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 | d1o58a_ | O-acetylserine sulfhydrylase (Cysteine synthase) | 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 <-- 1.469 --> HitDALI alignment (Z-score: 4.8 Raw score:403.90) d1gpma1 1 --wtPAKI--------------------------------iddavARIRE-QVGDDKVIL 25 :::: ::::: ::::::::: d1o58a_ 1 hhmmERLIgstpivrldsidsriflkleknnpggsvkdrpalfmiLDAEKrGLLKNGIVE 60 d1gpma1 26 GLSGGvdSSVTAMLLHRAIGkNLTCVFVDNgllrlneAEQVLDMFGdHFGLNIVHVPAEd 85 ::::: ::::::::::::: ::::::::: ::::::::: :::::::::::: d1o58a_ 61 PTSGN-mGIAIAMIGAKRGH-RVILTMPET------mSVERRKVLK-MLGAELVLTPGE- 110 d1gpma1 86 rflsalagendpeakrkiigrVFVEVFDEEALKL--EDVKWLAQGtiypdviesaakmgl 143 ::::::::::::: ::::::::: d1o58a_ 111 ---------------------LGMKGAVEKALEIsrETGAHMLNQ-------------fe 136 d1gpma1 144 vepLKELF---------------------------------------------------- 151 ::::: d1o58a_ 137 npyNVYSHqfttgpeilkqmdyqidafvagvgtggtisgvgrvlkgffgngvkivavepa 196 d1gpma1 152 -------------------------------------kdevrkiglelglpydmlyRHPF 174 :::: d1o58a_ 197 kspvlsggqpgkhaiqgigagfvpkildrsvidevitvedeeayemarylakkeglLVGI 256 d1gpma1 175 P------------------------------------ 175 : d1o58a_ 257 Ssganvaaalkvaqklgpdarvvtvapdhaerylsil 293 FAST alignment (Normalized score: 3.20 Raw score:724.00) d1gpma1 1 WTP-------------------------------------AKIIDDAVARIREQVGD--- 20 ::::::::::::: d1o58a_ 1 ---HHMMERLIGSTPIVRLDSIDSRIFLKLEKNNPGGSVKDRPALFMILDAEK----RGL 53 d1gpma1 21 --DKVILGLSGGVDSSVTAMLLHRAIGK---NLTCVFVDNGLLRLNE---AEQVLDMFGD 72 :::::::: ::::::::::::: ::::::: :::::::: : d1o58a_ 54 LKNGIVEPTS-GNMGIAIAMIGAK----RGHRVILTMP---------ETMSVERRKVL-K 98 d1gpma1 73 HFGLNIVHVPAEDRFLSALAGENDPEAKRKIIGRVFVEVFDEEALKLEDV--KWLAQGTI 130 :::::::: :::: :::::::::::::::: ::::: d1o58a_ 99 MLGAELVL-TPGE-----------------LGMKGAVEKALEISRE----TGAHMLN--- 133 d1gpma1 131 YPDVIESAAKMGLV----EPLKELFKDEVRKIGLELGLPYDMLYRHPFP----------- 175 ::::: d1o58a_ 134 --------------QFENPYNVY--------------------------SHQFTTGPEIL 153 d1gpma1 176 ------------------------------------------------------------ 176 d1o58a_ 154 KQMDYQIDAFVAGVGTGGTISGVGRVLKGFFGNGVKIVAVEPAKSPVLSGGQPGKHAIQG 213 d1gpma1 176 ------------------------------------------------------------ 176 d1o58a_ 214 IGAGFVPKILDRSVIDEVITVEDEEAYEMARYLAKKEGLLVGISSGANVAAALKVAQKLG 273 d1gpma1 176 -------------------- 176 d1o58a_ 274 PDARVVTVAPDHAERYLSIL 293 TMalign alignment (TM-score: 0.46 Raw score:81.21) d1gpma1 1 ----WTPAKI------------------------------I--DDA-VARIREQ-VGDDK 22 :::: : :: ::::::: ::::: d1o58a_ 1 HHMM--ERLIGSTPIVRLDSIDSRIFLKLEKNNPGGSVKDRPA-LFMILDAEKRGLLKNG 57 d1gpma1 23 VILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRLNEAEQVLDMFGDHFGLNIVHVP 82 :::::::: ::::::::::::::: ::::::: : : : :::::::: :::: ::::: d1o58a_ 58 IVEPTSGN-MGIAIAMIGAKRGHR-VILTMPE-T-M---S-VERRKVLK-MLGA-ELVLT 107 d1gpma1 83 AEDRFLSALAGENDPEAKRKIIGRVFVEVFDEEALKLEDVKWLAQGTIYPDVIESAAKMG 142 :: : ::::::::::::::: :::: :::::: d1o58a_ 108 PG--E---------------LGMKGAVEKALEISR-ETGA-HMLNQF------------- 135 d1gpma1 143 LVEPLKELFK-DEV-RK------------------------------------------- 157 :::::::::: ::: : d1o58a_ 136 ENPYNVYSHQFTTGP-EILKQMDYQIDAFVAGVGTGGTISGVGRVLKGFFGNGVKIVAVE 194 d1gpma1 158 ----------------------------------------------------------IG 159 d1o58a_ 195 PAKSPVLSGGQPGKHAIQGIGAGFVPKILDRSVIDEVITVEDEEAYEMARYLAKKEGL-- 252 d1gpma1 160 LELGLPYDMLYRHPF--------------------------------P 175 ::::::::: d1o58a_ 253 ------LVGISSGANVAAALKVAQKLGPDARVVTVAPDHAERYLSIL- 293 HHsearch alignment (Probability: 0.12 E-value:0.03) d1gpma1 12 ARIREQVGDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRLNEAEQVLDMFG 71 ::::::::::::::::::::::::::::::: :::::: :::::::: : : ::::: d1o58a_ 46 LDAEKRGLLKNGIVEPTSGNMGIAIAMIGAK-RGHRVI-LTMPETMS--V---E-RRKVL 97 d1gpma1 72 DHFGLNIVHVPAE 84 ::::::::::::: d1o58a_ 98 KMLGAELVLTPGE 110