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 | d1guda_ | D-allose-binding protein | Periplasmic binding protein-like I | Periplasmic binding protein-like I | 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 <-- 0.732 --> HitDALI alignment (Z-score: 8.9 Raw score:672.00) d1vlja_ 1 ------------------------------------------------------------ 1 d1guda_ 1 aaeyavvlktlsnpfwvdmkkgiedeaktlgvsvdifaspsegdfqsqlqlfedlsnkny 60 d1vlja_ 1 ------------------------------------hhhmenfvfhnptkivfgrgTIPK 24 :::: d1guda_ 61 kgiafaplssvnlvmpvarawkkgiylvnldekidmdnlkkaggnveafvttdnvaVGAK 120 d1vlja_ 25 IGEEIKNAG---IRKVLFLYGG---GSIKknGVYDQVVDSLKKH-GIEW-VEVSGVKpnP 76 ::::::::: :::::::::: :::: ::::::::::::: :::: ::::::: : d1guda_ 121 GASFIIDKLgaeGGEVAIIEGKagnASGE--ARRNGATEAFKKAsQIKLvASQPADW--D 176 d1vlja_ 77 VLSKVHEAVEVAKKEK-VEAVLGVGgGSVVDSAKAVAAGALyegdiwdafigkyqieKAL 135 :::::::::::::::: :::::::: ::::::::::::::: ::: d1guda_ 177 RIKALDVATNVLQRNPnIKAIYCAN-DTMAMGVAQAVANAG--------------ktGKV 221 d1vlja_ 136 PIFDVLtisaTGTEMNGnavitnektkekygvsSKALyPKVSIIDPsvqftlpkeqtvyg 195 :::::: ::::::: :::: :::::::: d1guda_ 222 LVVGTD---gIPEARKM---------------vEAGQ-MTATVAQN-------------- 248 d1vlja_ 196 avdaishileyyfdgsspeisneiaegtirtimkmterliekpddyEARAnlawsatial 255 :::: d1guda_ 249 ----------------padigatglklmvdaeksgkvipldkapefKLVD---------- 282 d1vlja_ 256 ngtmavgrrggewachriehslsalydiahgaglaivfpawmkyvyrknpaqferfakki 315 d1guda_ 283 ------------------------------------------------------------ 283 d1vlja_ 316 fgfegegeelilkgieafknwlkkvgapvslkdagipeedidkivdnvmllveknlkpkg 375 d1guda_ 283 ------------------------------------------------------------ 283 d1vlja_ 376 aslgrimvleredvreilklaak 398 d1guda_ 283 -----------------silvtq 288 FAST alignment (Normalized score: 2.28 Raw score:770.60) d1vlja_ 1 HHHMENFVFHNPTKIVFGRGTIPKIGEEIKNAGIR--KVLFLYGGGSIKK------NGVY 52 :::::::: :::: d1guda_ 1 -----------------------------------AAEYAVVLKT-----LSNPFWVDMK 20 d1vlja_ 53 DQVVDSLKKHGIEWVEVSGVKPNP-------VLSKVHEAVEVAKKEKVEAVLGVGGGS-- 103 ::::::::::::::::: ::::::::::::: ::::::::: d1guda_ 21 KGIEDEAKTLGVSVDIF-------ASPSEGDFQSQLQLFEDLSN-KNYKGIAFA----PL 68 d1vlja_ 104 VVDSAKAVAAGALYEGDIWDAFIGKYQIEK---ALPIFDVLTISATGTEMNGNAVITNEK 160 :::::::::::: :::::: d1guda_ 69 SSVNLVMPVARA------------------WKKGIYLVN--------------------- 89 d1vlja_ 161 TKEKYGVSSK-------------ALYPKVSIIDPSVQFTLPKEQTVYGAVDAISHILEYY 207 ::::::::: d1guda_ 90 ----------LDEKIDMDNLKKAGGNVEAFVT---------------------------- 111 d1vlja_ 208 FDGSSPE----------------------------------ISNEIAEGTIRTIMKMTER 233 :::::::::::::::: d1guda_ 112 -------TDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATEAFKK--- 161 d1vlja_ 234 LIEKPDDYEARANLAWSATIALNGTMAVGRRGGEWACHRIEHSLSALYDIAHGAGLAIVF 293 d1guda_ 162 ------------------------------------------------------------ 162 d1vlja_ 294 PAWMKYVYRKNPAQFERFAKKIFGFEGEGEELILKGIEAFKNWLKKVGAPVSLKDAGIPE 353 d1guda_ 162 ------------------------------------------------------------ 162 d1vlja_ 354 EDIDKIVDNVMLLVEKNLKPKGASLGRIMVLEREDVREILKLAAK--------------- 398 d1guda_ 162 ---------------------------------------------ASQIKLVASQPADWD 176 d1vlja_ 399 ------------------------------------------------------------ 399 d1guda_ 177 RIKALDVATNVLQRNPNIKAIYCANDTMAMGVAQAVANAGKTGKVLVVGTDGIPEARKMV 236 d1vlja_ 399 ---------------------------------------------------- 399 d1guda_ 237 EAGQMTATVAQNPADIGATGLKLMVDAEKSGKVIPLDKAPEFKLVDSILVTQ 288 TMalign alignment (TM-score: 0.30 Raw score:120.45) d1vlja_ 1 ------------------------------------------------------------ 1 d1guda_ 1 AAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFASPSEGDFQSQLQLFEDLSNKNY 60 d1vlja_ 1 ---------------------------------------------------HHHMENFVF 9 d1guda_ 61 KGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEKIDMDNLKKAGGNVEAFVT--------- 111 d1vlja_ 10 HNPTKIVFGR--GT-IP--KIGEEIKNAGIRKVLFLYGGG-SIKKNGVYDQVVDSLKKHG 63 :: :: :: ::::::::::::::::::::: ::::::::::::::::::: d1guda_ 112 --------TDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATEAFKKAS 163 d1vlja_ 64 -IEW-VEVSGVKPNPVLSKVHEAVEVAKKEKVEAVLGVGGGSVVDSAKAVAAGALYEGDI 121 ::: :::::::: :: ::::::::::::::::::::::::::::::::::::::: d1guda_ 164 QIKLVASQPADWD-RI-KALDVATNVLQRNPNIKAIYCANDTMAMGVAQAVANAGK---- 217 d1vlja_ 122 WDAFIGKYQIEKALPIFDVLTISATGTEMNGNAVITNEKTKEKYGVSSKALYPKVSIIDP 181 ::::::::: :::::: :::: :::::: :::: : d1guda_ 218 -----------TGKVLVVGT-DGIPEA-RKMV---------------EAGQMT-ATVA-Q 247 d1vlja_ 182 SVQFTLPKEQTVYGAVDAISHILEYYFDGSSPEISNEIAEGTIRTIMKMTER--LIE--- 236 : : :::::::: : d1guda_ 248 N-------------P-----------------------------ADIGATGLKL--MVDA 263 d1vlja_ 237 ------------KPDDYEARANLAWSATIALNGTMAVGRRGGEWACHRIEHSLSALYDIA 284 :::::: :: :: :: : d1guda_ 264 EKSGKVIPLDKAPEFKLV-DS--IL--VT--Q---------------------------- 288 d1vlja_ 285 HGAGLAIVFPAWMKYVYRKNPAQFERFAKKIFGFEGEGEELILKGIEAFKNWLKKVGAPV 344 d1guda_ 289 ------------------------------------------------------------ 289 d1vlja_ 345 SLKDAGIPEEDIDKIVDNVMLLVEKNLKPKGASLGRIMVLEREDVREILKLAAK 398 d1guda_ 289 ------------------------------------------------------ 289 HHsearch alignment (Probability: 0.91 E-value:0.00) d1vlja_ 37 VLFLYGGGSIKKNGVYDQVVDSLKKHGIEWVEVSGVKPNPVLSKVHEAVEVAKKEKVEAV 96 ::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::: d1guda_ 5 AVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFAS-PSEGDFQSQLQLFEDLSNKNYKGI 63 d1vlja_ 97 LGVGGGSVVDSAKAVAAGALYEGDIWDAFIGKYQIEKALPIFDVLTI 143 :::::::: ::::::::: ::::::::::::: d1guda_ 64 AFAPLSSV-NLVMPVARA----------------WKKGIYLVNLDEK 93