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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1ru8a_ | Putative N-type ATP pyrophosphatase PF0828 | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1fmta2 | Methionyl-tRNAfmet formyltransferase | Formyltransferase | Formyltransferase | α/β |
Query <-- 0.947 --> IntermediateDALI alignment (Z-score: 7.4 Raw score:643.70) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1ru8a_ 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1ru8a_ 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1ru8a_ 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1ru8a_ 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1ru8a_ 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvaknGFRSVLIGLSGGIDSALVAAIACDALgaqNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1ru8a_ 1 -----------------------GLADVAVLYSGGKDSNYALYWAIKNR-fsVKFLVTMV 36 query 361 SKYS-----sDHSKGdAAELARRTGLNFRTVSIEpmfdaymaslgltglaEENLQSRLRG 415 :::: ::::: :::::::::::::::::: :::::::::: d1ru8a_ 37 SENEesymytINANL-TDLQARALGIPLVKGFTQ---------------gEKEKEVEDLK 80 query 416 TTLMAIsnqEGHIVLAPGnkselavGYSTlyGDSVG------AYGPIKDVYKTSIFRLAE 469 :::::: ::::::::: :::: ::::: :::::::::::::::::: d1ru8a_ 81 RVLSGL---KIQGIVAGA------sKYQRkrIEKVAkelgleVYTPAWGRDAKEYMRELL 131 query 470 WRN------------------------------------raaaergqtppipEASItkpd 493 ::: :::: d1ru8a_ 132 NLGfkimvvgvsaygldeswlgrildesaleelitlnekykvhvageggefeTFVL---- 187 query 494 ypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfg 553 d1ru8a_ 188 -----------------------------------dmplfkykivvdkakkvwepctssg 212 query 554 kdrrlpitnrwregh 568 d1ru8a_ 213 kliieeahleskleh 227 FAST alignment (Normalized score: 3.54 Raw score:1270.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1ru8a_ 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1ru8a_ 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1ru8a_ 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1ru8a_ 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1ru8a_ 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQN-----VY 355 :::::::::::::::::::::::: :: d1ru8a_ 1 -----------------------GLADVAVLYSGGKDSNYALYWAIK------NRFSVKF 31 query 356 GVSMPSKYS----SDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLA---EEN 408 ::::::::: ::::::::::::::::::::::: ::: d1ru8a_ 32 LVTMVSENEESYMYTINANLTDLQARALGIPLVKGF------------------TQGEKE 73 query 409 LQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLY-----GDSVG-----------A 452 :::::::::::: ::: ::::: :::: : d1ru8a_ 74 KEVEDLKRVLSG--LKI-QGIVA---------------GASKYQRKR-IEKVAKELGLEV 114 query 453 YGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKP-------------------- 492 :::::::::::::::::: d1ru8a_ 115 YTPAWGRDAKEYMRELLN----------------------LGFKIMVVGVSAYGLDESWL 152 query 493 ----------DYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYP 542 :::::::: d1ru8a_ 153 GRILDESALEELITLNEK------------------------------------------ 170 query 543 PGTKISAKGFGKDRRLPITNRWREGH---------------------------------- 568 d1ru8a_ 171 --------------------------YKVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKV 204 query 569 ----------------------- 569 d1ru8a_ 205 WEPCTSSGKLIIEEAHLESKLEH 227 TMalign alignment (TM-score: 0.21 Raw score:120.91) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1ru8a_ 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1ru8a_ 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1ru8a_ 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1ru8a_ 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1ru8a_ 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 ::::::::::::::::::::::::::: ::::::::: d1ru8a_ 1 -----------------------GLADVAVLYSGGKDSNYALYWAIKNRF-SVKFLVTMV 36 query 361 SKYS-S---DHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGT 416 :::: : :::::::::::::::::::::::: : : ::::::::: d1ru8a_ 37 SENEESYMYTINANLTDLQARALGIPLVKGFTQ--G-------------E-KEKEVEDLK 80 query 417 TLMAISNQEGHIVLAPGNKSELAVGYSTL-YGDSV-G------AYGPIKDVYKTSIFRLA 468 :::::: ::::::::: :: : :: :::: : ::::::::::::::::: d1ru8a_ 81 RVLSGL--KIQGIVAGA---SK--Y--QRK-RIEKVAKELGLEVYTPAWGRDAKEYMREL 130 query 469 EWRNRAAAERGQTPPIPEASITK---P-DY----------------PVLDAILELYVDRD 508 ::: : : : :::: : :: ::::: d1ru8a_ 131 LNL-G----------F-K-IMVVGVSAYGLDESWLGRILDESALEELITLN--------- 168 query 509 TGADAIVAAGYDRELV-------------------------------------------- 524 ::: :: d1ru8a_ 169 ---------EKY--KVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWEPCTSSGKLIIE 217 query 525 ----------VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1ru8a_ 218 EAHLESKLEH-------------------------------------------- 227 HHsearch alignment (Probability: 0.87 E-value:0.00) query 324 GFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHS---KGDAAELARRTG 380 ::::::::::::::::::::::::::::::::::::::::::::: :::::::::::: d1ru8a_ 1 GLADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYMYTINANLTDLQARALG 60 query 381 LNFRTVSIEPMFDAYMASL 399 ::::::::::::::::::: d1ru8a_ 61 IPLVKGFTQGEKEKEVEDL 79
Intermediate <-- 0.992 --> HitDALI 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