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 | d1jfla2 | Aspartate racemase | Aspartate/glutamate racemase | ATC-like | α/β |
| Hit | d1vkza2 | Glycinamide ribonucleotide synthetase (GAR-syn), N-domain | PreATP-grasp domain | PreATP-grasp domain | α/β |
Query <-- 0.593 --> IntermediateDALI alignment (Z-score: 3.0 Raw score:191.90) query 1 slqLRLALNQ-------------------------------IDST------VGDIAGNAE 23 ::::::: :::: ::::::::: d1jfla2 1 --fKKAGLLAttgtivsgvyekefskygveimtptedeqkdVMRGiyegvkAGNLKLGRE 58 query 24 AILRWTRHSAEQGAHLVAF-PEMAltgypvedlalrssfveasrtalrelAARLaeegfg 82 ::::::::::::::::::: :::: :::: d1jfla2 59 LLLKTAKILEERGAECIIAgCTEV----------------------svvlKQDD-----l 91 query 83 ELPVLvgyldrsesaqpkygqpagaprnaaavlhrgrvaltfakhhlpnygvfdefryfv 142 ::::: d1jfla2 92 KVPLI------------------------------------------------------- 96 query 143 pgdtmpivrlhgvdialaicedlwqdggrvpaarsagaglllsvnaspyerdkddtrlel 202 d1jfla2 97 ------------------------------------------------------------ 97 query 203 vrkraqeagcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcvvldldlpaa 262 d1jfla2 97 ------------------------------------------------------------ 97 query 263 eaepptgvvddglridrlviseeplpayeaelaggyadrldadeevysalvvglrayvak 322 d1jfla2 97 ------------------------------------------------------------ 97 query 323 ngfrsvliglsggidsalvaaiacdalgaqnvygvsmpskyssdhskgdaaelarrtgln 382 d1jfla2 97 ------------------------------------------------------------ 97 query 383 frtvsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqeghivlapgnkselavgy 442 d1jfla2 97 ------------------------------------------------------------ 97 query 443 stlygdsvgaygpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldaile 502 d1jfla2 97 ------------------------------------------------------------ 97 query 503 lyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitn 562 d1jfla2 97 -------------------------------------------------dpmdviaevav 107 query 563 rwregh 568 d1jfla2 108 kvalek 113 FAST alignment (Normalized score: 1.63 Raw score:413.10) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1jfla2 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1jfla2 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1jfla2 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1jfla2 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1jfla2 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDS--ALVAAIACDALGA--QNVY 355 :::::::: :::: ::::::::: :::: d1jfla2 1 -------------------------FKKAGLLAT-TGTIVSGVYEKEFSK----YGVEIM 30 query 356 GVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLT------------- 402 : d1jfla2 31 T----------------------------------------------PTEDEQKDVMRGI 44 query 403 -------GLAEENLQSRLRGTTLMAISNQEG---HIVLAPGNKSELAVGYSTLYGDSVG- 451 :::::::::::::::::: ::::: d1jfla2 45 YEGVKAGNLKLGRELLLKTAKILEE------RGAECIIA--------------------G 78 query 452 ----------------AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYP 495 :::: d1jfla2 79 CTEVSVVLKQDDLKVPLIDP---------------------------------------- 98 query 496 VLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKD 555 d1jfla2 99 ------------------------------------------------------------ 99 query 556 RRLPITNRWREGH--------------- 