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 | d1gpja2 | Glutamyl tRNA-reductase middle domain | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 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 <-- 1.773 --> HitDALI alignment (Z-score: 5.0 Raw score:396.30) d1jmva_ 1 ----------------------MYKHILVAVDlseeSPILLKKAVGIAKRHDAKLSIIHv 38 :::::::::: ::::::::::::::::::::::: d1gpja2 1 segavsigsaavelaerelgslHDKTVLVVGA----GEMGKTVAKSLVDRGVRAVLVAN- 55 d1jmva_ 39 dvnfsdlytglidvnmssmqdristeTQKALLDLAESVdypISEKLSGSgdlgqVLSDAI 98 :::::::::::: :::::::: :::::: d1gpja2 56 -------------------------rTYERAVELARDL---GGEAVRFD-----ELVDHL 82 d1jmva_ 99 EqyDVDLLVTG-HHQDfwsklmssTRQVMNTI--------KIDMLVVPLR---------- 139 : :::::::: :::: :::::::: :::::::::: d1gpja2 83 A--RSDVVVSAtAAPH-----pviHVDDVREAlrkrdrrsPILIIDIANPrdveegveni 135 d1jmva_ 140 -----------------------d 140 d1gpja2 136 edvevrtiddlrviarenlerrrk 159 FAST alignment (Normalized score: 4.28 Raw score:638.70) d1jmva_ 1 MYK-----------------------HILVAVDLSEE--SPILLKKAVGIAKRHDAKLSI 35 ::::::: ::::::::::::: ::: ::: d1gpja2 1 ---SEGAVSIGSAAVELAERELGSLHDKTVLVV----GAGEMGKTVAKSLVD-RGV-RAV 51 d1jmva_ 36 IHVDVNFSDLYTGLIDVNMSSMQDRISTE--TQKALLDLAESVDYPISE---KLSG-SGD 89 ::: :::::::::: :::: ::: d1gpja2 52 LVA--------------------------NRTYERAVELAR--------DLGGEAVRFDE 77 d1jmva_ 90 LGQVLSDAIEQYDVDL-LVTGHHQDFWSK----------LMSSTRQVMNTI--KIDMLVV 136 ::::::: :::: :::::::::::: ::::::: d1gpja2 78 LVDHLAR---------SDVVV--------SATAAPHPVIHVDDVREALRKRDRRSPILII 120 d1jmva_ 137 PLRD------------------------------------- 140 :: d1gpja2 121 DI--ANPRDVEEGVENIEDVEVRTIDDLRVIARENLERRRK 159 TMalign alignment (TM-score: 0.47 Raw score:66.18) d1jmva_ 1 --------------------MY-KHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHVD 39 :: ::::::: : :: ::::::::::::: :::::::::: d1gpja2 1 SEGAVSIGSAAVELAERELGSLHDKTVLVV-G-AG-EMGKTVAKSLVDR-GVRAVLVANR 56 d1jmva_ 40 VNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIE 99 :: :::::::::: : :::::::::::::: : d1gpja2 57 ------------------------TY-ERAVELARDL---G-GEAVRFDELVDHLA--R- 84 d1jmva_ 100 QYDVDLLVTGHH--QDF-WSKLMSSTRQVMNTI-K-IDMLVVPLRD-------------- 140 : ::::::: ::: ::::::::::::: : :::::::::: d1gpja2 85 ---S-DVVVSATAAPHPV--IHVDDVREALRKRDRRSPILIIDIANPRDVEEGVENIEDV 138 d1jmva_ 141 --------------------- 141 d1gpja2 139 EVRTIDDLRVIARENLERRRK 159 HHsearch alignment (Probability: 0.13 E-value:0.08) d1jmva_ 101 YDVDLLVTGHHQDFWSKLMSSTRQVMNT--IKIDMLVVP 137 :::::::::::::::::::::::::::: ::::::::: d1gpja2 83 ARSDVVVSATAAPHPVIHVDDVREALRKRDRRSPILIID 121