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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1s3la_ | Putative phosphodiesterase MJ0936 | Metallo-dependent phosphatases | Metallo-dependent phosphatases | α+β |
| Hit | d1vl0a_ | DTDP-4-dehydrorhamnose reductase RfbD | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
Query <-- 1.015 --> IntermediateDALI alignment (Z-score: 6.5 Raw score:666.30) query 1 slqLRLALNQIDStvgdiagNAEAILRWTRHSAEQGAHLVAFPEMALtgypvedlalrss 60 :::::::::: ::::::::::::::::::::::::::: d1s3la_ 1 ---MKIGIMSDTH------dHLPNIRKAIEIFNDENVETVIHCGDFV------------- 38 query 61 fveaSRTALrELAARLaeegfgeLPVLV----gYLDRSesaqpkygqpagaprnaaavLH 116 ::::: :::::: ::::: ::::: :: d1s3la_ 39 ----SLFVI-KEFENL------nANIIAtygnnDGERC---------------klkewLK 72 query 117 RGR-vALTFAkhhlpnygvfdefryfvpgdtmPIVRLHGVDIALAICEDLwqdgGRVPAA 175 ::: ::::: :::::::::::::::::: :::::: d1s3la_ 73 DINeeNIIDD---------------------fISVEIDDLKFFITHGHHQ----SVLEMA 107 query 176 R-SAGAGLLLSVNASpyerdkddtrlelvrkRAQEaGCTTAYLAM--IGGQdelvfdgds 232 : ::::::::::::: :::: ::::::::: :::: d1s3la_ 108 IkSGLYDVVIYGHTH------------ervfEEVD-DVLVINPGEccGYLT--------- 145 query 233 ivvdrdgevvarapqFSEGCVVLDLDlpaaeaepptgvvddglridrlviseeplpayeA 292 ::::::::::: : d1s3la_ 146 ---------------GIPTIGILDTE---------------------------------K 157 query 293 ELAGgyadrldadeevysalvvglrayvakngfrsvliglsggidsalvaaiacdalgaq 352 :::: d1s3la_ 158 KEYR-------------------------------------------------------- 161 query 353 nvygvsmpskyssdhskgdaaelarrtglnfrtvsiepmfdaymaslgltglaeenlqsr 412 d1s3la_ 162 ------------------------------------------------------------ 162 query 413 lrgttlmaisnqeghivlapgnkselavgystlygdsvgaygpikdvyktsifrlaewrn 472 d1s3la_ 162 ------------------------------------------------------------ 162 query 473 raaaergqtppipeasitkpdypvldailelyvdrdtgadaivaagydrelvvktlrmvd 532 d1s3la_ 162 ------------------------------------------------------------ 162 query 533 taeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1s3la_ 162 --------------------------------eivl 165 FAST alignment (Normalized score: 2.92 Raw score:894.50) query 1 SLQL-RLALNQIDSTVGDIAG-----NAEAILRWTRHSAEQGAHLVAFPEMALTGYPVED 54 ::::: ::::::::::::::::::::: d1s3la_ 1 ----MKIGIM-----------SDTHDHLPNIRKAIEIFNDENVETVI------------- 32 query 55 LALRSSFVEASRT------------------------------ALRELAARLAEEGFGEL 84 ::::::::::: d1s3la_ 33 -------------HCGDFVSLFVIKEFENLNANIIATYGNNDGERCKLKEWLKD------ 73 query 85 PVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRVALTFAKHHLPNYGVFDEFRYFVPG 144 d1s3la_ 74 ------------------------------------------------------------ 74 query 145 D--------TMPIVRLHGVDIALAICEDLWQDGGRVPAARSA-GAGLLLSVNASPYERDK 195 :::::::::::::::: :::: ::::::::: ::::::::: d1s3la_ 74 -INEENIIDDFISVEIDDLKFFITH---GHHQ-SVLEMAIKSGLYDVVIYGH-------- 120 query 196 DDTRLELVRKRAQE---------AGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAP 