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 | d1gpma1 | GMP synthetase, central domain | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1p5ja_ | L-serine dehydratase | Tryptophan synthase beta subunit-like PLP-dependent enzymes | Tryptophan synthase beta subunit-like PLP-dependent enzymes | α/β |
Query <-- 2.152 --> IntermediateDALI alignment (Z-score: 17.0 Raw score:1273.10) query 1 DADEEVYSALVVGLRAYVAkngFRSVLIGLSGGIDSALVAAIACDALGaQNVYGVSMPSK 60 ::::::::::::::::::: :::::::::::::::::::::::::: ::::::::::: d1gpma1 1 WTPAKIIDDAVARIREQVG---DDKVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVDNG 56 query 61 YSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMAsLGLTGLAEENLQSRLRGTTLMAI 119 ::::::::::: :::::::::::::::::::::::: ::::::::::::::::::::::: d1gpma1 57 LLRLNEAEQVLdMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFDEE 115 query 120 SNQE--GHIVLAPGNKSELAVGystlygdsvgAYGPIKDVYKTSIFRLAEWRNraaaerg 177 :::: :::::::::::::::: ::::::::::::::::::::: d1gpma1 116 ALKLedVKWLAQGTIYPDVIES-----aakmgLVEPLKELFKDEVRKIGLELG------- 163 query 178 qtppIPEASITKpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrr 237 :::::::: d1gpma1 164 ----LPYDMLYR------------------------------------------------ 171 query 238 qyppgtkisakgfgkdrrlpitnrwregh 266 d1gpma1 172 -------------------------hpfp 175 FAST alignment (Normalized score: 13.11 Raw score:2830.00) query 1 DADEEVYSALVVGLRAYVAKNGF---RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSM 57 ::::::::::::::::: ::::::::::::::::::::::: :::::::::: d1gpma1 1 WTPAKIIDDAVARIREQ------VGDDKVILGLSGGVDSSVTAMLLHRA-IGKNLTCVFV 53 query 58 PSKYSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTL 116 :::::::::::::: :::::::::::::::::::::::::: :::::::::::::::::: d1gpma1 54 DNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGE-NDPEAKRKIIGRVFVEVF 112 query 117 MAISNQEG----HIVLAPGNKSELAVGYSTLYGDSVG-------AYGPIKDVYKTSIFRL 165 :::::: ::::::::::::: :::::::::::::::: d1gpma1 113 DEEALK--LEDVKWLAQGTIYPDVI------------ESAAKMGLVEPLKELFKDEVRKI 158 query 166 AEWRNRAAAERGQTP-PIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVK 224 ::: :::::::: d1gpma1 159 GLE------------LGLPYDMLY------------------------------------ 170 query 225 TLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----- 266 d1gpma1 171 ------------------------------------------RHPFP 175 TMalign alignment (TM-score: 0.53 Raw score:140.98) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 ::::::::::::::::::: :: :::::::::::::::::::::::: ::::::::::: d1gpma1 1 WTPAKIIDDAVARIREQVG--DD-KVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVDNG 56 query 61 YSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAI 119 ::::::::::: :::::::::::::::::::::::: ::::::::::::::::::::::: d1gpma1 57 LLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFDEE 115 query 120 SNQEG-H-IVLAPGNKSELAVG---YSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAA 174 ::::: : :::::::::::::: ::::::::::::::::::::::: d1gpma1 116 ALKLEDVKWLAQGTIYPDVIESAAK--------MGLVEPLKELFKDEVRKIGLELG---- 163 query 175 ERGQTPPIPEASITKPDY--PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTA 232 :::::::: :: d1gpma1 164 -------LPYDMLYR-HPFP---------------------------------------- 175 query 233 EYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1gpma1 176 ---------------------------------- 176 HHsearch alignment (Probability: 1.00 E-value:0.00) query 4 EEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSS 63 ::::::::::::::::: ::::::::::::::::::::::::::: :::::::::::: d1gpma1 4 AKIIDDAVARIREQVGD---DKVILGLSGGVDSSVTAMLLHRAIGKN-LTCVFVDNGLLR 59 query 64 DHSKGD-AAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQ 122 :::::: ::::::::::::::::::::::::::::::::: ::::::::::::::::::: d1gpma1 60 LNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGENDPEA-KRKIIGRVFVEVFDEEALK 118 query 123 EGHI-VLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPP 181 :::: :::::::::::::::::::: :::::::::::::::::::: d1gpma1 119 LEDVKWLAQGTIYPDVIESAAKMGL----VEPLKELFKDEVRKIGLELG----------- 163 query 182 IPEASITKPDYP 193 :::::::::::: d1gpma1 164 LPYDMLYRHPFP 175
