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 <-- 1.197 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1odza_) 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 d1odza_ Mannanase A,​ ManA(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 <-- 1.197 --> Hit
DALI alignment (Z-score: 10.8 Raw score:1341.80) d1kfwa1 1 -----------------------pltstvNGYRNVGYFaqwGVYGRAFQ-AKQL---dvS 33 ::::::::: :::::::: :::: : d1odza_ 1 vkpvtvklvdsqatmetrslfafmqeqrrHSIMFGHQHettQGLTITRTdGTQSdtfnaV 60 d1kfwa1 34 GTAknLTHINySFGNinnqtltCFMAnkaqgtgpngsdgagDAWADfgmgyaadksvsgk 93 ::: ::::: :::: :::: ::::: d1odza_ 61 GDF--AAVYG-WDTL------sIVAP---------------KAEGD-------------- 82 d1kfwa1 94 adtwdqplagSFNQLKQLKAKNpkLKVMISLG-------------gwtWSKNfsKAAAT- 139 :::::::::::: :::::::: :::: ::::: d1odza_ 83 ----------IVAQVKKAYARG--GIITVSSHfdnpktdtqkgvwpvgTSWDqtPAVVDs 130 d1kfwa1 140 ------EASRQKLVSSCIDLyIKGNlpnfegrggagaaAGIFDGIDIDWEWPgtNSGLag 193 :::::::::::::: :::: :::::::::::::: :::: d1odza_ 131 lpggayNPVLNGYLDQVAEW-ANNL--------kdeqgRLIPVIFRLYHENT--GSWFww 179 d1kfwa1 194 ngVDTVndRANFKALLAEFRKQLD--AYGStnnkKYVLSAFLPAN----PADIDAGGwdd 247 :::: :::::::::::::::: :::: ::::::::::: :::::::: d1odza_ 180 gdKQST--PEQYKQLFRYSVEYLRdvKGVR----NFLYAYSPNNFwdvtEANYLERY--- 230 d1kfwa1 248 paNFKSLDFGSIQGYDlhgawnptltghqaNLYDdpadprapskkfSADKAVKKYLaAGI 307 :::::::::::::: :::: :::::::::: ::: d1odza_ 231 -pGDEWVDVLGFDTYG----------pvadNADW----------frNVVANAALVA-RMA 268 d1kfwa1 308 D--pkQLGL-GLAA---------dNIATTKQKTDYIVS----KGLGGGMWWEL------- 344 : :::: :::: :::::::::::::: ::::::::::: d1odza_ 269 EargkIPVIsGIGIrapdieaglyDNQWYRKLISGLKAdpdaREIAFLLVWRNapqgvpg 328 d1kfwa1 345 ------SGDRN----------gELVGAMSDKFRaaapgpvteAAPP------ 374 ::::: ::::::::::: :::: d1odza_ 329 gtqvphYWVPAnrpeninngtlEDFQAFYADEF-tafnrdieQVYQrptliv 379 FAST alignment (Normalized score: 4.86 Raw score:1828.00) d1kfwa1 1 PLTSTVN------------------------------GYRNVGYFAQWGVYG-------- 22 :::::: d1odza_ 1 -------VKPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGH---------QHETTQGL 44 d1kfwa1 23 --RAFQA--KQLDVSGTAK----NLTHINYSFGNINNQTLTCFMANKAQGTGPNGSDGAG 74 ::::: ::::: ::::::: d1odza_ 45 TITRTDGTQSDTFN-----AVGDFAAVYGW------------------------------ 69 d1kfwa1 75 DAWADFGMGYAADKSVSGKADTWDQPLA------------GSFNQLKQLKAKNPKLKVMI 122 ::::::::::: ::::::: d1odza_ 70 ----------------------------DTLSIVAPKAEGDIVAQVKKAYA--RGGIITV 99 d1kfwa1 123 SLGGWTWS------------------------KNFSKAAA-----TEASRQKLVSSCIDL 153 : :::::: ::::::::::::::: d1odza_ 100 S-------SHFDNPKTDTQKGVWPVGTSWDQTPAVVDS--LPGGAYNPVLNGYLDQVAEW 150 d1kfwa1 154 YIKGNLPNFEGRGGAGAAAGIF-------------DGIDIDW--EWPGTNSGLAGNGVDT 198 :::: ::::::: d1odza_ 151 ----------------------ANNLKDEQGRLIPVIFR---LYHENTGSW--------- 176 d1kfwa1 199 VN--------DRANFKALLAEFRKQLDAYGSTNNK------KYVLSAFLP----ANPADI 240 ::::::::::::::::: ::::::::: :::::: d1odza_ 