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 | d1psda2 | Phosphoglycerate dehydrogenase | Formate/glycerate dehydrogenase catalytic domain-like | Flavodoxin-like | 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 <-- 0.738 --> HitDALI alignment (Z-score: 2.5 Raw score:239.00) d1jmva_ 1 --myKHILVAVdlseespiLLKKAVGIAKRHDA-KLSIIHVdvnfsdlytglidvnmssm 57 ::::::: :::::::::::::: ::::::: d1psda2 1 ekdkIKFLLVE-------gVHQKALESLRAAGYtNIEFHKG------------------- 34 d1jmva_ 58 qdristetqkalldlaesvdypiseklsgsgdLGQVLSDAIEqyDVDLLVTGHhqdfwsk 117 :::::::::: ::::::::: d1psda2 35 ------------------------------alDDEQLKESIR--DAHFIGLRS------- 55 d1jmva_ 118 lmsSTRQ-VMNTIK--IDMLVVP------------------------------------- 137 :::: :::::: ::::::: d1psda2 56 -rtHLTEdVINAAEklVAIGCFCigtnqvdldaaakrgipvfnapfsstqeaqeniglev 114 d1jmva_ 138 ---------------lrd 140 d1psda2 115 agklikysdngstlsavn 132 FAST alignment (Normalized score: 3.14 Raw score:426.50) d1jmva_ 1 MY----KHILVAVDLSEE----SPILLKKAVGIAKRHD---AKLSIIHVDVNFSDLYTGL 49 ::::: :::::::::: :::::: d1psda2 1 --EKDKIKFLL-------VEGVHQKALESLRA------AGYTNIEFH------------- 32 d1jmva_ 50 IDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSGSGD----LGQVLSDAIEQYDVDL 105 ::::::::: ::::: d1psda2 33 ----------------------------------------KGALDDEQLKESI--RDAHF 50 d1jmva_ 106 LVTGHHQDFWSKLMSS------TRQVMNTIK--IDMLV--------------------VP 137 ::: ::::::::: ::::: :: d1psda2 51 IGL-------------RSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFN 97 d1jmva_ 138 LRD--------------------------------- 140 :: d1psda2 98 AP-FSSTQEAQENIGLEVAGKLIKYSDNGSTLSAVN 132 TMalign alignment (TM-score: 0.33 Raw score:46.06) d1jmva_ 1 -MYKHILVAVD----------------------LSEESPILLKKAVGIAKRHDAKLSIIH 37 :::::::::: :::::::::::::: : ::::: d1psda2 1 EKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRD-A------HFIGL 53 d1jmva_ 38 VDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSGS---------- 87 :: :: :::::::::::::::::::: d1psda2 54 RS-------------------------RT-HLTEDVINAAEKLVAIGCFCIGTNQVDLDA 87 d1jmva_ 88 --------------G---DLGQVLSDAIEQYDV------------DLLVTGHHQDFWSKL 118 : ::::::::::::::: d1psda2 88 AAKRGIPVFNAPFSSTQEAQENIGLEVAGKLIKYSDNGSTLSAVN--------------- 132 d1jmva_ 119 MSSTRQVMNTIKIDMLVVPLRD 140 d1psda2 133 ---------------------- 133 HHsearch alignment (Probability: 0.00 E-value:0.54) d1jmva_ 4 HILVAVDLSEESPILL 19 :::::::::::::::: d1psda2 6 KFLLVEGVHQKALESL 21