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 | d1jmva_ | Universal stress protein A, UspA | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1jyea_ | Lac-repressor (lacR) core (C-terminal domain) | Periplasmic binding protein-like I | Periplasmic binding protein-like I | α/β |
Query <-- 1.476 --> IntermediateDALI alignment (Z-score: 6.4 Raw score:517.70) query 1 dadeevysalvvglrayvaknGFRSVLIGLSGGIDSALVAAIACDALG--aqNVYGVSMP 58 ::::::::::::::::::::::::::: :::::::: d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVGIAKrhdaKLSIIHVD 39 query 59 S------------------kysSDHSKGDAAELARRTG---lNFRTVSIepmfdaymasl 97 : :::::::::::::::: ::::::: d1jmva_ 40 VnfsdlytglidvnmssmqdriSTETQKALLDLAESVDypisEKLSGSG----------- 88 query 98 gltglaeenlqsrLRGTTLMAISNQEGH-IVLAPGNKseLAVG--YSTL----ygdsvgA 150 ::::::::::::::: :::::::: :::: :::: : d1jmva_ 89 -------------DLGQVLSDAIEQYDVdLLVTGHHQ--DFWSklMSSTrqvmntikidM 133 query 151 YGPiKDVYktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtgad 210 ::: :::: d1jmva_ 134 LVV-PLRD---------------------------------------------------- 140 query 211 aivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1jmva_ 141 -------------------------------------------------------- 141 FAST alignment (Normalized score: 4.82 Raw score:930.50) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQ------NVYG 54 ::::::::::::::::::::::::: :::: d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVGI----AKRHDAKLSI 35 query 55 VSMPSKYSS-----------------------DHSKGDAAELAR--RTGL-NFRTVSIEP 88 :::: :::::::::::: :::: ::::: d1jmva_ 36 IHVD-----VNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSG---- 86 query 89 MFDAYMASLGLTGLAEENLQSR--LRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY- 144 :::::::::::::: :::::::: d1jmva_ 87 ----------------------SGDLGQVLSDAIEQYDVDLLVTGHH------------Q 112 query 145 ------------GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDY 192 :::::: d1jmva_ 113 DFWSKLMSSTRQVMNTIK------------------------------------------ 130 query 193 PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGK 252 d1jmva_ 131 ------------------------------------------------------------ 131 query 253 DRRLPITNRWREGH---------- 266 d1jmva_ 131 --------------IDMLVVPLRD 140 TMalign alignment (TM-score: 0.33 Raw score:88.21) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALG--AQNVYGVSMP 58 ::::::::::::::::::::::::::: :::::::::: d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHVD 39 query 59 SK---------------------YSSDHSKGDAAELARRT--GLNFRTVSIEPMFDAYMA 95 :: :: :::::::::::: ::::::::: d1jmva_ 40 VNFSDLYTGLIDVNMSSMQDRIS--TE-TQKALLDLAESVDYPISEKLSGS--------- 87 query 96 SLGLTGLAEENLQSRLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG---- 149 : ::::::::::::::: ::::::: ::::::::: ::: :: d1jmva_ 88 ------------G--DLGQVLSDAIEQYDVDLLVTGHH-QDFWSKLMS--STRQVMNTIK 130 query 150 --AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDT 207 ::: :: : :: d1jmva_ 131 IDMLV-VP-L-RD----------------------------------------------- 140 query 208 GADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1jmva_ 141 ----------------------------------------------------------- 141 HHsearch alignment (Probability: 0.05 E-value:0.16) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :::::::::::::::::::::::::::::::::::::::::::::: ::::: :::::: d1jmva_ 56 SMQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQY-DVDLL--VTGHHQ 112 query 61 YSSDHSKGDAAELARRTGLNFRTVSIEP 88 :::::::::::::::::::::::::::: d1jmva_ 113 DFWSKLMSSTRQVMNTIKIDMLVVPLRD 140
