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 | d1tx2a_ | Dihydropteroate synthetase | Dihydropteroate synthetase-like | TIM beta/alpha-barrel | α/β |
| Hit | d5ruba1 | Ribulose 1,5-bisphosphate carboxylase-oxygenase | RuBisCo, C-terminal domain | TIM beta/alpha-barrel | α/β |
Query <-- 0.687 --> IntermediateDALI alignment (Z-score: 2.9 Raw score:483.20) query 1 ---------------SLQLRLALN----qidstvgdiagnAEAILRWTRHSAEQGAHLVA 41 ::::::::: :::::::::::::::::::: d1tx2a_ 1 kwdydlrcgeytlnlNEKTLIMGIlnvtpdsfsdggsyneVDAAVRHAKEMRDEGAHIID 60 query 42 fpemALTGypvedlalrSSFVEASRTALRELAARLAeEGFGeLPVLVGYldrsesaqpky 101 :::: ::::::::::::::::::: :::: ::::::: d1tx2a_ 61 ---iGGES-------faKVSVEEEIKRVVPMIQAVS-KEVK-LPISIDT----------- 97 query 102 gqpagaprnaaavlhrGRVALT-FAKHhlpnygvfdefryfvPGDT-mpivrlhgvdiaL 159 :::::: :::: :::: : d1tx2a_ 98 -----ykaevakqaieAGAHIInDIWG--------------aKAEPkiaevaahydvpiI 138 query 160 AICE---------dlwQDGGR----vpaarsagaglllsvnaspyerdkDDTRLELVRKR 206 :::: ::::: ::::::::::: d1tx2a_ 139 LMHNrdnmnyrnlmadMIADLydsikiakdagvrdeniildpgigfaktPEQNLEAMRNL 198 query 207 aQEAG---ctTAYLAmiggqdelvFDGD------------------sivVDRDGevvara 245 :::: ::::: :::: ::::: d1tx2a_ 199 -EQLNvlgypVLLGT-------srKSFIghvldlpveerlegtgatvclGIEKG------ 244 query 246 pqfsegCVVLdldlpaaeaepptgvvddglridrlviseeplpayeaeLAGGyadrldad 305 :::: :::: d1tx2a_ 245 cefvrvHDVK-----------------------------------emsRMAK-------- 261 query 306 eevysalvvglrayvakngfrsvliglsggidsalvaaiacdalgaqnvygvsmpskyss 365 d1tx2a_ 262 ------------------------------------------------------------ 262 query 366 dhskgdaaelarrtglnfrtvsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqe 425 d1tx2a_ 262 ------------------------------------------------------------ 262 query 426 ghivlapgnkselavgystlygdsvgaygpikdvyktsifrlaewrnraaaergqtppip 485 d1tx2a_ 262 ------------------------------------------------------------ 262 query 486 easitkpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgt 545 d1tx2a_ 262 ------------------------------------------------------------ 262 query 546 kisakgfgkdrrlpitnrwregh 568 d1tx2a_ 262 ---------------mmdamigk 269 FAST alignment (Normalized score: 1.23 Raw score:478.70) query 1 ----------------SLQLRLALNQIDSTVGD---IAGNAEAILRWTRHSAEQGAHLVA 41 ::::::::::::::::: :::::::::::::::::::::::: d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIID 60 query 42 FPEMALTGYPVEDLALRSSFVEASRTALRELAARLAEEGF-------------------- 81 :: d1tx2a_ 61 IG--------------------------------------GESFAKVSVEEEIKRVVPMI 82 query 82 ------GELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRVALTFAKHHLPNYGVF 135 ::::::: d1tx2a_ 83 QAVSKEVKLPISI----------------------------------------------- 95 query 136 DEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDK 195 d1tx2a_ 96 ------------------------------------------------------------ 96 query 196 DDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVL 255 d1tx2a_ 96 ------------------------------------------------------------ 96 query 256 DLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVG 315 d1tx2a_ 96 ------------------------------------------------------------ 96 query 316 LRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVS----------------- 358 d1tx2a_ 96 -------------------------------------------DTYKAEVAKQAIEAGAH 112 query 359 ----------------------------MPSKYSSDHSKGDAAELARRTGLNFRTVSIEP 390 :::: d1tx2a_ 113 IINDIWGAKAEPKIAEVAAHYDVPIILMHNRD---------------------------- 144 query 391 MFDAYMASLG----LTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLY 446 :::::::::::::::::::: d1tx2a_ 145 ----------NMNYRNLMADMIADLYDSIKIAKD-------------------------- 168 query 447 GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVD 506 d1tx2a_ 169 ------------------------------------------------------------ 169 query 507 RDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWRE 566 d1tx2a_ 169 ------------------------------------------------------------ 169 query 567 GH---------------------------------------------------------- 568 d1tx2a_ 169 --AGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPV 226 query 569 ------------------------------------------- 569 d1tx2a_ 227 EERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 269 TMalign alignment (TM-score: 0.25 Raw score:142.24) query 1 --SLQL------RLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPV 52 :::: ::: : :::: :::: ::: d1tx2a_ 1 KWDYDLRCGEYTLNL------------------------N-EKTL--IMGI--LNV---- 27 query 53 EDLALRSSFV--E-ASRTALRELAARLAEEGFGELPVLVGYLDR---SESAQPKYGQPAG 106 :: ::::: : :::::::::::::: ::: :::::::::: :: : : d1tx2a_ 28 --TP-DSFSDGGSYNEVDAAVRHAKEMR-DEG--AHIIDIGGESFAK---VS--V-E--- 72 query 107 APR-NAA-AV--LHRGRV-ALTFAKHHLPNYGVFDEFRYFVPGDTMPIV-RLHGVDIALA 160 ::: ::: :: :::::: ::::::::: :::::::: : ::::: d1tx2a_ 73 EEIKRVVPMIQAVSKEVKLPISIDTYKA-------------EVAKQAIEA-G---AHIIN 115 query 161 ICEDLWQDGGRVPAARSAGAGLLLSVNASP-YERD-K---DD-TRLELVRKRAQE--AGC 212 :::::::::::::::::: : ::::::::: :::: : :: :::::::::::: ::: d1tx2a_ 116 DIWGAKAEPKIAEVAAHY-D-VPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRD 173 query 213 T-TAYLAMIGG-QDELV-FD--GD--SIVVDRDGEVVARAPQFSE-GCVVLDLDLPAAEA 264 : ::::::::: ::: :: :: ::::: :::::::: ::: d1tx2a_ 174 ENIILDPGIGFA--KTPEQNLEAMRNLEQLN--VLGYPVLL-GTSR-------------- 214 query 265 EPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNG 324 :::::::: ::::: d1tx2a_ 215 ----------------------------------------------KSFIGHVL-DLPVE 227 query 325 FR----------------------------------------SVLIGLSGGIDSALVAAI 344 :: d1tx2a_ 228 ERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK------------------ 