Intermediate <-- 1.463 --> HitDALI alignment (Z-score: 4.9 Raw score:337.00) d1gpma1 1 -----------------------------------wtpakiidDAVARIREQvGDDKVIL 25 ::::::::: ::::::: d1p5ja_ 1 geplhvktpirdsmalskmagtsvylkmdsaqpsgsfkirgigHFCKRWAKQ-GCAHFVC 59 d1gpma1 26 GLSGgVDSSVTAMLLHRAIGKnLTCVFVDNgllrlneAEQVLDMFGdHFGLNIVHVPAed 85 :::: :::::::::::::::: :::::::: ::::::::: ::::::::::: d1p5ja_ 60 SSAG-NAGMAAAYAARQLGVP-ATIVVPGT------tPALTIERLK-NEGATCKVVGE-- 108 d1gpma1 86 rflsalagendpeakrkiigrvFVEVFDEEALKL--EDVK-WLAQG-------------- 128 :::::::::::: :::: ::::: d1p5ja_ 109 ----------------------LLDEAFELAKALakNNPGwVYIPPfddpliweghasiv 146 d1gpma1 129 ------------------------------------------------------------ 129 d1p5ja_ 147 kelketlwekpgaialsvggggllcgvvqglqecgwgdvpviametfgahsfhaattagk 206 d1gpma1 129 ------------------------------------------------------------ 129 d1p5ja_ 207 lvslpkitsvakalgvktvgsqalklfqehpifsevisdqeavaaiekfvddekilvepa 266 d1gpma1 129 ------tiypdviesaakmglveplkelfkdevrkiglelglpydmlyrhpfp 175 d1p5ja_ 267 cgaalaavyshviqklqlegnlrtplpslvvivcggsnislaqlralkeqlgm 319 FAST alignment (Normalized score: 3.15 Raw score:744.30) d1gpma1 1 WTP--------------------------------------AKIIDDAVARIREQVG--D 20 ::::::::::::: : d1p5ja_ 1 ---GEPLHVKTPIRDSMALSKMAGTSVYLKMDSAQPSGSFKIRGIGHFCKRWAK---QGC 54 d1gpma1 21 DKVILGLSGGVDSSVTAMLLHRAIGK---NLTCVFVDNGLLRLNEAEQVLDMFGDHFGLN 77 ::::: :::::::::::::::: :::::: :::: :::::::: :::::: d1p5ja_ 55 AHFVC-SSAGNAGMAAAYAARQ----LGVPATIVV--PGTT----PALTIERL-KNEGAT 102 d1gpma1 78 IVHVPAEDRFLSALAGENDPEAKRKI--IGRVFVEVFDEEALKLEDVKWLAQGTIYPDVI 135 :::: :::::::::::::::::: ::::: d1p5ja_ 103 CKVV----------------------GELLDEAFELAKALAKNNPG-WVYIP-------- 131 d1gpma1 136 ESAAKMGLVE-----PLKELFKDEVRKIGLELGLPYDMLYRHPFP--------------- 175 :::: d1p5ja_ 132 ----------PFDDPLIWE--------------------------GHASIVKELKETLWE 155 d1gpma1 176 ------------------------------------------------------------ 176 d1p5ja_ 156 KPGAIALSVGGGGLLCGVVQGLQECGWGDVPVIAMETFGAHSFHAATTAGKLVSLPKITS 215 d1gpma1 176 ------------------------------------------------------------ 176 d1p5ja_ 216 VAKALGVKTVGSQALKLFQEHPIFSEVISDQEAVAAIEKFVDDEKILVEPACGAALAAVY 275 d1gpma1 176 -------------------------------------------- 176 d1p5ja_ 276 SHVIQKLQLEGNLRTPLPSLVVIVCGGSNISLAQLRALKEQLGM 319 TMalign alignment (TM-score: 0.48 Raw score:84.15) d1gpma1 1 ----WTPAKI-----------------------ID-----DA--VARIREQVG-DDKVIL 25 :::: :: :: ::::::::: :::::: d1p5ja_ 1 GEPL--HVKTPIRDSMALSKMAGTSVYLKMDSAQPSGSFKIRGIGHFCKRWAKQGCAHFV 58 d1gpma1 26 GLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRLNEAEQVLDMFGDHFGLNIVHVPAED 85 ::::::::::::::::: :: :::::::: : :: : :::::::: :::: ::::::: d1p5ja_ 59 CSSAGNAGMAAAYAARQ-LG-VPATIVVP-G-TT--P-ALTIERLK-NEGA-TCKVVGE- 108 d1gpma1 86 RFLSALAGENDPEAKRKIIGRVFVEVFDEEALKLEDVKWLAQGT---------------- 129 : :: :::::::::::::::: :::::: d1p5ja_ 109 -L----------------LD-EAFELAKALAKNNPGW-VYIPPFDDPLIWEGHASIVKEL 149 d1gpma1 130 ------------------IYP--------------------------------------- 132 ::: d1p5ja_ 150 KETLWEKPGAIALSVGGGGLLCGVVQGLQECGWGDVPVIAMETFGAHSFHAATTAGKLVS 209 d1gpma1 133 ----------------D-VIESAA--------------------------------KMGL 143 : :::::: d1p5ja_ 210 LPKITSVAKALGVKTVGSQALKLFQEHPIFSEVISDQEAVAAIEKFVDDEKILVEP---- 265 d1gpma1 144 VEPLKELFK------------------------------DEVRKIGLELGLPYDM-LYR- 171 :: :::: : ::::: :: d1p5ja_ 266 -------ACGAALAAVYSHVIQKLQLEGNLRTPLPSLVVIVCG--G----SNISLA-QLR 311 d1gpma1 172 -H------PFP 175 : d1p5ja_ 312 ALKEQLGM--- 319 HHsearch alignment (Probability: 0.20 E-value:0.02) d1gpma1 20 DDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRLNEAEQVLDMFGDHFGLNIV 79 ::::::::::::::::::::::: :::::: ::::::: ::: ::::::::::::: d1p5ja_ 53 GCAHFVCSSAGNAGMAAAYAARQ-LGVPAT-IVVPGTT-----PAL-TIERLKNEGATCK 104 d1gpma1 80 HVP 82 ::: d1p5ja_ 105 VVG 107