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: T0542_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.956 --> Intermediate <-- 0.726 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) 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 <-- 1.956 --> Intermediate
DALI alignment (Z-score: 6.1 Raw score:664.70) query 1 slqLRLALNqidstvgdiagNAEAILRWTRHSAEQGAHLVAFPEMALTgypvedlalrss 60 :::::: :::::::::::::::::::::::::::: d1s3la_ 1 ---MKIGIM------sdthdHLPNIRKAIEIFNDENVETVIHCGDFVS------------ 39 query 61 fveasrtalRELAARLaeEGFGeLPVLV---gYLDRsesaqpkygqpagaprnaaavlhR 117 ::::::: :::: ::::: :::: : d1s3la_ 40 ---------LFVIKEF--ENLN-ANIIAtygnNDGE-------------rcklkewlkdI 74 query 118 GRVALTFAkhhlpnygvfdefryfvpgdtmPIVRLHGVDIALAICEDLwqdgGRVPAAR- 176 :::::::: :::::::::::::::::: ::::::: d1s3la_ 75 NEENIIDD---------------------fISVEIDDLKFFITHGHHQ----SVLEMAIk 109 query 177 SAGAGLLLSVNASpyerdkddtrlelvrkRAQEaGCTTAYLAM-IGGQdelvfdgdsivv 235 ::::::::::::: :::: ::::::::: :::: d1s3la_ 110 SGLYDVVIYGHTH------------ervfEEVD-DVLVINPGEcCGYL------------ 144 query 236 drdgevvarapQFSEGCVVLDLDLpaaeaepptgvvddglridrlviseeplpayeaela 295 ::::::::::::: d1s3la_ 145 -----------TGIPTIGILDTEK-----------------------------------k 158 query 296 ggyadrl 302 d1s3la_ 159 eyreivl 165 FAST alignment (Normalized score: 4.01 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 DRL----------- 302 d1s3la_ 155 ---TEKKEYREIVL 165 TMalign alignment (TM-score: 0.40 Raw score:119.85) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 ::::::::::: :: :::::::::::::::::::::::::: d1s3la_ 1 ---MKIGIMSDTHD-----HL-PNIRKAIEIFNDENVETVIHCGDFVS------------ 39 query 61 FVEASRTALRELAARLAEEGFGELPVLVGY--LDRSE-SAQPKYGQPAGAPRNAAA-VLH 116 : :: ::: :: ::: :::::::: ::::: ::: :: d1s3la_ 40 ----L--FV-IKE-FE--NLN-ANIIATYGNNDGERCK---------------LKEW-LK 72 query 117 -RGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAA 175 ::::::::: :::::::::::::::::: :: :::::: d1s3la_ 73 DINEENIIDD---------------------FISVEIDDLKFFITHGHH-QS--VLEMAI 108 query 176 RSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAM-IGGQDELVFDGDSIV 234 :::::::::::::: :: ::: ::: ::::::::: ::: :: d1s3la_ 109 KSGLYDVVIYGHTH---------ER-VFE--EVD-DVLVINPGECCGY-----LT----- 145 query 235 VDRDGEVVARAPQFSEGCVVLDL-DLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAE 293 :::::::::: :: d1s3la_ 146 -------------GIPTIGILDTEKK---------------------------------- 158 query 294 LAGGYA-DRL 302 :::::: d1s3la_ 159 EYREIVL--- 165 HHsearch alignment (Probability: 0.38 E-value:0.00) query 4 LRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAF 42 ::::::: :::::::::::::::::::::::::: d1s3la_ 1 MKIGIMS------DTHDHLPNIRKAIEIFNDENVETVIH 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