246 :::::::: d1s3la_ 121 --------------THERVFEEVDDVLVINP----------------------------- 137 query 247 -------QFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYA 299 :::::::::: d1s3la_ 138 GECCGYLTGIPTIGILD------------------------------------------- 154 query 300 DRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSM 359 d1s3la_ 155 ------------------------------------------------------------ 155 query 360 PSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLM 419 d1s3la_ 155 ------------------------------------------------------------ 155 query 420 AISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERG 479 d1s3la_ 155 ------------------------------------------------------------ 155 query 480 QTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRR 539 d1s3la_ 155 ------------------------------------------------------------ 155 query 540 QYPPGTKISAKGFGKDRRLPITNRWREGH----------- 568 d1s3la_ 155 -----------------------------TEKKEYREIVL 165 TMalign alignment (TM-score: 0.14 Raw score:78.14) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1s3la_ 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1s3la_ 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1s3la_ 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1s3la_ 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1s3la_ 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLS-GG-IDSALVAAIACDALGAQNVYGVS 358 ::::::::: :: :::::::::::::: ::::::: d1s3la_ 1 ------------------------MKIGIMSDTHDHLPNIRKAIEIFNDEN--VETVIHC 34 query 359 MPSKYSSDHSKGDAAELARRTGLNFRTVSIE----------------------P------ 390 :: ::: ::: ::::::::::::::::: : d1s3la_ 35 GD---FVS--LFV-IKEFENLNANIIATYGNNDGERCKLKEWLKDINEENIIDDFISVEI 88 query 391 ---------MFDAY------------------MASLGLTGLAEENLQSRLRGTTLMA--- 420 :: :: :::: :: ::: d1s3la_ 89 DDLKFFITHGH-HQSVLEMAIKSGLYDVVIYG--------------HTHE-RV-FEEVDD 131 query 421 ISNQEGHIVLAPGNKSELAVGYSTLYGDSV--------GAYGPIKDVYKTSIFRLAEWRN 472 ::: ::::::: : ::::::::: :::::: d1s3la_ 132 -VLV--INPGECC---G----YLTGIPTIGILDTEKKEYREIVL---------------- 165 query 473 RAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVD 532 d1s3la_ 166 ------------------------------------------------------------ 166 query 533 TAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1s3la_ 166 ------------------------------------ 166 HHsearch alignment (Probability: 0.34 E-value:0.00) query 4 LRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAF 42 :::::: ::::::::::::::::::::::::::: d1s3la_ 1 MKIGIM------SDTHDHLPNIRKAIEIFNDENVETVIH 33
