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 | 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 <-- 2.423 --> IntermediateDALI alignment (Z-score: 17.0 Raw score:1263.90) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1gpma1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1gpma1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1gpma1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1gpma1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1gpma1 1 ------------------------------------------------------------ 1 query 301 rlDADEEVYSALVVGLRAYVAkngFRSVLIGLSGGIDSALVAAIACDALGaQNVYGVSMP 360 ::::::::::::::::::: :::::::::::::::::::::::::: ::::::::: d1gpma1 1 --WTPAKIIDDAVARIREQVG---DDKVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVD 54 query 361 SKYSS-DHSKGDAAELARRTGLNFRTVSIEPMFDAYMAsLGLTGLAEENLQSRLRGTTLM 419 ::::: :::::::::::::::::::::::::::::::: ::::::::::::::::::::: d1gpma1 55 NGLLRlNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFD 113 query 420 AISNQE--GHIVLAPGNKSELAVGystlygdsvgAYGPIKDVYKTSIFRLAEWRNraaae 477 :::::: :::::::::::::::: ::::::::::::::::::::: d1gpma1 114 EEALKLedVKWLAQGTIYPDVIES-----aakmgLVEPLKELFKDEVRKIGLELG----- 163 query 478 rgqtppIPEASITKpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeyk 537 :::::::: d1gpma1 164 ------LPYDMLYR---------------------------------------------- 171 query 538 rrqyppgtkisakgfgkdrrlpitnrwregh 568 d1gpma1 172 ---------------------------hpfp 175 FAST alignment (Normalized score: 8.89 Raw score:2802.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1gpma1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1gpma1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1gpma1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1gpma1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1gpma1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF---RSVLIGLSGGIDSALVAAIACDALGAQNVYGV 357 ::::::::::::::::: ::::::::::::::::::::::: :::::::: d1gpma1 1 --WTPAKIIDDAVARIREQ------VGDDKVILGLSGGVDSSVTAMLLHRA-IGKNLTCV 51 query 358 SMPSKYSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGT 416 :::::::::::::::: :::::::::::::::::::::::::: :::::::::::::::: d1gpma1 52 FVDNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGE-NDPEAKRKIIGRVFVE 110 query 417 TLMAISNQEG----HIVLAPGNKSELAVGYSTLYGDSVG-------AYGPIKDVYKTSIF 465 :::::::: ::::::::::::: :::::::::::::: d1gpma1 111 VFDEEALK--LEDVKWLAQGTIYPDVI------------ESAAKMGLVEPLKELFKDEVR 156 query 466 RLAEWRNRAAAERGQTP-PIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELV 524 ::::: :::::::: d1gpma1 157 KIGLE------------LGLPYDMLY---------------------------------- 170 query 525 VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----- 568 d1gpma1 171 --------------------------------------------RHPFP 175 TMalign alignment (TM-score: 0.27 Raw score:151.12) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1gpma1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1gpma1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1gpma1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 : d1gpma1 1 --------------W--------------------------------------------- 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1gpma1 2 ------------------------------------------------------------ 2 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::::::::::::: :: :::::::::::::::::::::::: ::::::::: d1gpma1 2 ---TPAKIIDDAVARIREQVG--DD-KVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVD 54 query 361 SKYSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLM 419 ::::::::::::: :::::::::::::::::::::::: ::::::::::::::::::::: d1gpma1 55 NGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFD 113 query 420 AISNQEG-H-IVLAPGNKSELAVG---YSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRA 474 ::::::: : :::::::::::::: ::::::::::::::::::::::: d1gpma1 114 EEALKLEDVKWLAQGTIYPDVIESAAK--------MGLVEPLKELFKDEVRKIGLELG-- 163 query 475 AAERGQTPPIPEASITKPDY--PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVD 532 :::::::: :: d1gpma1 164 ---------LPYDMLYR-HPFP-------------------------------------- 175 query 533 TAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1gpma1 176 ------------------------------------ 176 HHsearch alignment (Probability: 1.00 E-value:0.00) query 306 EEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSS 365 ::::::::::::::::: :::::::::::::::::::::::::::::::::::::::: d1gpma1 4 AKIIDDAVARIREQVGD---DKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRL 60 query 366 DHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQE 425 ::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::: d1gpma1 61 NEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGEN-DPEAKRKIIGRVFVEVFDEEALKL 119 query 426 GHI-VLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPI 484 ::: :::::::::::::::::::: ::::::::::::::::::: :::::::::::: d1gpma1 120 EDVKWLAQGTIYPDVIESAAKMGL----VEPLKELFKDEVRKIGLEL-GLPYDMLYRHPF 174 query 485 P 485 : d1gpma1 175 P 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