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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1k92a1 | Argininosuccinate synthetase, N-terminal domain | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1m1na_ | Nitrogenase iron-molybdenum protein, alpha chain | (Helical backbone( metal receptor | Chelatase-like | α/β |
Query <-- 1.588 --> IntermediateDALI alignment (Z-score: 11.2 Raw score:922.90) query 1 dadeevysalvvGLRAyvakngfRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMPSK 60 :::: ::::::::::::::::::::::::: :::::::::: d1k92a1 1 -------ttilkHLPV------gQRIGIAFSGGLDTSAALLWMRQKGA--VPYAYTANLG 45 query 61 Y-SSDHsKGDAAELARRTGL-NFRTVSIEPMFDAYMASLG-----------ltGLAEENL 107 : :::: ::::::::::::: ::::::::::::::::::: ::::::: d1k92a1 46 QpDEED-YDAIPRRAMEYGAeNARLIDCRKQLVAEGIAAIqcgafhnttggltYFNTTPL 104 query 108 QSRLRGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIKD- 156 :::::::::::::::::: :::::::: :::: :::: ::::::: d1k92a1 105 GRAVTGTMLVAAMKEDGVnIWGDGSTY-----KGNDierFYRYglltnaelqIYKPWLDt 159 query 157 --vyktSIFRLAEWRNRAAAergqtppipeasITKPDYpvldailelyvdrdtgadaiva 214 :::::::::::::: :::::: d1k92a1 160 dfidelGGRHEMSEFMIACG---------fdyKMSVEK---------------------- 188 query 215 agydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1k92a1 189 ---------------------------------------------------- 189 FAST alignment (Normalized score: 6.79 Raw score:1519.00) query 1 DADEEVYSALVVGLRAYVAKNGF----------RSVLIGLSGGIDSALVAAIACDALGAQ 50 :::::::::::::::::::::: d1k92a1 1 -----------------------TTILKHLPVGQRIGIAFSGGLDTSAALLWMRQ----- 32 query 51 ---NVYGVSMPSKYSSDH------SKGDAAELARRTG-LNFRTVSIEPMFDAYMA---SL 97 ::::::::: ::::::::::::: ::::::::::::::::: :: d1k92a1 33 KGAVPYAYTANL------GQPDEEDYDAIPRRAMEYGAENARLIDCRKQLVAEGIAAIQC 86 query 98 GLTG----------LAEENLQSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY-- 144 :: ::::::::::::::::::::::: :::::::::: d1k92a1 87 GA--FHNTTGGLTYFNTTPLGRAVTGTMLVAAMKEDGVNIWGDGSTYK----------GN 134 query 145 ----GDSVG---------AYGPIKD----------VYKTSIFRLAEWRNRAAAERGQTPP 181 :::: :::: :::::::::::: d1k92a1 135 DIERFYRY-GLLTNAELQIYKP---WLDTDFIDELGGRHEMSEFMIA------------- 177 query 182 IPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPP 241 d1k92a1 178 ------------------------------------------------------------ 178 query 242 GTKISAKGFGKDRRLPITNRWREGH----------- 266 d1k92a1 178 -------------------------CGFDYKMSVEK 188 TMalign alignment (TM-score: 0.49 Raw score:130.18) query 1 ----DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVS 56 ::: :: :::::::::::::::::::::::::: :::::: d1k92a1 1 TTIL-----------KHL---PV---GQRIGIAFSGGLDTSAALLWMRQKGA--VPYAYT 41 query 57 MPSKYSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAYMASLG---LT--------GLAE 104 ::::::::::::::::::::::: ::::::::::::::::::: :: :::: d1k92a1 42 ANLGQPDEEDYDAIPRRAMEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNT 101 query 105 ENLQSRLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTL-YGDS--V-------GAYGP 153 ::::::::::::::::::::: :::::: :: ::::: ::: : ::::: d1k92a1 102 TPLGRAVTGTMLVAAMKEDGVNIWGDGS---TY--KGNDIE-RFYRYGLLTNAELQIYKP 155 query 154 IKD---VY-KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGA 209 ::: :: ::::::::::::::: : ::: ::: :: d1k92a1 156 WLDTDFIDE-LGGRHEMSEFMIACG-----F-DYK--MSV-EK----------------- 188 query 210 DAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1k92a1 189 --------------------------------------------------------- 189 HHsearch alignment (Probability: 0.97 E-value:0.00) query 24 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 82 ::::::::::::::::::::::: ::::::::::::::::::::::::::::::: ::: d1k92a1 11 QRIGIAFSGGLDTSAALLWMRQK--GAVPYAYTANLGQPDEEDYDAIPRRAMEYGAENAR 68 query 83 TVSIEPMFDAYMASLGLTGLAEENLQSR-----------LRGTTLMAISNQEGHIVLAPG 131 :::::::::::::::::::::::::::: ::::::::::::::::::::: d1k92a1 69 LIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKEDGVNIWGDG 128 query 132 ------NKSELAVGYSTLYGDSVGAYGPIKDVY-------KTSIFRLAEWRNRAAAERGQ 178 :::::::::::::::::: :::::::: :::::::::::::::::::: d1k92a1 129 STYKGNDIERFYRYGLLTNAELQI-YKPWLDTDFIDELGGRHEMSEFMIACGFDYKMSVE 187 query 179 T 179 : d1k92a1 188 K 188
