGGIHFTGDDYP----VDAFSARLRAFSDRYGVQIYLEPG 216 ::::: ::::::::::::::::: :::: d1kfwa1 305 ----------AGIDPKQLGLG-----------LAADNIATTKQKTDYIVSKGL-GGGM-- 340 query 217 EASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGK 276 d1kfwa1 341 ------------------------------------------------------------ 341 query 277 SCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVR 336 d1kfwa1 341 ------------------------------------------------------------ 341 query 337 EFTYADYEQSLS---------------------------------- 348 d1kfwa1 341 ------------WWELSGDRNGELVGAMSDKFRAAAPGPVTEAAPP 374 TMalign alignment (TM-score: 0.41 Raw score:142.97) query 1 -----------------MIETPYY-LID-KAKLTRNMERIAH-VREKSGAKALLALKC-- 38 : :: :: :::::::: ::::::::::::::: d1kfwa1 1 PLTSTVNGYRNVGYFAQ------WG-VYG--RA-FQAKQLDVSGTAKNLTHINYSFGNIN 50 query 39 -----------------------FAT--WS----------------------V-FDLMRD 50 ::: :: : :::::: d1kfwa1 51 NQTLTCFMANKAQGTGPNGSDGAGDAWADFGMGYAADKSVSGKADTWDQPLAGSFNQLKQ 110 query 51 YM------DGTTSSS-------L------------FE-VR--LGRER------------- 69 :: ::::::: : :: :: ::::: d1kfwa1 111 LKAKNPKLKVMISLGGWTWSKNFSKAAATEASRQKLVSSCIDLYIKGNLPNFEGRGGAGA 170 query 70 ---FGKETHAYSVAY---------------G--DN--EIDEVV-SH----------ADKI 96 :::::::::::: : :: :::::: :: :::: d1kfwa1 171 AAGIFDGIDIDWEWPGTNSGLAGNGVDTVNDRANFKALLAEFRKQLDAYGSTNNKKYVLS 230 query 97 I-FN--S--IS--QLERFADKAAGIARGLRLN---------------PQ----------- 123 : :: : :: :::: :::::::::::::: :: d1kfwa1 231 AFLPANPADIDAGGWDD-PANFKSLDFGSIQGYDLHGAWNPTLTGHQANLYDDPADPRAP 289 query 124 -R-LGEWD-VPKVERVMDRI-NGFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDWVS 179 : ::::: ::::::::::: :::::::: :::::::::::::::: :::::: d1kfwa1 290 SKKFSADKAVKKYLAAGIDPKQLGLGLAA-------DNIATTKQKTDYIVSK--GLGGGM 340 query 180 LGGGIHFTGDDYPVDAFSARLRAFSDRY-GVQI------YLEPGEASITKSTTLEVTVLD 232 :::::::: :: ::::::::::::: :::: d1kfwa1 341 WWELSGDR----NG-ELVGAMSDKFRAAAPGPVTEAAPP--------------------- 374 query 233 TLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEE 292 d1kfwa1 375 ------------------------------------------------------------ 375 query 293 LKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1kfwa1 375 -------------------------------------------------------- 375 HHsearch alignment (Probability: 0.05 E-value:0.48) query 99 NSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDR------------------- 139 ::::::::::::::::::::::::::::::::::::::::: d1kfwa1 103 GSFNQLKQLKAKNPKLKVMISLGGWTWSKNFSKAAATEASRQKLVSSCIDLYIKGNLPNF 162 query 140 ------------INGFMIHN-------------NCENKDFGLFDRMLGEIEERFGALI-- 172 :::::::: ::::::::::::::::::::::::: d1kfwa1 163 EGRGGAGAAAGIFDGIDIDWEWPGTNSGLAGNGVDTVNDRANFKALLAEFRKQLDAYGST 222 query 173 ----ARVDWVSLGGGIHFTGDDYPVDAFSARLRAF 203 ::::::::::::::::::::::::::::::: d1kfwa1 223 NNKKYVLSAFLPANPADIDAGGWDDPANFKSLDFG 257
