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_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.159 --> Intermediate <-- 0.992 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1fmta2) through the intermediate protein (d1ru8a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ru8a_ Putative N-​type ATP pyrophosphatase PF0828Adenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1fmta2 Methionyl-​tRNAfmet formyltransferaseFormyltransferaseFormyltransferaseα/β

Supporting Alignments

Query <-- 1.159 --> Intermediate
DALI alignment (Z-score: 6.9 Raw score:641.00) query 1 dadeevysalvvglrayvaknGFRSVLIGLSGGIDSALVAAIACDALgaqNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1ru8a_ 1 ---------------------GLADVAVLYSGGKDSNYALYWAIKNR-fsVKFLVTMVSE 38 query 61 YS-----sDHSKGdAAELARRTGLNFRTVSIEpmfdaymaslgltglaEENLQSRLRGTT 115 :: ::::: :::::::::::::::::: :::::::::::: d1ru8a_ 39 NEesymytINANL-TDLQARALGIPLVKGFTQ---------------gEKEKEVEDLKRV 82 query 116 LMAIsnqEGHIVLAPGnkselavGYSTlyGDSVG------AYGPIKDVYKTSIFRLAEWR 169 :::: ::::::::: :::: ::::: :::::::::::::::::::: d1ru8a_ 83 LSGL---KIQGIVAGA------sKYQRkrIEKVAkelgleVYTPAWGRDAKEYMRELLNL 133 query 170 N------------------------------------raaaergqtppipEASItkpdyp 193 : :::: d1ru8a_ 134 GfkimvvgvsaygldeswlgrildesaleelitlnekykvhvageggefeTFVL------ 187 query 194 vldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkd 253 d1ru8a_ 188 ---------------------------------dmplfkykivvdkakkvwepctssgkl 214 query 254 rrlpitnrwregh 266 d1ru8a_ 215 iieeahleskleh 227 FAST alignment (Normalized score: 5.12 Raw score:1259.00) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQN-----VYGV 55 :::::::::::::::::::::::: :::: d1ru8a_ 1 ---------------------GLADVAVLYSGGKDSNYALYWAIK------NRFSVKFLV 33 query 56 SMPSKYSSDHS--------KGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLA---E 104 ::::::: ::::::::::::::::::: : d1ru8a_ 34 TMVSENE----ESYMYTINANLTDLQARALGIPLVKGF------------------TQGE 71 query 105 ENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLY-----GDSVG---------- 149 :::::::::::::: ::: ::::: :::: d1ru8a_ 72 KEKEVEDLKRVLSG--LKI-QGIVA---------------GASKYQRKR-IEKVAKELGL 112 query 150 -AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKP------------------ 190 ::::::::::::::::::: d1ru8a_ 113 EVYTPAWGRDAKEYMRELLN----------------------LGFKIMVVGVSAYGLDES 150 query 191 ------------DYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQ 238 :::::::: d1ru8a_ 151 WLGRILDESALEELITLNEK---------------------------------------- 170 query 239 YPPGTKISAKGFGKDRRLPITNRWREGH-------------------------------- 266 d1ru8a_ 171 ----------------------------YKVHVAGEGGEFETFVLDMPLFKYKIVVDKAK 202 query 267 ------------------------- 267 d1ru8a_ 203 KVWEPCTSSGKLIIEEAHLESKLEH 227 TMalign alignment (TM-score: 0.41 Raw score:109.76) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 ::::::::::::::::::::::::::: ::::::::::: d1ru8a_ 1 ---------------------GLADVAVLYSGGKDSNYALYWAIKNRF-SVKFLVTMVSE 38 query 61 YS-S---DHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTL 116 :: : :::::::::::::::::::::::: : : ::::::::::: d1ru8a_ 39 NEESYMYTINANLTDLQARALGIPLVKGFTQ--G-------------E-KEKEVEDLKRV 82 query 117 MAISNQEGHIVLAPGNKSELAVGYSTL-YGDSV-G------AYGPIKDVYKTSIFRLAEW 168 :::: ::::::::: :: : :: :::: : ::::::::::::::::::: d1ru8a_ 83 LSGL--KIQGIVAGA---SK--Y--QRK-RIEKVAKELGLEVYTPAWGRDAKEYMRELLN 132 query 169 RNRAAAERGQTPPIPEASITK---P-DY----------------PVLDAILELYVDRDTG 208 : : : : :::: : :: ::::: d1ru8a_ 133 L-G----------F-K-IMVVGVSAYGLDESWLGRILDESALEELITLN----------- 168 query 209 ADAIVAAGYDRELV---------------------------------------------- 222 ::: :: d1ru8a_ 169 -------EKY--KVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWEPCTSSGKLIIEEA 219 query 223 --------VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1ru8a_ 220 HLESKLEH-------------------------------------------- 227 HHsearch alignment (Probability: 0.94 E-value:0.00) query 22 GFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHS----KGDAAELARRT 77 ::::::::::::::::::::::::: ::::::::::::::::::: ::::::::::: d1ru8a_ 1 GLADVAVLYSGGKDSNYALYWAIKN-RFSVKFLVTMVSENEESYMYTINANLTDLQARAL 59 query 78 GLNFRTVSIEPMFDAYMASL 97 :::::::::::::::::::: d1ru8a_ 60 GIPLVKGFTQGEKEKEVEDL 79