177 --FWWGDKQSTPEQYKQLFRYSVEYLR--------DVKGVRNFLYAYSPNNFWDVTEANY 226 d1kfwa1 241 DAGGWDDPA---NFKSLDFGSIQGYDLHGAWNPTLTGHQANLYDDPADPRAPSKKF---- 293 :: ::::::::::: d1odza_ 227 LE-------RYPGDEWVDVLGFD---------------------------------TYGP 246 d1kfwa1 294 ---------SADKAVKKYLAAGIDPKQLGLGLAAD------------------------- 319 ::::::::::: d1odza_ 247 VADNADWFRNVVANAALVAR---------------MAEARGKIPVISGIGIRAPDIEAGL 291 d1kfwa1 320 -NIATTKQKTDYIVS----KGLGGGMWWELSGDRN------------------------- 349 :::::::::::::: :::::::::: d1odza_ 292 YDNQWYRKLISGLKADPDAREIAFLLVWR------NAPQGVPGGTQVPHYWVPANRPENI 345 d1kfwa1 350 ----GELVGAMSDKFRAAAPGPVTEAAPP--------------------- 374 ::::::::: d1odza_ 346 NNGTLEDFQAFYA----------------DEFTAFNRDIEQVYQRPTLIV 379 TMalign alignment (TM-score: 0.56 Raw score:209.94) d1kfwa1 1 P-----------------LT--STVNGY---RNVGYFAQWGVYGRAF-Q-AKQL-DVS-- 33 : :: :::::: :::::::::::::::: : :::: ::: d1odza_ 1 VKPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGHQHETTQGLTITRTDGTQSDTFNAV 60 d1kfwa1 34 GTAKNLTHINYSFGNINNQTLTCFMANKAQGTGPNGSDGAGDAWADFGMGYAADKSVSGK 93 ::: :: :::::::: :::: :: ::: d1odza_ 61 GDF-AA-VYGWDTLS-------IVAP--------------KA--EGD------------- 82 d1kfwa1 94 ADTWDQPLAGSFNQLKQLKAKNPKLKVMISLGG------------W--TWSKNFSKAAA- 138 :::::::::::: ::::::::: : ::::::::::: d1odza_ 83 ----------IVAQVKKAYARG--GIITVSSHFDNPKTDTQKGVWPVGTSWDQTPAVVDS 130 d1kfwa1 139 TEAS-RQKLVSSCIDLYIKGNLPNFEGRGGAGAAA-----GIFDGIDIDWEWPGTNSGLA 192 :::: :::::::::::::::: :: :: ::::::::::::: :: :: d1odza_ 131 LPGGAYNPVLNGYLDQVAEWA---------NN-LKDEQGRLIPVIFRLYHENT-GS-WF- 177 d1kfwa1 193 GNGVDTVNDRANFKALLAEFRKQLDAYGSTNNKKYVLSAFLPANPADIDAGGWDDPANFK 252 ::::::::::::::::::::::::::: :: :::::::::::::::::::::::::::: d1odza_ 178 -WWGDKQSTPEQYKQLFRYSVEYLRDVK-GV-RNFLYAYSPNNFWDVTEANYLERYPGDE 234 d1kfwa1 253 SLDFGSIQGYDLHGAWNPTLTGHQANLYDDPADPRAPSKKFSADKAVKKYLAAG-IDPKQ 311 ::::::::: :::: :::::::: ::::::::::::: ::::: d1odza_ 235 WVDVLGFDT-YGPV------ADNADWFR-------------NVVANAALVARMAEARGKI 274 d1kfwa1 312 LGL-GLAA------------DNIATTKQKTDYIVSKGLGGGMWWELS------------- 345 ::: :::: ::::::::::::::::::::::::::: d1odza_ 275 PVISGIGIRAPDIEAGLYDNQWYRKLISGLKADPDAREIAFLLVWRNAPQGVPGGTQVPH 334 d1kfwa1 346 --GDRN------------GELVGAMSDKFR----AAAPG-PVTEAAPP---- 374 :::: ::::::: :::: : :::::: d1odza_ 335 YWVPANRPENINNGTLEDFQAFYAD-EFTAFNRD----IE--QVYQRPTLIV 379 HHsearch alignment (Probability: 0.21 E-value:0.09) d1kfwa1 144 QKLVSSCIDLYIKGN-LPNFEGRGGAGAAAGIFDGIDIDWEWPGTNSGLAGNGVDTVNDR 202 ::::::::::::::: :::: ::::::::::::::::::::::: ::: d1odza_ 141 NGYLDQVAEWANNLKDEQGR----LIPVIFRLYHENTGSWFWWGDKQ----------STP 186 d1kfwa1 203 ANFKALLAEFRKQLDAYGSTNNKKYVLSAFLPANPADIDAGGWDDPANFKSLDFGSIQGY 262 :::::::::::::::::: :::::::::::::::::::::: ::::::::::::::: d1odza_ 187 EQYKQLFRYSVEYLRDVK---GVRNFLYAYSPNNFWDVTEANY--LERYPGDEWVDVLGF 241 d1kfwa1 263 DLHGAW 268 :::::: d1odza_ 242 DTYGPV 247