HorA Server Transitive Detail

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


Query <-- 1.015 --> Intermediate <-- 0.765 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1dbqa_) through the intermediate protein (d1s3la_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1s3la_ Putative phosphodiesterase MJ0936Metallo-​dependent phosphatasesMetallo-​dependent phosphatasesα+β
Hit d1dbqa_ Purine repressor (PurR),​ C-​terminal domainPeriplasmic binding protein-​like IPeriplasmic binding protein-​like Iα/β

Supporting Alignments

Query <-- 1.015 --> Intermediate
DALI 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 <-- 0.765 --> Hit
DALI alignment (Z-score: 4.4 Raw score:328.60) d1s3la_ 1 MKIGIMSD-----------------------------THDHLPNIRKAIEIFNDENVETV 31 :::::::: ::::::::::::::::::::::: d1dbqa_ 1 KSIGLLATsseaayfaeiieavekncfqkgytlilgnAWNNLEKQRAYLSMMAQKRVDGL 60 d1s3la_ 32 IHCGDFVSLFVIKEFENL-NANIIATYGNndgerCKLKewlkdineenIIDD-------- 82 :::::::::::::::::: :::::::::: :::: :::: d1dbqa_ 61 LVMCSEYPEPLLAMLEEYrHIPMVVMDWG---eaKADF----------TDAVidnafegg 107 d1s3la_ 83 ------------------------------------------------------------ 83 d1dbqa_ 108 ymagrylierghreigvipgpagrlagfmkameeamikvpeswivqgdfepesgyramqq 167 d1s3la_ 83 ------------------------------------------------------------ 83 d1dbqa_ 168 ilsqphrptavfcggdimamgalcaademglrvpqdvsligydnvrnaryftpalttihq 227 d1s3la_ 83 ----FISV----eIDDLkffithghhqsVLEMaiksglydvviyghthervfeevddvlv 134 :::: :::: :::: d1dbqa_ 228 pkdsLGETafnmlLDRIvnkreepqsieVHPR---------------------------- 259 d1s3la_ 135 inpgeccgyltgiptigildtekkeyreivl 165 d1dbqa_ 260 --------------lierrsvadgpfrdyrr 276 FAST alignment (Normalized score: 2.62 Raw score:558.90) d1s3la_ 1 MKIGIM-----------------------------SDTHDHLPNIRKAIEIFNDENVETV 31 :::::: ::::::::::::::::::::::::: d1dbqa_ 1 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGL 60 d1s3la_ 32 IHCGDF--VSLFVIKEFEN-LNANIIATYGNNDGERCKLKEWLKDIN-EENIIDDFISVE 87 :::: ::::::::::: ::::::::: ::::: :::: d1dbqa_ 61 LVMC--SEYPEPLLAMLEEYRHIPMVVMD---WGEAK----------ADFTD-------- 97 d1s3la_ 88 IDDLKFFITHG------------------------------------------------- 98 d1dbqa_ 98 -----------AVIDNAFEGGYMAGRYLIERGHREIGVIPGPAGRLAGFMKAMEEAMIKV 146 d1s3la_ 99 ---------HHQSVLEMAIKSGLYDVVIYGHTHERVFEEVDDVLVINPGECCGYLTGIPT 149 ::::::::::: d1dbqa_ 147 PESWIVQGDFEPESGYRAMQ---------------------------------------- 166 d1s3la_ 150 IGILDTEKKEYREIVL-------------------------------------------- 165 d1dbqa_ 167 ----------------QILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYD 210 d1s3la_ 166 ------------------------------------------------------------ 166 d1dbqa_ 211 NVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGP 270 d1s3la_ 166 ------ 166 d1dbqa_ 271 FRDYRR 276 TMalign alignment (TM-score: 0.40 Raw score:65.40) d1s3la_ 1 MKIGIMSD-----------------------------THDHLPNIRKAIEIFNDENVETV 31 :::::::: ::::::::::::::::::::::: d1dbqa_ 1 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGL 60 d1s3la_ 32 IHCGDFVSLFVIKEFENL-NANIIATYGNNDGERCKLKEWLKDINEENIIDDF------- 83 :::::::::::::::::: ::::::::: : ::: :::: ::::: d1dbqa_ 61 LVMCSEYPEPLLAMLEEYRHIPMVVMDW--G--EAK--ADFT------DAVIDNAFEGGY 108 d1s3la_ 84 ------------------------------------------------------------ 84 d1dbqa_ 109 MAGRYLIERGHREIGVIPGPAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQI 168 d1s3la_ 84 ------------ISVEIDDLKFFITHGHHQ--------------------------SVLE 105 ::: :::: d1dbqa_ 169 LSQPHRPTAVFC---------------GGDIMAMGALCAADEMGLRVPQDVSLIGYDNVR 213 d1s3la_ 106 --------------MAIKSGLYDVVI---------------------------------- 117 ::: : ::: d1dbqa_ 214 NARYFTPALTTIHQPKD----S-LGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVAD 268 d1s3la_ 118 --------YGHTHERVFEEVDDVLVINPGECCGYLTGIPTIGILDTEKKEYREIVL 165 d1dbqa_ 269 GPFRDYRR------------------------------------------------ 276 HHsearch alignment (Probability: 0.67 E-value:0.00) d1s3la_ 4 GIMSDTHDHLPNIRKAIEIFNDENVETVIHCGDFVSLFVIKEFENL-NANIIATY 57 :::::::::::::::::::::::::::::::::::::::::::::: :::::::: d1dbqa_ 33 LILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMD 87