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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1vlja_ | NADH-dependent butanol dehydrogenase A (TM0820) | Dehydroquinate synthase-like | Dehydroquinate synthase-like | multi |
| Hit | d1v16b2 | Branched-chain alpha-keto acid dehydrogenase | TK C-terminal domain-like | TK C-terminal domain-like | α/β |
Query <-- 0.611 --> IntermediateDALI 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 <-- 0.801 --> HitDALI alignment (Z-score: 4.5 Raw score:379.90) d1vlja_ 1 hhhmenfvfhnptkivfgrgtipkigeeiknagirKVLFLYGgGSIKknGVYDQVVDSLK 60 ::::::: :::: ::::::::::: d1v16b2 1 -------------------pyniplsqaeviqegsDVTLVAW-GTQV--HVIREVASMAK 38 d1vlja_ 61 K-HGIEWVEVSGVKPNPVlsKVHEAVEVAKkeKVEAVLGVG-----gGSVVDSAKAVAAG 114 : :::::::::::::::: :::::::::: ::::::::: ::::::::::::: d1v16b2 39 EkLGVSCEVIDLRTIIPW--DVDTICKSVI--KTGRLLISHeapltgGFASEISSTVQEE 94 d1vlja_ 115 ALYegdiwdafigkyqiekaLPIFDVLtISATgtemngnavitnektkekygvsskalyp 174 ::: ::::::: :::: d1v16b2 95 CFL--------------nleAPISRVC-GYDT---------------------------p 112 d1vlja_ 175 kvsiidPSVQftlpkeqtvygavdaishileyyfdgsspeisneiaegtirtimkmterl 234 :::: d1v16b2 113 fphifePFYI-------------------------------------------------- 122 d1vlja_ 235 iekpddyearanlawsatialngtmavgrrggewachriehslsalydiahgaglaivfp 294 d1v16b2 123 ------------------------------------------------------------ 123 d1vlja_ 295 awmkyvyrknpaqferfakkifgfegegeelilkgieafknwlkkvgapvslkdagipee 354 d1v16b2 123 ------------------------------------------------------------ 123 d1vlja_ 355 didkivdnvmllveknlkpkgaslgrimvleredvreilklaak 398 d1v16b2 123 ----------------------------pdkwkcydalrkminy 138 FAST alignment (Normalized score: 2.75 Raw score:643.30) d1vlja_ 1 HHHMENFVFHNPTKIVFGRGTIPKIGEEIKNAGIR----------------KVLFLYGGG 44 ::::::: d1v16b2 1 -----------------------------------PYNIPLSQAEVIQEGSDVTLVAW-- 23 d1vlja_ 45 SIKKNGVYDQVVDSLKK----HGIEWVEVSGV----KPNPVLSKVHEAVEVAKKEKVEAV 96 ::::::::::::: :::::::: :::: :::::::::::: ::: d1v16b2 24 ----GTQVHVIREVASMAKEKLGVSCEVI---DLRTIIPW---DVDTICKSVIKT--GRL 71 d1vlja_ 97 LGVGG-------GSVVDSAKAVAAGALYEGDIWDAFIGKYQIEKA-----LPIFDVLTIS 144 ::: :::::::::::::: ::::::: d1v16b2 72 LIS--HEAPLTGGFASEISSTVQEEC-------------------FLNLEAPISRVC--- 107 d1vlja_ 145 ATGTEMNGNAVITNEKTKEKYGVSSKALYPKVSIIDPSVQFTLPKEQTVYGAVDAISHIL 204 d1v16b2 108 ------------------------------------------------------------ 108 d1vlja_ 205 EYYFDGSSPEISNEIAEGTIRTIMKMTERLIEKPDDYEARANLAWSATIALNGTMAVGRR 264 d1v16b2 108 ------------------------------------------------------------ 108 d1vlja_ 265 GGEWACHRIEHSLSALYDIAHGAGLAIVFPAWMKYVYRKNPAQFERFAKKIFGFEGEGEE 324 d1v16b2 108 ------------------------------------------------------------ 108 d1vlja_ 325 LILKGIEAFKNWLKKVGAPVSLKDAGIPEEDIDKIVDNVMLLVEKNLKPKGASLGRIMVL 384 d1v16b2 108 ------------------------------------------------------------ 108 d1vlja_ 385 EREDVREILKLAAK------------------------------- 398 d1v16b2 108 --------------GYDTPFPHIFEPFYIPDKWKCYDALRKMINY 138 TMalign alignment (TM-score: 0.21 Raw score:85.00) d1vlja_ 1 ---------------HHHMENFVFHNPTKIVFGRGTIPKIGEEIKNAGIRKVLFLYGGGS 45 :::::::: :: d1v16b2 1 PYNIPLSQAEVIQEG----------------------------------SDVTLVAW-GT 25 d1vlja_ 46 IKKNGVYDQVVDSLK-KHGIEWVEVSGVKPNPVLSKVHEAVEVAKKEKVEAVLGVG-G-- 101 ::: :::::::::: ::::::::::::: :::::::::::::: ::::::::: : d1v16b2 26 QVH--VIREVASMAKEKLGVSCEVIDLRT--IIPWDVDTICKSVI--KTGRLLISHEAPL 79 d1vlja_ 102 --GSVVDSAKAVAAGALYEGDIWDAFIGKYQIEKAL--PIFDVLTISATGTEMNGNAVIT 157 ::::::::::::::: ::: :::::: ::: d1v16b2 80 TGGFASEISSTVQEECF----------------LNLEAPISRVC-GYD------------ 110 d1vlja_ 158 NEKTKEKYGVSSKALYPKVSIIDPSVQFTLPKEQTVYGAVDAISHILEYYFDGSSPEISN 217 :: d1v16b2 111 -------------------------------------TP--------------------- 112 d1vlja_ 218 EIAEGTIRTIMKMTERLIEKPDDYEARA-NLA---------------WSATIALNGTMAV 261 : : : :::::: : d1v16b2 113 -------------F--P---H-IFEPFYI--PDKWKCYDALRKMINY------------- 138 d1vlja_ 262 GRRGGEWACHRIEHSLSALYDIAHGAGLAIVFPAWMKYVYRKNPAQFERFAKKIFGFEGE 321 d1v16b2 139 ------------------------------------------------------------ 139 d1vlja_ 322 GEELILKGIEAFKNWLKKVGAPVSLKDAGIPEEDIDKIVDNVMLLVEKNLKPKGASLGRI 381 d1v16b2 139 ------------------------------------------------------------ 139 d1vlja_ 382 MVLEREDVREILKLAAK 398 d1v16b2 139 ----------------- 139 HHsearch alignment (Probability: 0.06 E-value:0.08) d1vlja_ 35 RKVLFLYGGGSIKKNGVYDQVVDSLK-KHGIEWVEVSGVKPNPVLSKVHEAVEVAKKEKV 93 :::::::::::::: ::::::::: ::::::::::::::::::: :::::::::::: d1v16b2 16 SDVTLVAWGTQVHV---IREVASMAKEKLGVSCEVIDLRTIIPWDV--DTICKSVIKTGR 70 d1vlja_ 94 EAVL 97 :::: d1v16b2 71 LLIS 74