269 query 345 ACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGL 404 d1tx2a_ 270 ------------------------------------------------------------ 270 query 405 AEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSI 464 d1tx2a_ 270 ------------------------------------------------------------ 270 query 465 FRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELV 524 d1tx2a_ 270 ------------------------------------------------------------ 270 query 525 VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1tx2a_ 270 -------------------------------------------- 270 HHsearch alignment (Probability: 0.05 E-value:0.02) query 494 YPVLDAILELYVDRDTGADAIV---AAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAK 550 :::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: d1tx2a_ 156 IADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRK 215 query 551 GF 552 :: d1tx2a_ 216 SF 217
Intermediate <-- 0.670 --> HitDALI alignment (Z-score: 11.5 Raw score:1272.20) d1tx2a_ 1 --kwdyDLRCgeYTLN---lNEKTLIMGILN-VTPDsfsdggsynEVDAAVRHAKEMRDe 54 :::: :::: ::::::::::: :::: :::::::::::::: d5ruba1 1 gpsvniSALW--KVLGrpevDGGLVVGTIIKpKLGL---------RPKPFAEACHAFWL- 48 d1tx2a_ 55 GAHIIDI---GGESFAkvsveEEIKRvVPMIQAVSKEVK------LPISIDTY------K 99 ::::::: :::::: ::::: :::::::::::: :::::::: : d5ruba1 49 GGDFIKNdepQGNQPF----aPLRDT-IALVADAMRRAQdetgeaKLFSANITaddpfeI 103 d1tx2a_ 100 AEVAKQAIEAG-----aHIINDIW--gaKAEP-KIAEVAAhyDVPIILMHN-RDNM-NYR 149 ::::::::::: ::::::: :::: ::::::: ::::::::: :::: ::: d5ruba1 104 IARGEYVLETFgenashVALLVDGyvagAAAItTARRRFP--DNFLHYHRAgHGAVtSPQ 161 d1tx2a_ 150 N-lmADMIADLYDSIKIAkdagvrdenIILDPGIgfaktpeqnleamrNLEQ-LNVLG-- 205 : :::::::::::::: ::::::: :::: ::::: d5ruba1 162 SkrgYTAFVHCKMARLQG--------aSGIHTGT-------------sSDRAiAYMLTqd 200 d1tx2a_ 206 ----------------YPVLLGTSrksfighvldlpveerleGTGATVCLGIEKG---CE 246 :::::::: ::::::::::::: :: d5ruba1 201 eaqgpfyrqswggmkaCTPIISGG------------------MNALRMPGFFENLgnaNV 242 d1tx2a_ 247 FVRVHD------------VKEMSRMAKMMDAM---------------------------- 266 :::::: :::::::::::::: d5ruba1 243 ILTAGGgafghidgpvagARSLRQAWQAWRDGvpvldyarehkelarafesfpgdadqiy 302 d1tx2a_ 267 ------igk 269 d5ruba1 303 pgwrkalgv 311 FAST alignment (Normalized score: 6.63 Raw score:1918.00) d1tx2a_ 1 KWDYDLRCGEYTLNL------------------NEKTLIMGILNVTPDSFSDGGSYN--- 39 :::::::::: d5ruba1 1 ---------------GPSVNISALWKVLGRPEVDGGLVVGTII--------------KPK 31 d1tx2a_ 40 ---EVDAAVRHAKEMRDEGAHIIDIGGESFA---------KVSVEEEIKRVVPMIQAVSK 87 :::::::::::::: :::::: :::::::::::::::::::: d5ruba1 32 LGLRPKPFAEACHAFWL-GGDFIK-------NDEPQGNQPFAPLRDTIALVADAMRRAQD 83 d1tx2a_ 88 EV--KLPISIDT--YKAEVAKQAIEAGA------------HIINDIWGAKA-EPKIAEVA 130 :: :::::::: ::::::::::: ::::: :::: :::::::: d5ruba1 84 ETGEAKLFSANITADDPFEIIARGE---YVLETFGENASHVALLV--DGYVAGAAAITTA 138 d1tx2a_ 