Intermediate <-- 0.992 --> Hit
DALI alignment (Z-score: 7.8 Raw score:496.60) d1ru8a_ 1 -GLADVAVLYSGGKdSNYALYWAIKNRFSVKFLVTMVseneesymytINANLT-DLQARA 58 ::::::::::::: :::::::::::::::::::::: :::::: :::::: d1fmta2 1 sESLRIIFAGTPDF-AARHLDALLSSGHNVVGVFTQP--------drPLMPSPvKVLAEE 51 d1ru8a_ 59 LGIPLVKGFTqgekekEVEDLKRVLSGLKIQGIVAGaskyqrkRIEKVAKEL-GLEVYTp 117 :::::::::: :::::::::::::::::::: ::::::::: :::::: d1fmta2 52 KGLPVFQPVS-----lRPQENQQLVAELQADVMVVV---ayglILPKAVLEMpRLGCIN- 102 d1ru8a_ 118 AWGRD---------------------------------------------------akEY 126 ::::: :: d1fmta2 103 VHGSLlprwrgaapiqrslwagdaetgvtimqmdvgldtgdmlyklscpitaedtsgtLY 162 d1ru8a_ 127 MRELLNlgfkimvvgvsaygldeswlgrildesaleelitlnekykvhvageggefetfv 186 :::::: d1fmta2 163 DKLAEL------------------------------------------------------ 168 d1ru8a_ 187 ldmplfkykivvdkakkvwepctssgkliieeahleskleh 227 d1fmta2 169 ---------gpqglittlkqladgtakpevqdetlvtyaek 200 FAST alignment (Normalized score: 4.30 Raw score:916.90) d1ru8a_ 1 GL---ADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEES---YMYTINANLTDL 54 ::::::: :::::::::::::::::::::::: :::: :::::: d1fmta2 1 --SESLRIIFAG-TPDFAARHLDALLSSGHNVVGVFT--------QPDRPLM--PSPVKV 47 d1ru8a_ 55 QARALGIPLVKGFTQGEKEKE----VEDLKRVLSGLKIQGIVAGASKYQ-------RKRI 103 :::::::::::: :::::::::::::::::: :::: d1fmta2 48 LAEEKGLPVFQP---------VSLRPQENQQLVAELQADVMVV------VAYGLILPKAV 92 d1ru8a_ 104 EKVAKELGL---EVYTPAWGR--------------------------------------- 121 ::: :::: d1fmta2 93 LEM------PRLGCIN-----VHGSLLPRWRGAAPIQRSLWAGDAETGVTIMQMDVGLDT 141 d1ru8a_ 122 ----------------DAKEYMRELLNLGFKIMVVGVSAYGLDESWLGRILDESALEELI 165 :::::::::: d1fmta2 142 GDMLYKLSCPITAEDTSGTLYDKLAE---------------------------------- 167 d1ru8a_ 166 TLNEKYKVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWEPCTSSGKLIIEEAHLESKL 225 d1fmta2 168 ------------------------------------------------------------ 168 d1ru8a_ 226 EH--------------------------------- 227 d1fmta2 168 --LGPQGLITTLKQLADGTAKPEVQDETLVTYAEK 200 TMalign alignment (TM-score: 0.39 Raw score:87.70) d1ru8a_ 1 -GLADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYMYTINANLTDLQARAL 59 ::::::::::::: ::::::::::::::::::::::: : : : ::::::::::: d1fmta2 1 SESLRIIFAGTPDF-AARHLDALLSSGHNVVGVFTQPD--R-P---L-MPSPVKVLAEE- 51 d1ru8a_ 60 GIPLVKGFTQGEKEKEVE-DLKRVLSGLKIQGIVAGAS-KYQRKRIEKVAKELGLEVYTP 117 ::::::::: :::: ::::::::::::::::::: :: ::::::: :::::::: d1fmta2 52 KGLPVFQPV-----SLRPQENQQLVAELQADVMVVVAYG-LI--LPKAVLE-MPRLGCIN 102 d1ru8a_ 118 AWGRD---------A---------KEYM---------------------RELLNLGFKIM 138 ::::: : :::: d1fmta2 103 VHGSLLPRWRGAAPIQRSLWAGDAETGVTIMQMDVGLDTGDMLYKLSCP----------- 151 d1ru8a_ 139 VVGVSAYGLDESWLGRILDESALEELI-TLNEKYKVHVA---GEGGEFETF---VLDM-- 189 :::::::: :: : : d1fmta2 152 -------------------ITAEDTSGT---------LYDKL--------AELG---PQG 172 d1ru8a_ 190 ---------------------------PLFKYKIVVDKAKKVWEPCTSSGKLIIEEAHLE 222 : d1fmta2 173 LITTLKQLADGTAKPEVQDETLVTYAE---------------------K----------- 200 d1ru8a_ 223 SKLEH 227 d1fmta2 201 ----- 201 HHsearch alignment (Probability: 0.72 E-value:0.00) d1ru8a_ 6 AVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYMYTINANLTDLQARALGIPLVK 65 :::::::::::::::::::::::::::::::::: ::::::::::::::::::: d1fmta2 6 IIFAGTPDFAARHLDALLSSGHNVVGVFTQPDRP-------LMPSPVKVLAEEKGLPVFQ 58 d1ru8a_ 66 GFTQGEKEKEVEDLKRVLSGLKIQGIVA-GASKY 98 ::::: :::::::::::::::::: ::::: d1fmta2 59 PVSLR-----PQENQQLVAELQADVMVVVAYGLI 87