Intermediate <-- 0.650 --> HitDALI alignment (Z-score: 2.4 Raw score:416.00) d1k92a1 1 ------------------------------------------------------------ 1 d1m1na_ 1 msreevesliqevlevypekarkdrnkhlavndpavtqskkciisnkksqpglmtirgca 60 d1k92a1 1 ------------------------------------------------------------ 1 d1m1na_ 61 yagskgvvwgpikdmihishgpvgcgqysragrrnyyigttgvnafvtmnftsdfqekdi 120 d1k92a1 1 ------------------------------------------------------------ 1 d1m1na_ 121 vfggdkklaklidevetlfplnkgisvqsecpigligddiesvskvkgaelsktivpvrc 180 d1k92a1 1 ------------------------------------------------------------ 1 d1m1na_ 181 egfrgvsqslghhiandavrdwvlgkrdedttfastpydvaiigdyniggdawssrille 240 d1k92a1 1 ------------------------------------------------------------ 1 d1m1na_ 241 emglrcvaqwsgdgsiseieltpkvklnlvhcyrsmnyisrhmeekygipwmeynffgpt 300 d1k92a1 1 -----------------------------------ttilkhlPVGQRIGIAFSGGlDTSA 25 ::::::::::::: :::: d1m1na_ 301 ktieslraiaakfdesiqkkceeviakykpeweavvakyrprLEGKRVMLYIGGL-RPRH 359 d1k92a1 26 ALLWMRQKGAVPYAYTanlgqpdeeDYDAIpRRAMEYG-aeNARLIDcrkqlvaegiaai 84 :::::::::::::::: ::::: ::::::: :::::: d1m1na_ 360 VIGAYEDLGMEVVGTG-----yefaHNDDY-DRTMKEMgdsTLLYDD------------- 400 d1k92a1 85 qcgafhnttggltyfnttplgravTGTMLVAAMKEDGVNIWGDGStykgndieRFYRYGL 144 ::::::::::::::::::::: ::::::: d1m1na_ 401 -----------------------vTGYEFEEFVKRIKPDLIGSGI--------KEKFIFQ 429 d1k92a1 145 LtnAELQIYKP--WLDTdfIDELGG------rhemsefmiacgfdykmsvek 188 : :::::::: :::: :::::: d1m1na_ 430 K--MGIPFREMhsWDYS--GPYHGFdgfaifardmdmtlnnpcwkklqapwe 477 FAST alignment (Normalized score: 0.73 Raw score:217.50) d1k92a1 1 TTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRAM 60 d1m1na_ 1 ------------------------------------------------------------ 1 d1k92a1 61 EYGAENARLIDC------------------------------------------------ 72 d1m1na_ 1 ------------MSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKK 48 d1k92a1 73 ------------------------------------------------------------ 73 d1m1na_ 49 SQPGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVT 108 d1k92a1 73 ------------------------------------------------------------ 73 d1m1na_ 109 MNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKG 168 d1k92a1 73 ------------------------------------------------------------ 73 d1m1na_ 169 AELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNI 228 d1k92a1 73 ------------------------------------------------------------ 73 d1m1na_ 229 GGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYG 288 d1k92a1 73 ---------RKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKEDGV- 122 ::::::::::::: d1m1na_ 289 IPWMEYNFFGPTKTIESLRAIA-------------------------------------A 311 d1k92a1 123 ----------------------------------NIWGDGSTYKGNDIERFYRYGLLTNA 148 ::::::: :::::::::::::: : d1m1na_ 312 KFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYI--GGLRPRHVIGAYED--L 367 d1k92a1 149 ELQIYKPWLDTDFIDEL-----------------------------GGRHEMSEFMIACG 179 :::: ::::::::::: d1m1na_ 368 GMEV-------------VGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVK--- 411 d1k92a1 180 FDYKMSVEK--------------------------------------------------- 188 d1m1na_ 412 ---------RIKPDLIGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDM 462 d1k92a1 189 --------------- 189 d1m1na_ 463 TLNNPCWKKLQAPWE 477 TMalign alignment (TM-score: 0.38 Raw score:70.81) d1k92a1 1 ------------------------------------------------------------ 1 d1m1na_ 1 MSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIRGCA 60 d1k92a1 1 ------------------------------------------------------------ 1 d1m1na_ 61 YAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDI 120 d1k92a1 1 ------------------------------------------------------------ 1 d1m1na_ 121 VFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRC 180 d1k92a1 1 ------------------------------------TTILKHLPVGQRIGIA-FSGG-LD 22 ::::::: :::: :: d1m1na_ 181 EGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFAST---------PYDVAIIGDYNIGGD 231 d1k92a1 23 TSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRAMEYGAENARLIDCRKQLVAEGIA 82 :::::::::::::::::::: : :: ::: d1m1na_ 232 AWSSRILLEEMGLRCVAQWS---------G--DG------------SIS----------- 257 d1k92a1 83 AIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKEDGVNIWGDGSTYKGNDIERFYRY 142 :: :::: :::::::::: ::::::::: d1m1na_ 258 -----------------------------EI-ELTP--KVKLNLVHCY---RSMNYISRH 282 d1k92a1 143 GLLTNAELQIYKPW-----L-DTDFI-----------------D------E--------- 164 ::::: :::::::: : ::::: : : d1m1na_ 283 MEEKY-GIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRP 341 d1k92a1 165 ------------------L-GG-------------------------------------- 167 : :: d1m1na_ 342 RLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDV 401 d1k92a1 168 -------------------------------------------RHEMSEFMIA----CGF 180 :::::::::: d1m1na_ 402 TGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFAR--- 458 d1k92a1 181 DYKM------------------SVEK 188 : d1m1na_ 459 ---DMDMTLNNPCWKKLQAPWE---- 477 HHsearch alignment (Probability: 0.50 E-value:0.00) d1k92a1 106 RAVTGTMLVAAMKEDGVNIWGDGSTYKGNDIER 138 ::::::::::::::::::::::::::::::::: d1m1na_ 353 GGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYD 385