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 | d1jx6a_ | Quorum-sensing signal (autoinducer-2) binding protein LuxP | 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 <-- 0.698 --> HitDALI alignment (Z-score: 5.6 Raw score:639.90) d1vlja_ 1 ------------------------------------------------------------ 1 d1jx6a_ 1 gywgyqefldefpeqrnltnalseavraqpvplskptqrpikisvvypgqqvsdywvrni 60 d1vlja_ 1 ------------------------------------------------------------ 1 d1jx6a_ 61 asfekrlyklninyqlnqvftrpnadikqqslslmealksksdyliftldttrhrkfveh 120 d1vlja_ 1 ----------------hhhmenfvfhnptkivfgrGTIPKIGEEIKNAG--iRKVLFLYG 42 :::::::::::::: :::::::: d1jx6a_ 121 vldstntklilqnittpvrewdkhqpflyvgfdhaEGSRELATEFGKFFpkhTYYSVLYF 180 d1vlja_ 43 G-GSIKknGVYDQVVDSLKK-HGIEW-VEVSGVKpnPVLSKVHEAVEVAKKEK-VEAVLG 98 : :::: :::::::::::: ::::: ::::::: ::::::::::::::::: :::::: d1jx6a_ 181 SeGYIS-dVRGDTFIHQVNRdNNFELqSAYYTKA--TKQSGYDAAKASLAKHPdVDFIYA 237 d1vlja_ 99 VGGgSVVDSAKAVAAGALyegdiwdafigkyqieKALPIFDVLtisaTGTEMNGnavitn 158 ::: :::::::::::::: ::::::::: ::::::: d1jx6a_ 238 CST-DVALGAVDALAELG---------------rEDIMINGWG---gGSAELDA------ 272 d1vlja_ 159 ektkekygvsSKALyPKVSIIDPSvqftlpkeqtvygavdaishileyyfdgsspeisne 218 :::: ::::::::: d1jx6a_ 273 ---------iQKGD-LDITVMRMN------------------------------------ 286 d1vlja_ 219 iaegtirtimkmterliekpddyearanlawsatialngtmavgrrggewachriehsls 278 d1jx6a_ 287 ------------------------------------------------------------ 287 d1vlja_ 279 alydiahgaglaivfpawmkyvyrknpaqferfakkifgfegegeelilkgieafknwlk 338 d1jx6a_ 287 ------------------------------------------------------------ 287 d1vlja_ 339 kvgapvslkdagipeedidkivdnvmllveknlkpkgaslgrimvleredvreilklaak 398 d1jx6a_ 287 --------ddtgiamaeaikwdledkpvptvysgdfeivtkadsperiealkkrafrysd 338 FAST alignment (Normalized score: 1.67 Raw score:611.30) d1vlja_ 1 HHHMENFVFHNPTKIVFGRGTIPKIGEEIKNAGI-------------------------- 34 d1jx6a_ 1 ----------------------------------GYWGYQEFLDEFPEQRNLTNALSEAV 26 d1vlja_ 35 --------------RKVLFLYGGGSIKKN----------GVYDQVVDSLKK--HGIEWVE 68 ::::::: :::::::::::: ::::::: d1jx6a_ 27 RAQPVPLSKPTQRPIKISVVY--------PGQQVSDYWVRNIASFEKRLYKLNINYQLNQ 78 d1vlja_ 69 VSGVKPN-PVLSKVHEAVEVAKKEKVEAVLGVGGGSVVDS-------AKAVAAGALYEGD 120 : :::: :::::::::::::::::::::: ::::::::: d1jx6a_ 79 V-FTRP-NADIKQQSLSLMEALKSKSDYLI----------FTLDTTRHRKFVEHVL---- 122 d1vlja_ 121 IWDAFIGKYQIEK---ALPIFDVLTISATGTEMNGNAVITNEKTKEKYGVSSKAL----- 172 :::::: d1jx6a_ 123 -------------DSTNTKLIL---------------------------------QNITT 136 d1vlja_ 173 --------YPKVSIIDPSVQFTLPKEQTVYGAVDAISHILEYYFDGSSPEISNEIAEGTI 224 :::::::: d1jx6a_ 137 PVREWDKHQPFLYVGF-------------------------------------------- 152 d1vlja_ 225 RTIMKMTERLIEKPDDYEARANLAWSATIALNGTMAVGRRGGEWACHRIEHSLSALYDIA 284 d1jx6a_ 153 ------------------------------------------------------------ 153 d1vlja_ 285 HGAGLAIVFPAWMKYVYRKNPAQFERFAKKIFGFEGEGEELILKGIEAFKNWLKKVGAPV 344 d1jx6a_ 153 ------------------------------------------------------------ 153 d1vlja_ 345 SLKDAGIPEEDIDKIVDNVMLLVEKNLKPKGASLGRIMVLEREDVREILKLAAK------ 398 