568 d1jfla2 99 -------------MDVIAEVAVKVALEK 113 TMalign alignment (TM-score: 0.13 Raw score:76.04) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1jfla2 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1jfla2 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1jfla2 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1jfla2 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1jfla2 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::: d1jfla2 1 ----------------------------------------------------FKKAGLLA 8 query 361 SKYSSDHSK--GDAAELARRTGLNFRTV-S--IEPMFDAY--MASLGL-TGLAE-ENLQS 411 : :: :: ::::::::::::::::: : :: ::::: :: ::::: :: : d1jfla2 9 T--TG--TIVSGVYEKEFSKYGVEIMTPTEDEQK-DVMRGIY----EGVKAGNLK-LG-R 57 query 412 RLRGTTLMAISNQEGHIVLAP-GNKSELAVGYSTLYGD-SVG--A--YGPI--KDVYKTS 463 :::::::::::::: :::::: :::::: ::: : :::: :::: : d1jfla2 58 ELLLKTAKILEERG-AECIIAG----------CTEVSVVLKQDDLKVPLIDPM-DVIA-E 104 query 464 IFRLAEWRNRAAAERGQTPPIPEASITKPDYP---VLDAILELYVDRDTGADAIVAAGYD 520 :::: : : d1jfla2 105 VAVK-V-------------------------ALEK------------------------- 113 query 521 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1jfla2 114 ------------------------------------------------ 114 HHsearch alignment (Probability: 0.04 E-value:0.07) query 16 GDIAGNAEAILRWTRHSAEQGAHLVAF 42 ::::::::::::::::::::::::::: d1jfla2 51 GNLKLGRELLLKTAKILEERGAECIIA 77
Intermediate <-- 1.003 --> HitDALI alignment (Z-score: 4.0 Raw score:235.00) d1jfla2 1 fKKAGLLATTGTIvsGVYEKEFSKYGVEIMTPtedeqkdvmrgiyegvkagnlklgreLL 60 :::::::::::: ::::::::::::::::: :: d1vkza2 1 -VRVHILGSGGRE--HAIGWAFAKQGYEVHFY-----------pgnagtkrdgtnhpyEG 46 d1jfla2 61 LKTAKILEergaECIIAGCtEVSVVLKQddlkVPLIDpmdviaevavkvalek 113 :::::::: ::::::: :::::::: ::::: d1vkza2 47 EKTLKAIP---eEDIVIPG-SEEFLVER----SNVFG------pvkevarleg 85 FAST alignment (Normalized score: 3.47 Raw score:339.70) d1jfla2 1 FKKAGLLATTGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKAGNLKLGRE-- 58 :::::::::::: :::::::::::::::: d1vkza2 1 -VRVHILGSGGRE--HAIGWAFAKQGYEVHF---------------------------YP 30 d1jfla2 59 --------------LLLKTAKILEERGA---ECIIAGCTEVSVVLKQDDLKVPLIDPMDV 101 :::::::: :::::: ::::::: d1vkza2 31 GNAGTKRDGTNHPYEGEKTLKA------IPEEDIVIP-GSEEFLV--------------- 68 d1jfla2 102 IAEVAVKVALEK----------------- 113 d1vkza2 69 ------------ERSNVFGPVKEVARLEG 85 TMalign alignment (TM-score: 0.43 Raw score:48.71) d1jfla2 1 FKKAGLLATTGTIVSGVYEKEFSKYGVEIMTP------------TEDEQKDVMRGIYEGV 48 ::::::: :::: :::::::::::::::::: : :: d1vkza2 1 -VRVHILG-SGGR-EHAIGWAFAKQGYEVHFYPGNAGTKRDGTNH--PY----------- 44 d1jfla2 49 KAGNLKLGRELLLKTAKILEERGAECIIAGCTEVSVVLKQDDLKVPLID----------P 98 :::::::: : ::::::::: ::::::: : ::::: d1vkza2 45 ----------EGEKTLKA-I--PEEDIVIPG-SEEFLVE---R-SNVFGPVKEVARLEG- 85 d1jfla2 99 MDVIAEVAVKVALEK 113 d1vkza2 86 --------------- 86 HHsearch alignment (Probability: 0.01 E-value:0.23) d1jfla2 3 KAGLLATTGTIVSGVYEKEFSKYGVEI-MTPTEDEQKDVMRGIYEGVKAGNLKLGRELLL 61 ::::::::: :::::::::::::::: ::::::::::: ::::: :: d1vkza2 2 RVHILGSGG--REHAIGWAFAKQGYEVHFYPGNAGTKRD-------GTNHP-------YE 45 d1jfla2 62 KTAKILEERGAECIIAGCTEVSVVLKQDDLKVPLIDPMDVIAE 104 :::::::::::::::::::: ::: :::::::::::::: d1vkza2 46 GEKTLKAIPEEDIVIPGSEE-FLV-----ERSNVFGPVKEVAR 82