Intermediate <-- 1.384 --> HitDALI alignment (Z-score: 6.6 Raw score:441.50) d1jmva_ 1 myKHILVAVDL--SEESPILLKKAVGIAKRHDAKLSIIHVDVNFsdlytglidvnmssmq 58 ::::::::: ::::::::::::::::::::::::::::::: d1jyea_ 1 --LLIGVATSSlaLHAPSQIVAAILSRADQLGASVVVSMVERSG---------------- 42 d1jmva_ 59 dristetqkalldlaesvdypiseklsgsGDLGQVLSDAIEqYDVDLLVTGhhqdfwskL 118 :::::::::::: ::::::::: : d1jyea_ 43 ----------------------------vEACKTAVHNLLA-QRVSGLIIN-----yplD 68 d1jmva_ 119 MSSTRQVMNTIK-IDMLVV----------PLR---------------------------- 139 :::::::::::: :::::: ::: d1jyea_ 69 DQDAIAVEAACTnVPALFLdvsdqtpinsIIFshedgtrlgvehlvalghqqiallagpl 128 d1jmva_ 140 ------------------------------------------------------------ 140 d1jyea_ 129 ssvsarlrlagwhkyltrnqiqpiaeregdwsamsgfqqtmqmlnegivptamlvandqm 188 d1jmva_ 140 ------------------------------------------D----------------- 140 : d1jyea_ 189 algamraitesglrvgadisvvgyddtedsscyipplttikqDfrllgqtsvdrllqlsq 248 d1jmva_ 141 ----------------------- 141 d1jyea_ 249 gqavkgnqllpvslvkrkttlap 271 FAST alignment (Normalized score: 4.03 Raw score:784.30) d1jmva_ 1 MYKHILVAVD--LSEESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQ 58 :::::::: :::::::::::::::::::::::::::::: d1jyea_ 1 --LLIGVATSSLALHAPSQIVAAILSRADQLGASVVVSMVER------------------ 40 d1jmva_ 59 DRISTETQKALLDLAESVDYPISEKLSGSGD-LGQVLSDAIE---QYDVDLLVTGHHQDF 114 :::::::::: ::::::::: d1jyea_ 41 -------------------------------SGVEACKTAVHNLLAQRVSGLII------ 63 d1jmva_ 115 WSK----LMSSTRQVMNT-IKIDMLVVPLRD----------------------------- 140 ::::::::::: ::::::: d1jyea_ 64 ---NYPLDDQDAIAVEAACTNVPALF-----LDVSDQTPINSIIFSHEDGTRLGVEHLVA 115 d1jmva_ 141 ------------------------------------------------------------ 141 d1jyea_ 116 LGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEG 175 d1jmva_ 141 ------------------------------------------------------------ 141 d1jyea_ 176 IVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLL 235 d1jmva_ 141 ------------------------------------ 141 d1jyea_ 236 GQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAP 271 TMalign alignment (TM-score: 0.50 Raw score:70.66) d1jmva_ 1 MYKHILVAVDL--SEESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQ 58 ::::::::: :::::::::::::::::::::::::::::::: d1jyea_ 1 --LLIGVATSSLALHAPSQIVAAILSRADQLGASVVVSMVERSGV--------------- 43 d1jmva_ 59 DRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQDFWSKL 118 :::: ::::::::::::::::::: : : d1jyea_ 44 -----------------------------EACK-TAVHNLLAQRVSGLIINYP-L---D- 68 d1jmva_ 119 MSSTRQVMNTI-KIDMLVV-----------PL---------------------------- 138 ::::::::::: ::::::: :: d1jyea_ 69 DQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPL 128 d1jmva_ 139 ------------------------------------------------------------ 139 d1jyea_ 129 SSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQM 188 d1jmva_ 139 -----------------------RD----------------------------------- 140 :: d1jyea_ 189 ALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQ 248 d1jmva_ 141 ----------------------- 141 d1jyea_ 249 GQAVKGNQLLPVSLVKRKTTLAP 271 HHsearch alignment (Probability: 0.37 E-value:0.02) d1jmva_ 16 PILLKKAVGIAKRHDAK 32 ::::::::::::::::: d1jyea_ 16 SQIVAAILSRADQLGAS 32