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 | d1o13a_ | Hypothetical protein TM1816 | Nitrogenase accessory factor-like | Ribonuclease H-like motif | 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 <-- 0.843 --> HitDALI alignment (Z-score: 2.8 Raw score:255.00) d1k92a1 1 ttilkhlpvgQRIGIAFSGgldtsaallwmrqkgavpyaytanlgqpdeedydaipRRAM 60 ::::::::: :::: d1o13a_ 1 ----------MIIAIPVSE-------------------------------------NRGK 13 d1k92a1 61 E----------------------ygaENARLIDC-RKQLvaegiaaiqcgafhnttgglt 97 : :::::::: :::: d1o13a_ 14 DspisehfgrapyfafvkvknnaiadISVEENPLaQDHV--------------------- 52 d1k92a1 98 yfnttplgravtgtMLVAAMKEDGVNIWGDGStykgndIERFYRYGLLtnAELQIYKP-- 155 :::::::::::::::::: :::::::::: :::::::: d1o13a_ 53 ------------hgAVPNFVKEKGAELVIVRG-----iGRRAIAAFEA--MGVKVIKGas 93 d1k92a1 156 --------wlDTDFidelggrhemsefmiacgfdykmsvek 188 :::: d1o13a_ 94 gtveevvnqyLSGQ--------------------------- 107 FAST alignment (Normalized score: 2.74 Raw score:388.90) d1k92a1 1 TTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIP--RR 58 ::::::: :: d1o13a_ 1 ----------MIIAIPV---------------------------------------SENR 11 d1k92a1 59 AMEY----------------------GAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGL 96 :: ::::::::: d1o13a_ 12 GK--DSPISEHFGRAPYFAFVKVKNNAIADISVEE------------------------- 44 d1k92a1 97 TYFNTTPLGRAVTGT----------MLVAAMKEDGVNIWGDGSTYKGND---IERFYRYG 143 :::::::::::::::: :::::::: d1o13a_ 45 ---------------NPLAQDHVHGAVPNFVKEKGAELVIV--------RGIGRRAIAAF 81 d1k92a1 144 LLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACGFDYKMSVEK--------------- 188 :: :::::: d1o13a_ 82 EA--MGVKVI-----------------------------------KGASGTVEEVVNQYL 104 d1k92a1 189 --- 189 d1o13a_ 105 SGQ 107 TMalign alignment (TM-score: 0.31 Raw score:57.94) d1k92a1 1 TTILKHLPVGQRIGIAFSGGL--DTSAA-----LLWMRQKGAVPYAYTANLGQPDEEDYD 53 ::::::::::: :::: ::: d1o13a_ 1 ----------MIIAIPVSENRGK-DSPISEHFG-------------RAP----------- 25 d1k92a1 54 AIPRRAM-------EYG-AENARLIDC-R-KQLVAEGIAAIQCGAFHNTTGGLTYFNTTP 103 :: :: : ::::::::: : ::: d1o13a_ 26 -YF--AFVKVKNNA--IADISVEENPLAQDHVH--------------------------- 53 d1k92a1 104 LGRAVTGTMLVAAMKEDGVNIWGDGSTYKGNDIERFYRYGLLTNA-ELQIYKPWLDTDFI 162 : :: :::::::::::::::: : : ::::::::: :::::::: : d1o13a_ 54 ----G--AV-PNFVKEKGAELVIVRG------I-G-RRAIAAFEAMGVKVIKGA----S- 93 d1k92a1 163 DELGGRHEM--SEF---------MIACGFDYKMSVEK 188 : : : d1o13a_ 94 --G-----TVE--EVVNQYLSGQ-------------- 107 HHsearch alignment (Probability: 0.02 E-value:0.03) d1k92a1 112 MLVAAMKEDGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYK 154 ::::::::::::::::::::::::: ::::::::::: d1o13a_ 55 AVPNFVKEKGAELVIVRGIGRRAIA-------AFEAMGVKVIK 90