Intermediate <-- 1.101 --> HitDALI alignment (Z-score: 2.9 Raw score:317.40) d1s3la_ 1 -MKIGIMS---------------------------dTHDHLPNIRKAIEIFNdenVETVI 32 ::::::: :::::::::::::::: ::::: d1vl0a_ 1 hMKILITGangqlgreiqkqlkgknveviptdvqdlDITNVLAVNKFFNEKK---PNVVI 57 d1s3la_ 33 HCGD---------------fVSLFVIKE-FENL---NANIIATY---------------- 57 :::: :::::::: :::: :::::::: d1vl0a_ 58 NCAAhtavdkceeqydlaykINAIGPKNlAAAAysvGAEIVQIStdyvfdgeakepitef 117 d1s3la_ 58 ------gnndGERCKLKEWLKDINEENIIDD----------------------------- 82 ::::::::::::::::::::: d1vl0a_ 118 devnpqsaygKTKLEGENFVKALNPKYYIVRtawlygdgnnfvktminlgkthdelkvvh 177 d1s3la_ 83 ---------------------fisveiddlkffithghhqsvlemaiksglydvviyght 121 d1vl0a_ 178 dqvgtptstvdlarvvlkvideknygtfhctckgicswydfaveifrltgidvkvtpctt 237 d1s3la_ 122 hervfeevddvlvinpgeccgyltgiptigildtekkeyreivl 165 d1vl0a_ 238 eefprpakrpkysvlrnymlelttgditrewkeslkeyidllqm 281 FAST alignment (Normalized score: 2.75 Raw score:592.00) d1s3la_ 1 -MKIGIMSDT-------------------------------HDHLPNIRKAIEIFNDENV 28 ::::: :::::::::::: :::: d1vl0a_ 1 HMKILI----TGANGQLGREIQKQLKGKNVEVIPTDVQDLDITNVLAVNKFFN---EKKP 53 d1s3la_ 29 ETVIHCGDFV-------------------SLFVIKEFE-----NLNANIIATYGNN---- 60 :::::: :::::::: :::::::::::: d1vl0a_ 54 NVVINC----AAHTAVDKCEEQYDLAYKINAIGPKNL-AAAAYSVGAEIVQISTD-YVFD 107 d1s3la_ 61 -------------------DGERCKLKEWLKDINEENIIDDFISVEIDDLKFFITHGHHQ 101 ::::::::::::::::::::: d1vl0a_ 108 GEAKEPITEFDEVNPQSAYGKTKLEGENFVKALNPKYYIV-------------------- 147 d1s3la_ 102 SVLEMAIKSGLYDVVIYGHTHERVFEEVDDVLVINPGECCGYLTGIPTIGILDTEKKEYR 161 d1vl0a_ 148 ------------------------------------------------------------ 148 d1s3la_ 162 EIVL-------------------------------------------------------- 165 d1vl0a_ 148 ----RTAWLYGDGNNFVKTMINLGKTHDELKVVHDQVGTPTSTVDLARVVLKVIDEKNYG 203 d1s3la_ 166 ------------------------------------------------------------ 166 d1vl0a_ 204 TFHCTCKGICSWYDFAVEIFRLTGIDVKVTPCTTEEFPRPAKRPKYSVLRNYMLELTTGD 263 d1s3la_ 166 ------------------ 166 d1vl0a_ 264 ITREWKESLKEYIDLLQM 281 TMalign alignment (TM-score: 0.43 Raw score:70.56) d1s3la_ 1 -MKIGIMS-----------------------DT---HDHLPNIRKAIEIFNDENVETVIH 33 ::::::: :: :::: :::::::::::::::::: d1vl0a_ 1 HMKILITGANGQLGREIQKQLKGKNVEVIPTDVQDL-DITN-VLAVNKFFNEKKPNVVIN 58 d1s3la_ 34 CGDF------------VS---LFVIKEF-ENL--N-ANIIATYG-N-------------- 59 :::: :: ::::::: ::: : :::::::: : d1vl0a_ 59 CAAHTAVDKCEEQYDLAYKINAIGPKNLAAAAYSVGAEIVQISTDYVFDGEAKEPITEFD 118 d1s3la_ 60 ------NDGE-RCKLKEWLKDINEENIIDDFISVEIDDLKFFITHGHHQ----------- 101 :::: :::::::::::::::::::: ::::: d1vl0a_ 119 EVNPQSAYGKTKLEGENFVKALNPKYYIVRT-------------AWLYGDGNNFVKTMIN 165 d1s3la_ 102 ------------------SVLEMAI-KSGLYDVV-------------------------- 116 :::: :: ::::: d1vl0a_ 166 LGKTHDELKVVHDQVGTPTSTV-DLA---RVVLKVIDEKNYGTFHCTCKGICSWYDFAVE 221 d1s3la_ 117 ------------------------------------------------------------ 117 d1vl0a_ 222 IFRLTGIDVKVTPCTTEEFPRPAKRPKYSVLRNYMLELTTGDITREWKESLKEYIDLLQM 281 d1s3la_ 117 IYGHTHERVFEEVDDVLVINPGECCGYLTGIPTIGILDTEKKEYREIVL 165 d1vl0a_ 282 ------------------------------------------------- 282 HHsearch alignment (Probability: 0.08 E-value:0.03) d1s3la_ 15 NIRKAIEIFNDENVETVIHCGDFV 38 :::::::::::::::::::::::: d1vl0a_ 40 NVLAVNKFFNEKKPNVVINCAAHT 63