Intermediate <-- 1.440 --> Hit
DALI alignment (Z-score: 13.2 Raw score:1641.60) d1kfwa1 1 --plTSTVngyRNVGYFAQW-GVYGR----------------------------aFQAKQ 29 :::: ::::::::: ::::: ::::: d1qhoa4 1 sssaSVKG---DVIYQIIIDrFYDGDttnnnpaksyglydptkskwkmywggdleGVRQK 57 d1kfwa1 30 LDvsGTAK-NLTHINYSFGninnqtltcFMANKaqGTGPNgsDGAG-----------DAW 77 :: :::: :::::::::: ::::: ::::: :::: ::: d1qhoa4 58 LP--YLKQlGVTTIWLSPV---------LDNLD-tLAGTD--NTGYhgywtrdfkqiEEH 103 d1kfwa1 78 ADFgmgyaadksvsgkadtwdqpLAGSFNQLKQLKAKNpkLKVMISLGgwtWSKN----- 132 ::: ::::::::::::::: :::::::: :::: d1qhoa4 104 FGN--------------------WTTFDTLVNDAHQNG--IKVIVDFV---PNHStpfka 138 d1kfwa1 133 ----------------------------------------------------------fS 134 : d1qhoa4 139 ndstfaeggalynngtymgnyfddatkgyfhhngdisnwddryeaqwknftdpagfslaD 198 d1kfwa1 135 KAAATEASRQKLVSSCIDlYIKGnlpnfegrggagaaagIFDGIDIDWEWPgtnsglagn 194 :::::::::::::::::: :::: :::::::::::: d1qhoa4 199 LSQENGTIAQYLTDAAVQ-LVAH----------------GADGLRIDAVKH--------- 232 d1kfwa1 195 gvdtvndraNFKALLAEFRKQLDAYGstnnkKYVLSAFLPANP---ADIDagGWDDpANF 251 ::::::::::::::::: :::::::::::: :::: :::: ::: d1qhoa4 233 ---------FNSGFSKSLADKLYQKK-----DIFLVGEWYGDDpgtANHL--EKVR-YAN 275 d1kfwa1 252 K-SLDFgSIQGydlhgawnptltghqANLYD-----DPADprapskkfsaDKAVKKYLAA 305 : :::: :::: ::::: :::: :::::::::: d1qhoa4 276 NsGVNV-LDFD-------------lnTVIRNvfgtfTQTM-------ydlNNMVNQTGNE 314 d1kfwa1 306 GIDPKQLGLGLA--------------adNIATTKqKTDYIvskgLGGGMWWElSGDR--- 348 :::::::::::: :::::: ::::: :::::::: :::: d1qhoa4 315 YKYKENLITFIDnhdmsrflsvnsnkanLHQALA-FILTS----RGTPSIYY-GTEQyma 368 d1kfwa1 349 -------------------nGELVGAMSDKFRAAAPGPVteaapp 374 ::::::::::::::::::: d1qhoa4 369 ggndpynrgmmpafdttttaFKEVSTLAGLRRNNAAIQY------ 407 FAST alignment (Normalized score: 5.16 Raw score:2014.00) d1kfwa1 1 PLTSTVNG-------YRNVGYFAQWGVY-----------------------------GRA 24 ::::::::: ::: d1qhoa4 1 --------SSSASVKGDVIYQIII----DRFYDGDTTNNNPAKSYGLYDPTKSKWKMYWG 48 d1kfwa1 25 FQAKQLDVSGTA-------KNLTHINYSFGNINNQTLTCF---MANKAQGTGPNGSDGAG 74 :::::::: :::::::::: :::::: d1qhoa4 49 GDLEGVRQ----KLPYLKQLGVTTIWLSP-----------VLDNLDTLA----------- 82 d1kfwa1 75 DAWADFGMGYAADKSVSGKADTWDQP------------------------LAGSFNQLKQ 110 :::::::::: d1qhoa4 83 --------------------------GTDNTGYHGYWTRDFKQIEEHFGNWTTFDTLVND 116 d1kfwa1 111 LKAKNPKLKVMISLGGWTWSKNFSK----------------------------------- 135 ::: :::::::: d1qhoa4 117 AHQ--NGIKVIVD------------FVPNHSTPFKANDSTFAEGGALYNNGTYMGNYFDD 162 d1kfwa1 136 -------------------------------------AAATEASRQKLVSSCIDLYIKGN 158 :::::::::::::::: d1qhoa4 163 ATKGYFHHNGDISNWDDRYEAQWKNFTDPAGFSLADLSQENGTIAQYLTDAAV------- 215 d1kfwa1 159 LPNFEGRGGAGAAA----GIFDGIDIDWEWPGTNSGLAGNGVDTVN------DRANFKAL 208 :::::::: :::::::: d1qhoa4 216 --------------QLVAHGADGLRI--------------------DAVKHFNSGFSKSL 