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 | d1usga_ | Leucine-binding protein | Periplasmic binding protein-like I | Periplasmic binding protein-like I | 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 <-- 0.964 --> HitDALI alignment (Z-score: 3.8 Raw score:279.30) d1s3la_ 1 ------------------------------------------------------------ 1 d1usga_ 1 ddikvavvgamsgpiaqwgdmefngarqaikdinakggikgdklvgveyddacdpkqava 60 d1s3la_ 1 ------------------------------------------------------------ 1 d1usga_ 61 vankivndgikyvighlcssstqpasdiyedegilmispgatnpeltqrgyqhimrtagl 120 d1s3la_ 1 ------------------MKIGIMSD-----------------------------tHDHL 13 :::::::: :::: d1usga_ 121 dssqgptaakyiletvkpQRIAIIHDkqqygeglarsvqdglkaananvvffdgitAGEK 180 d1s3la_ 14 PnIRKAIEIFNDENVETVIHCGDFVS-lFVIKEFE--NLNANIIATYGnndgeRCKLKEW 70 : :::::::::::::::::::::::: ::::::: ::::::::::: ::::::: d1usga_ 181 D-FSALIARLKKENIDFVYYGGYYPEmgQMLRQARsvGLKTQFMGPEG---vgNASLSNI 236 d1s3la_ 71 lkDINEENIIDD--------------fisveiddlkffithghhqsvlemaiksglydvv 116 :::::::::: d1usga_ 237 agDAAEGMLVTMpkrydqdpanqgivdalkadkkdpsgpyvwityaavqslatalertgs 296 d1s3la_ 117 iyghthervfeevddvlvinpgeccgyltgiptigildtekkeyreivl 165 d1usga_ 297 deplalvkdlkangantvigplnwdekgdlkgfdfgvfqwhadgsstka 345 FAST alignment (Normalized score: 2.09 Raw score:499.10) d1s3la_ 1 --MKIGIM----------------------------------------SDTHDHLPNIRK 18 :::::: :::::::::::: d1usga_ 1 DDIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAKGGIKGDKLVGVEYDDACDPKQAVA 60 d1s3la_ 19 AIEIFNDENVETVIHCG-DFVSLFVIKEF-----ENLNANIIATYGNNDGE----RCKLK 68 ::::::::::::: :::::::::: ::::::::: ::::: d1usga_ 61 VANKIVNDGIKYV----IGHLCSSSTQP-ASDIYEDEGILMIS--------PGATNPELT 107 d1s3la_ 69 EWLKDI--NEENIIDDFISVEIDDLKFFITHGHHQSVLEMAIKSGLYDVVIYGHTHERVF 126 : :::::: d1usga_ 108 Q-----RGYQHIMR---------------------------------------------- 116 d1s3la_ 127 EEVDDVLVINPGECCGYLTGIPTIGILDTEKKEYREIVL--------------------- 165 d1usga_ 117 ---------------------------------------TAGLDSSQGPTAAKYILETVK 137 d1s3la_ 166 ------------------------------------------------------------ 166 d1usga_ 138 PQRIAIIHDKQQYGEGLARSVQDGLKAANANVVFFDGITAGEKDFSALIARLKKENIDFV 197 d1s3la_ 166 ------------------------------------------------------------ 166 d1usga_ 198 YYGGYYPEMGQMLRQARSVGLKTQFMGPEGVGNASLSNIAGDAAEGMLVTMPKRYDQDPA 257 d1s3la_ 166 ------------------------------------------------------------ 166 d1usga_ 258 NQGIVDALKADKKDPSGPYVWITYAAVQSLATALERTGSDEPLALVKDLKANGANTVIGP 317 d1s3la_ 166 ---------------------------- 166 d1usga_ 318 LNWDEKGDLKGFDFGVFQWHADGSSTKA 345 TMalign alignment (TM-score: 0.40 Raw score:66.36) d1s3la_ 1 ------------------------------------------------------------ 1 d1usga_ 1 DDIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAKGGIKGDKLVGVEYDDACDPKQAVA 60 d1s3la_ 1 -----------------------------------------------------------M 1 d1usga_ 61 VANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMISPGATNPELTQRGYQHIMRTAG- 119 d1s3la_ 2 KIGIMSDTHDHLPNIRKAIEIFNDE-NVE-TVIHCG-DFVSLFV-IKEFENL----NANI 53 :::::::::::::::: ::: :::::: ::::::: ::::::: :::: d1usga_ 120 ---------LDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARSVQDGLKAANANVV 170 d1s3la_ 54 IATYGNNDGERCKLKEWLKDINEENIIDD-----F--ISV--E-IDDL-KF-FI-THGHH 100 :::::: : ::: : :::: : : ::::: d1usga_ 171 -----------------------FFDGITAGEKDFSALIARLKKENIDF-VY-YGGYYPE 205 d1s3la_ 101 QSVLEMAIKSGLYDV-V-IYG---HTHE-RV--FEEVDDVLVIN-PGECCGY-------- 143 :::::::: ::::: : ::: :::: :: :: :::: ::::::: d1usga_ 206 MGQMLRQA--RSVGLKTQFMGPEGVGNASLSNI--AG---DAAEGMLVTMPKRYDQDPAN 258 d1s3la_ 144 ---------------LTG------------------------------------------ 146 :: d1usga_ 259 QGIVDALKADKKDPS-GPYVWITYAAVQSLATALERTGSDEPLALVKDLKANGANTVIGP 317 d1s3la_ 147 -------------IPTIGI-----LDTEKKEYREIVL 165 :::::: :::: d1usga_ 318 LNWDEKGDLKGFDFGVFQWHADGS---------STKA 345 HHsearch alignment (Probability: 0.17 E-value:0.01) d1s3la_ 4 GIMSDTHDHLPNIRKAIEIFNDENVETVI-HCGDFVSLFVIKEFENLNANIIA 55 ::::::::::::::::::::::::::::: ::::::::::::::::::::::: d1usga_ 46 GVEYDDACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMIS 98