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 <-- 2.134 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1g5ba_) 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 d1g5ba_ lambda ser/​thr protein phosphataseMetallo-​dependent phosphatasesMetallo-​dependent phosphatasesα+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 <-- 2.134 --> Hit
DALI alignment (Z-score: 9.2 Raw score:780.10) d1s3la_ 1 ------------MKIGIMSDTHDHLPNIRKAIEIfNDEN--vETVIHCGDFV-----SLF 41 :::::::::::::::::::::: :::: :::::::::: ::: d1g5ba_ 1 mryyekidgskyRNIWVVGDLHGCYTNLMNKLDT-IGFDnkkDLLISVGDLVdrgaeNVE 59 d1s3la_ 42 VIKEFEnlnANIIATYGNNDG------------------------------------ERC 65 :::::: :::::::::::: ::: d1g5ba_ 60 CLELIT--fPWFRAVRGNHEQmmidglsergnvnhwllngggwffnldydkeilakaLAH 117 d1s3la_ 66 KLKEwlkdineeniIDDFISVEIDDLKFFITHG-------------------HHQSV--- 103 :::: ::::::::::::::::::: ::::: d1g5ba_ 118 KADE----------LPLIIELVSKDKKYVICHAdypfdeyefgkpvdhqqviWNRERisn 167 d1s3la_ 104 --lemaiKSGLYDVVIYGHTHE--RVFEEvddvLVINPGEccGYLTGIPTIGILDTEkke 159 ::::::::::::::: ::::: ::::::: ::::::::::::::: d1g5ba_ 168 sqngivkEIKGADTFIFGHTPAvkPLKFA----NQMYIDT-gAVFCGNLTLIQVQGA--- 219 d1s3la_ 160 yreivl 165 d1g5ba_ 220 ------ 220 FAST alignment (Normalized score: 6.43 Raw score:1223.00) d1s3la_ 1 ------------MKIGIMSDTHDHLPNIRKAIEIFNDENV-------ETVIHCGDFV--- 38 :::::::::::::::::::::: :::::::: d1g5ba_ 1 MRYYEKIDGSKYRNIWVVGDLHGCYTNLMNKLDT------IGFDNKKDLLISVGD--LVD 52 d1s3la_ 39 ----SLFVIKEFENLNA--NIIATYGNNDGE----------------------------- 63 ::::::::: ::::::::: d1g5ba_ 53 RGAENVECLELIT----FPWFRAVRGNH---EQMMIDGLSERGNVNHWLLNGGGWFFNLD 105 d1s3la_ 64 ------RCKLKEWLKDINEENI---IDDFISVEIDDLKFFITH----------------- 97 ::::::: ::::::::::::::::: d1g5ba_ 106 YDKEILAKALAHK---------ADELPLIIELVSKDKKYVIC-HADYPFDEYEFGKPVDH 155 d1s3la_ 98 ---GHHQSVLEMAI--------KSGLYDVVIYGHTHE----RVFEEVDDVLVIN-PGECC 141 :::::::: ::::::::::: ::::::: :::: :::: d1g5ba_ 156 QQVIWNRERIS---NSQNGIVKEIKGADTFIFG----HTPAVKPLKFA--NQMYIDTGA- 205 d1s3la_ 142 GYLTGIPTIGILDTEKKEYREIVL---- 165 :::::::::: d1g5ba_ 206 -VFCGNLTLIQ-------------VQGA 219 TMalign alignment (TM-score: 0.63 Raw score:103.56) d1s3la_ 1 ------------MKIGIMSDTHDHLPNIRKAIEIFNDEN--VETVIHCGDFV-----SLF 41 ::::::::::::::::::::::: ::: ::::::::::: ::: d1g5ba_ 1 MRYYEKIDGSKYRNIWVVGDLHGCYTNLMNKLDTI-GFDNKKDLLISVGDLVDRGAENVE 59 d1s3la_ 42 VIKEFENLNANIIATYGNND--GE----------------------------------RC 65 :::::: : ::::::::::: :: :: d1g5ba_ 60 CLELIT-F-PWFRAVRGNHEQMMIDGLSERGNVNHWLLNGGGWFFNLDYDKEILAKALAH 117 d1s3la_ 66 KLKEWLKDINEENIIDDFISVEIDDLKFFITHG-------------------HHQSVL-- 104 :::: ::::::::::::::::::: :::::: d1g5ba_ 118 KADE----------LPLIIELVSKDKKYVICHADYPFDEYEFGKPVDHQQVIWNRERISN 167 d1s3la_ 105 E-----MAIKSGLYDVVIYGHTHE-RVFEEVDDVLVINPGECCGYLTGIPTIGILDTEKK 158 : :::::::::::::::: :::::: : ::::::: ::: :::::::::::: d1g5ba_ 168 SQNGIV--KEIKGADTFIFGHTPAVKPLKFA--N-QMYIDTG-AVF-CGNLTLIQVQGA- 219 d1s3la_ 159 EYREIVL 165 d1g5ba_ 220 ------- 220 HHsearch alignment (Probability: 1.00 E-value:0.00) d1s3la_ 2 KIGIMSDTHDHLPNIRKAIEIFN-DENVETVIHCGDFVSLFV-----IKEFENLNANIIA 55 ::::::::::::::::::::::: :::::::::::::::::: :::::: ::::: d1g5ba_ 14 NIWVVGDLHGCYTNLMNKLDTIGFDNKKDLLISVGDLVDRGAENVECLELITF--PWFRA 71 d1s3la_ 56 TYGNNDGERCKLKEWL--------------------------KDINEENIIDDFISVEID 89 :::::::::::::::: :::::::::::::::::: d1g5ba_ 72 VRGNHEQMMIDGLSERGNVNHWLLNGGGWFFNLDYDKEILAKALAHKADELPLIIELVSK 131 d1s3la_ 90 DLKFFITHGHHQSVLE------------------------MAIKSGLYDVVIYGHTHERV 125 :::::::::::::::: :::::::::::::::::::: d1g5ba_ 132 DKKYVICHADYPFDEYEFGKPVDHQQVIWNRERISNSQNGIVKEIKGADTFIFGHTPAVK 191 d1s3la_ 126 FEEVDDVLVINPGECCGYLTGIPTIGILD 154 :::::::::::::::: :::::::::: d1g5ba_ 192 PLKFANQMYIDTGAVF---CGNLTLIQVQ 217