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 | d1k92a1 | Argininosuccinate synthetase, N-terminal domain | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
Query <-- 0.999 --> 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 <-- 0.998 --> HitDALI alignment (Z-score: 11.4 Raw score:891.80) d1gpma1 1 wtpakiiddavARIReqvGDDKVILGLSGGVDSSVTAMLLHRAIGkNLTCVFVDNGL-LR 59 :::: ::::::::::::::::::::::::::: ::::::::::: :: d1k92a1 1 -------ttilKHLP---VGQRIGIAFSGGLDTSAALLWMRQKGA-VPYAYTANLGQpDE 49 d1gpma1 60 LNeAEQVLDMFGdHFGL-NIVHVPAEDRFLSALAGEN------------dPEAKRKIIGR 106 :: ::::::::: :::: ::::::::::::::::::: :::::::::: d1k92a1 50 ED-YDAIPRRAM-EYGAeNARLIDCRKQLVAEGIAAIqcgafhnttggltYFNTTPLGRA 107 d1gpma1 107 VFVEVFDEEALKLEdVKWLAQGTiypDVIE------------saaKMGLVEP-----LKE 149 :::::::::::::: :::::::: :::: ::::::: ::: d1k92a1 108 VTGTMLVAAMKEDG-VNIWGDGS---TYKGndierfyryglltnaELQIYKPwldtdFID 163 d1gpma1 150 L--FKDEVRKIGLELGLPYDmlYRHPfp 175 : ::::::::::::::::: :::: d1k92a1 164 ElgGRHEMSEFMIACGFDYK--MSVE-k 188 FAST alignment (Normalized score: 9.74 Raw score:1767.00) d1gpma1 1 WTPAKIIDDAVARIRE------QVGDDKVILGLSGGVDSSVTAMLLHRAIGK---NLTCV 51 :::::::::::::::::::::::::: ::::: d1k92a1 1 ----------------TTILKHLPVGQRIGIAFSGGLDTSAALLWMRQ----KGAVPYAY 40 d1gpma1 52 FVDNGLLRL-----NEAEQVLDMFGDHFGL-NIVHVPAEDRFLSALAGENDP-------- 97 :::: :::::::::: ::::: ::::::::::::::::: d1k92a1 41 TANL-----GQPDEEDYDAIPRRA-MEYGAENARLIDCRKQLVAEGIA----AIQCGAFH 90 d1gpma1 98 --------EAKRKIIGRVFVEVFDEEALKLEDVKWLAQGTIYPDVIESA----------- 138 ::::::::::::::::::::: :::::::::: d1k92a1 91 NTTGGLTYFNTTPLGRAVTGTMLVAAMKE-DGVNIWGDGS---------TYKGNDIERFY 140 d1gpma1 139 -------AKMGLVEPLKE----------LFKDEVRKIGLELGLPYDMLYRHPFP------ 175 :::::::: :::::::::::::: d1k92a1 141 RYGLLTNAELQIYKP---WLDTDFIDELGGRHEMSEFMIACG------------FDYKMS 185 d1gpma1 176 --- 176 d1k92a1 186 VEK 188 TMalign alignment (TM-score: 0.67 Raw score:116.78) d1gpma1 1 -----WTPAKIIDDAVARIREQVGDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDN 55 : ::::::::::::::::::::::::::::: ::::::::: d1k92a1 1 TTILK-------------H--LPVGQRIGIAFSGGLDTSAALLWMRQKGA-VPYAYTANL 44 d1gpma1 56 GL-LRLNEAEQVLDMFGDHFGL-NIVHVPAEDRFLSALA-GE----N-------DPEAKR 101 :: :::: ::::::::: :::: :::::::::::::::: :: : :::::: d1k92a1 45 GQPDEED-YDAIPRRAM-EYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTT 102 d1gpma1 102 KIIGRVFVEVFDEEALKLEDVKWLAQGTIYPDVIES---------------AAK-MGLVE 145 ::::::::::::::::::: :::::::: :: :: : ::::: d1k92a1 103 PLGRAVTGTMLVAAMKEDG-VNIWGDGS---TY-KGNDIERFYRYGLLTNA--ELQIYKP 155 d1gpma1 146 --P--LKE--LFKDEVRKIGLELGLPYDMLYRHPFP 175 : ::: :::::::::::::::::: ::::: d1k92a1 156 WLDTDFIDELGGRHEMSEFMIACGFDYK--MSVEK- 188 HHsearch alignment (Probability: 1.00 E-value:0.00) d1gpma1 15 REQVGDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRLNEAEQVLDMFGDHF 74 :::::::::::::::::::::::::::: ::::::::::::::::::: ::::::::::: d1k92a1 5 KHLPVGQRIGIAFSGGLDTSAALLWMRQ-KGAVPYAYTANLGQPDEED-YDAIPRRAMEY 62 d1gpma1 75 GLN-IVHVPAEDRFLSALAGEN-----------DPEAKRKIIGR-VFVEVFDEEALKLED 121 ::: :::::::::::::::::: ::::::::::: :::::::::::: :: d1k92a1 63 GAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE-DG 121 d1gpma1 122 VKWLAQGTIYPDVI---------ESAAKMGLVEPLKEL-------FKDEVRKIGLELGLP 165 :::::::::::::: ::::::::::::::: ::::::::::::::: d1k92a1 122 VNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACGFD 181 d1gpma1 166 YDMLYR 171 :::::: d1k92a1 182 YKMSVE 187