131 AH--YDVPIILMHNR------DNMNYRNLMA---DMIADLYDSIKIAKDAGVRDEN---I 176 :: ::::::::: :::::: ::::::::::: : d5ruba1 139 RRRFPDNFLHYHR--AGHGAVTSPQSK----RGYTAFVHCKMARL-----------QGAS 181 d1tx2a_ 177 ILDPGIGFAKTPEQNLEAMR---NLEQLNVL--------------------GYPVLLGTS 213 :::: ::::::: ::::::: d5ruba1 182 GIHT----------------GTSSDRAIAY-MLTQDEAQGPFYRQSWGGMKACTPIIS-- 222 d1tx2a_ 214 RKSFIGHVLDLPVEERLEG---TGATVCLGIE--KGC-EFVRVH-------------DVK 254 :::::::::: ::: ::::: ::: d5ruba1 223 -------------------GGMNALRMPGFFENLGNANVILTA-GGGAFGHIDGPVAGAR 262 d1tx2a_ 255 EMSRMAKMMDAMIGK--------------------------------------- 269 :::::::::: d5ruba1 263 SLRQAWQAWR-----DGVPVLDYAREHKELARAFESFPGDADQIYPGWRKALGV 311 TMalign alignment (TM-score: 0.60 Raw score:160.76) d1tx2a_ 1 ---KWDYDLRC-GEY-TLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEG 55 :::::: :: :::::::::::::::::::: :: :: :::::::::: :: d5ruba1 1 GPS--VNISALW-KVLGRPEVDGGLVVGTIIKPKLG-LR-PK-PFAEACHAFW-LG---- 49 d1tx2a_ 56 AHIIDIGGESFAKVSVE-EEIKRVVPMIQAVSKEVK-----LPISIDTYKA-----E--V 102 : :::::::: ::::: :::::::::::::::::: :::::::::: : : d5ruba1 50 G-DFIKNDEP--QGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIAR 106 d1tx2a_ 103 AKQAIEAG---A--HIINDIWGAKAEPKIAEVAAHY-DVPIILMHN-RDN--MN-YRNLM 152 :::::::: : :::::::::::::::::::::: ::::::::: ::: :: :::: d5ruba1 107 GEYVLETFGENASHVALLVDGYVAGAAAITTARRRFPDNFLHYHRAGHGAVTSPQSKRG- 165 d1tx2a_ 153 ADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRN-LEQLN---V----- 203 :::::::::::::: ::::::: : ::::: ::::: : d5ruba1 166 YTAFVHCKMARLQG---------ASGIHTG--------T-SSDRAIAYMLTQDEAQGPFY 207 d1tx2a_ 204 ---L---GYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVH----D- 252 : :::::::::: :::::::::::::: :::::::: : d5ruba1 208 RQSWGGMKACTPIISGG--------------MNALRMPGFFENLG-NANVILTAGGGAFG 252 d1tx2a_ 253 --------VKEMSRMAKMMDAMI------------------------------------G 268 ::::::::::::::: d5ruba1 253 HIDGPVAGARSLRQAWQAWRDGVPVLDYAREHKELARAFESFPGDADQIYPGWRKALGV- 311 d1tx2a_ 269 K 269 d5ruba1 312 - 312 HHsearch alignment (Probability: 0.50 E-value:0.03) d1tx2a_ 15 LNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESFAKVSVEEE 74 ::::::::::: ::::::::::::::::::::::::::::::::::::::::: d5ruba1 18 VDGGLVVGTII--------KPKLGLRPKPFAEACHAFWLGGDFIKNDEPQGNQPFAPLRD 69 d1tx2a_ 75 -IKRVVPMIQAVSKEV--KLPISIDTY--KA-EVA---KQAIEAGAH-------IINDIW 118 ::::::::::::::: ::::::::: :: ::: ::::::::: :::::: d5ruba1 70 TIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVLETFGENASHVALLVDGYV 129 d1tx2a_ 119 GAKAEPKIAEVAAHYDVPIILM-HNRDNMNY--RNLMADMIADLYDSIKIAKDAGVRDEN 175 :: ::::::::::::::::: :::::::: ::::::::::::::::: ::::: d5ruba1 130 AG---AAAITTARRRFPDNFLHYHRAGHGAVTSPQSKRGYTAFVHCKMAR--LQGAS--- 181 d1tx2a_ 176 IILDPGIGFAKTPEQNLEAMRNLEQ 200 :::::::: :::::::::::::::: d5ruba1 182 GIHTGTSS-DRAIAYMLTQDEAQGP 205