241 d1kfwa1 209 LAEFRKQLDAYGSTNNKKYVLSAFLPAN-----PADIDAGGWDDPANFKSL--------- 254 ::::::: :::::::::: :::::: d1qhoa4 242 ADKLYQK---------KDIFLVGEWY--GDDPGTANHLE------------KVRYANNSG 278 d1kfwa1 255 DFGSIQGYDLHGAWNPTLTGHQANLYDDPADPRAPSKKF-------------------SA 295 ::::: :: d1qhoa4 279 VNVLD----------------------------------FDLNTVIRNVFGTFTQTMYDL 304 d1kfwa1 296 DKAVKKYLAAG--IDPKQLGLGLAA------------DNIATTKQKTDYIVSKGLGGGMW 341 ::::::::: :::::::::: ::::::::::::::::: ::::: d1qhoa4 305 NNMVNQTGN--EYKYKENLITFI--DNHDMSRFLSVNSNKANLHQALAFILTSR-GTPSI 359 d1kfwa1 342 WELSGDRN----------------------GELVGAMSDKFRAAAPGPVTEAAPP----- 374 :::: ::::::::::::: d1qhoa4 360 -YYGT---EQYMAGGNDPYNRGMMPAFDTTTTAFKEVSTLAGL------------RRNNA 403 d1kfwa1 375 ---- 375 d1qhoa4 404 AIQY 407 TMalign alignment (TM-score: 0.57 Raw score:213.17) d1kfwa1 1 PLTSTVNGYRNVGYFAQWG--V-----Y-------------------GRAF--QAKQLDV 32 :::::: :::::::::::: : : :::: ::::::: d1qhoa4 1 SSSASV-KGDVIYQIIIDRFYDGDTTNNNPAKSYGLYDPTKSKWKMYWGGDLEGVRQKLP 59 d1kfwa1 33 SGTAKNLTHINYSFGNINNQTLTCFMANKAQGTG-PNGS----DGAG---DAWADFGMGY 84 ::::::::::::::: :::::::::: ::: :::: ::::::: d1qhoa4 60 YLKQLGVTTIWLSPV---------LDNLDTLAGTD-NTGYHGYWTRDFKQIEEHFGN--- 106 d1kfwa1 85 AADKSVSGKADTWDQPLAGSFNQLKQLKAKNPKLKVMISLGGWTWSK------------- 131 ::: :::::::::::: :::::::::::::: d1qhoa4 107 ---------------WTT--FDTLVNDAHQNG-IKVIVDFVPNHSTPFKANDSTFAEGGA 148 d1kfwa1 132 -------------------N---------------FS------------KAAATEASRQK 145 : :: ::::::::::: d1qhoa4 149 LYNNGTYMGNYFDDATKGYFHHNGDISNWDDRYEAQWKNFTDPAGFSLADLSQENGTIAQ 208 d1kfwa1 146 LVSSCIDLYIKGNLPNFEGRGGAGAAAGIFDGIDIDWEWPGTNSGLAGNGVDTVNDRANF 205 ::::::::::: :: :::::::: ::: : : d1qhoa4 209 YLTDAAVQLVA---------------HG-ADGLRIDA-VKH--------------F--N- 234 d1kfwa1 206 KALLAEFRKQLDAYGSTNNKKYVLSAFLPANPADIDAGGWDDPANFKSLDFGSIQGYDLH 265 ::::::::::::: : :::::::::::::::::::::::::::::::::::::::: d1qhoa4 235 SGFSKSLADKLYQ-K----KDIFLVGEWYGDDPGTANHLEKVRYANNSGVNVLDFDLNT- 288 d1kfwa1 266 GAWNPTLTGHQANLYDDPAD---PRAPSKKFSADKAVKKYLAAGIDPKQLGLGLA----- 317 ::::::::::: :::::::::::::::::::::::: d1qhoa4 289 ---------VIRNVFGTFTQTMY--------DLNNMVNQTGNEYKYKENLITFIDNHDMS 331 d1kfwa1 318 ADN-----IATTKQKTDYIVSKGLGGGMWWEL----------------SGDRNG-E-LVG 354 ::: ::::::::::::: :::::::::: :::::: : ::: d1qhoa4 332 RFLSVNSNKANLHQALAFILT-SRGTPSIYYGTEQYMAGGNDPYNRGMMPAFDTTTTAFK 390 d1kfwa1 355 AMSDKFRAA--APGPVTEAAPP 374 ::::::::: :::::: d1qhoa4 391 EVSTLAGLRRNNAAIQY----- 407 HHsearch alignment (Probability: 0.13 E-value:0.01) d1kfwa1 139 TEASRQKLVSSCIDLYIKGNLPNFEGRGGAGAAAGIFDGIDIDWEWPGTNSGLAGNGVDT 198 ::::::: :::::::::::: :::::::::: d1qhoa4 203 NGTIAQY-LTDAAVQLVAHG----------------ADGLRIDAVK-------------- 231 d1kfwa1 199 VNDRANFKALLAEFRKQLDAY 219 ::::::::::::::::: d1qhoa4 232 ----HFNSGFSKSLADKLYQK 248