d1jx6a_ 153 ------------------------------------------------------DHAEGS 158 d1vlja_ 399 ------------------------------------------------------------ 399 d1jx6a_ 159 RELATEFGKFFPKHTYYSVLYFSEGYISDVRGDTFIHQVNRDNNFELQSAYYTKATKQSG 218 d1vlja_ 399 ------------------------------------------------------------ 399 d1jx6a_ 219 YDAAKASLAKHPDVDFIYACSTDVALGAVDALAELGREDIMINGWGGGSAELDAIQKGDL 278 d1vlja_ 399 ------------------------------------------------------------ 399 d1jx6a_ 279 DITVMRMNDDTGIAMAEAIKWDLEDKPVPTVYSGDFEIVTKADSPERIEALKKRAFRYSD 338 TMalign alignment (TM-score: 0.32 Raw score:128.99) d1vlja_ 1 ------------------------------------------------------------ 1 d1jx6a_ 1 GYWGYQEFLDEFPEQRNLTNALSEAVRAQPVPLSKPTQRPIKISVVYPGQQVSDYWVRNI 60 d1vlja_ 1 ------------------------------------------------------------ 1 d1jx6a_ 61 ASFEKRLYKLNINYQLNQVFTRPNADIKQQSLSLMEALKSKSDYLIFTLDTTRHRKFVEH 120 d1vlja_ 1 -------------------------------HHHMENFVFHNPTKIVFG-RGTIPKIGEE 28 :: :::::::::: d1jx6a_ 121 VLDSTNTKLILQNITTPVREWDKHQPFLYVG----------------FDHAEGSRELATE 164 d1vlja_ 29 IKNAGI--RKVLFLYGGGSIKKNGVYDQVVDSLKK-HGIEW-VEVSGVKPNPVLSKVHEA 84 :::::: ::::::::::::::::::::::::::: ::::: ::::::: ::: :::::: d1jx6a_ 165 FGKFFPKHTYYSVLYFSEGYISDVRGDTFIHQVNRDNNFELQSAYYTKA-TKQ-SGYDAA 222 d1vlja_ 85 VEVAKKEK-VEAVLGVGGGSVVDSAKAVAAGALYEGDIWDAFIGKYQIEKALPIFDVLTI 143 :::::::: :::::::: :::::::::::::::: ::::::: : d1jx6a_ 223 KASLAKHPDVDFIYACS-TDVALGAVDALAELGR---------------EDIMING-W-- 263 d1vlja_ 144 SATGTEMNGNAVITNEKTKEKYGVSSKALYPKVSIIDPSVQFTLPKEQTVYGAVDAISHI 203 :::::::::: :::::: :::::: :: d1jx6a_ 264 GGGSAELDAI---------------QKGDLD-ITVMRM-------------ND------- 287 d1vlja_ 204 LEYYFDGSSPEISNEIAEGTIRTIMKMTERLI--E------KPDDYEARANLAW-SAT-- 252 :::::::::: : ::::: :: :: :: d1jx6a_ 288 ----------------------DTGIAMAEAIKWDLEDKPVPTVYS--GD--FEI-VTKA 320 d1vlja_ 253 I-ALNGTMAV----GRRGGEWACHRIEHSLSALYDIAHGAGLAIVFPAWMKYVYRKNPAQ 307 : :::::::: d1jx6a_ 321 DSPERIEALKKRAF---------------------------------------------- 334 d1vlja_ 308 FERFAKKIFGFEGEGEELILKGIEAF-KNWLKKVGAPVSLKDAGIPEEDIDKIVDNVMLL 366 :: : d1jx6a_ 335 ------RY-----------------SD--------------------------------- 338 d1vlja_ 367 VEKNLKPKGASLGRIMVLEREDVREILKLAAK 398 d1jx6a_ 339 -------------------------------- 339 HHsearch alignment (Probability: 0.84 E-value:0.00) d1vlja_ 35 RKVLFLY-GG-GSIKKNGVYDQVVDSLKKHGIEWVEVS-GVKPNPVLSKVHEAVEVAKKE 91 ::::::: :: ::::::::::::::::::::::::::: ::::::::::::::::::::: d1jx6a_ 41 IKISVVYPGQQVSDYWVRNIASFEKRLYKLNINYQLNQVFTRPNADIKQQSLSLMEALKS 100 d1vlja_ 92 KVEAVLGVGGGSVV-DSA-KAVAAGALYEGDIWDAFIGKYQIEKALPIFDVLTISAT--- 146 :::::::::::::: ::: :::: ::::::::::::::: d1jx6a_ 101 KSDYLIFTLDTTRHRKFVEHVLD-------------------STNTKLILQNITTPVREW 141 d1vlja_ 147 -GTEMNGNAVITNEKTKEKYGVSS--KA--LYPKVSIIDPSVQFTLPKEQTVYGAVDAIS 201 ::::::: ::::::::::::::: :: :::::::: :::::::::::::::::::: d1jx6a_ 142 DKHQPFLY-VGFDHAEGSRELATEFGKFFPKHTYYSVL--YFSEGYISDVRGDTFIHQVN 198 d1vlja_ 202 HILE-YYFDGSSPEISNEIAEGTIRTIMKM 230 :::: ::::::::::::::::::::::::: d1jx6a_ 199 RDNNFELQSAYYTKATKQSGYDAAKASLAK 228