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 <-- 0.726 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1nata_) 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 d1nata_ Sporulation response regulator Spo0FCheY-​likeFlavodoxin-​likeα/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 <-- 0.726 --> Hit
DALI alignment (Z-score: 4.7 Raw score:326.90) d1s3la_ 1 -MKIGIMSD-----------------thdhlpNIRKAIEIFNDENVETVIHCGDFvslFV 42 :::::::: ::::::::::::::::::::::: :: d1nata_ 1 nEKILIVDDqygirillnevfnkegyqtfqaaNGLQALDIVTKERPDLVLLDMKIpgmDG 60 d1s3la_ 43 IKEFENLN-----ANIIATYgnnDGERCKLKEWLKDINeeNIIDD------fISVE---I 88 :::::::: ::::::: ::::::::::::::: ::::: :::: : d1nata_ 61 IEILKRMKvidenIRVIIMT---AYGELDMIQESKELG-aLTHFAkpfdideIRDAvkkY 116 d1s3la_ 89 DDLkffithghhqsvlemaiksglydvviyghthervfeevddvlvinpgeccgyltgip 148 ::: d1nata_ 117 LPL--------------------------------------------------------- 119 d1s3la_ 149 tigildtekkeyreivl 165 d1nata_ 120 ----------------- 120 FAST alignment (Normalized score: 3.26 Raw score:456.80) d1s3la_ 1 -MKIGIMSDTHDHLP-------------------------NIRKAIEIFNDENVETVIHC 34 :::::: :::::::::::::::::::: d1nata_ 1 NEKILIV--------DDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLD 52 d1s3la_ 35 GDFVSL-----FVIKEFEN-----LNANIIATYGNNDGERCKLKEWLKDINEE---NIID 81 : :::::::: :::::::::::: :::::::::: :::: d1nata_ 53 M-----KIPGMDGIEILKRMKVIDENIRVIIMTAYG---ELDMIQESKE----LGALTHF 100 d1s3la_ 82 -DFISVEIDDLKFFITHGHHQSVLEMAIKSGLYDVVIYGHTHERVFEEVDDVLVINPGEC 140 :::: d1nata_ 101 AKPFD------------------------------------------------------- 105 d1s3la_ 141 CGYLTGIPTIGILDTEKKEYREIVL-------------- 165 d1nata_ 106 -------------------------IDEIRDAVKKYLPL 119 TMalign alignment (TM-score: 0.40 Raw score:65.82) d1s3la_ 1 -MKIGIMSDT---------------------HDHLPNIRKAIEIFNDENVETVIHCGDFV 38 ::::::::: :::::::::::::::::::: :::: d1nata_ 1 NEKILIVDDQYGIRILLNEVFNKEGYQTFQA----ANGLQALDIVTKERPDLVLL-DMKI 55 d1s3la_ 39 S-LFVIKEFENL---N--ANIIATYGNNDGERCKLKEWLKDINEENIIDD--F----I-S 85 : :::::::::: : ::::::: ::::::::::::::: :::::: : : : d1nata_ 56 PGMDGIEILKRMKVIDENIRVIIMT---AYGELDMIQESKELG-ALTHFAKPFDIDEIRD 111 d1s3la_ 86 V-E--IDDLKFFITHGHHQSVLEMAIKSGLYDVVIYGHTHERVFEEVDDVLVINPGECCG 142 : : ::: d1nata_ 112 AVKKYLPL---------------------------------------------------- 119 d1s3la_ 143 YLTGIPTIGILDTEKKEYREIVL 165 d1nata_ 120 ----------------------- 120 HHsearch alignment (Probability: 0.35 E-value:0.01) d1s3la_ 17 RKAIEIFNDENVETVIHC---GDFVSLFVIKEFENLN--ANIIATYGNNDGE 63 :::::::::::::::::: :::::::::::::::: ::::::::::::: d1nata_ 35 LQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELD 86