Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011318900.1 AVA_RS10680 2-isopropylmalate synthase
Query= curated2:O26819 (496 letters) >NCBI__GCF_000204075.1:WP_011318900.1 Length = 531 Score = 354 bits (908), Expect = e-102 Identities = 218/522 (41%), Positives = 308/522 (59%), Gaps = 35/522 (6%) Query: 2 QVRVLDTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKI-- 59 ++ + DTTLRDGEQ PG +L +EKL IA ++ LG DIIEAG A S G+ E + KI Sbjct: 7 RIIIFDTTLRDGEQCPGATLNIDEKLAIAKQLARLGVDIIEAGFAFASPGDFEAVHKIAQ 66 Query: 60 ---TSEGLRAEICSFARAVREDIDAAISCDVDS----VHLVVPTSDLHLEHKLRKTREEV 112 T G ICS ARA +DI AA + +H + TSD+HL++KL+KTR EV Sbjct: 67 TVGTENG--PVICSLARARHDDIKAAAEAIKPAAKGRIHTFIATSDIHLQYKLKKTRPEV 124 Query: 113 LEQAVDCTEYAVDHGILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTPE 172 + A + YA VE S ED+ RSD +FL + I AGA I DTVG TP Sbjct: 125 IAIAEEMVAYAKSFTDDVEFSPEDAGRSDPEFLYQVLERAIAAGATTINIPDTVGYTTPS 184 Query: 173 RSYEFYRGLSEL-----GAPLSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGN 227 +G+ E A +SVH HND GLAVAN L ++ GA ++ TINGIGERAGN Sbjct: 185 EFGAIIKGIKENVPNIDQAIISVHGHNDLGLAVANFLEAVKNGARQLECTINGIGERAGN 244 Query: 228 AALEEVVVALK--------------SLYDVDTSINIEMLYETSRMVARMTGVYLQPNKAI 273 AALEE+V+A+ + T+I+ + +Y+TSR+V+ +TG+ +QPNKAI Sbjct: 245 AALEELVMAMHVRRQYFNPFLGRHPDSEEPLTNIDTKQIYKTSRLVSNLTGMLVQPNKAI 304 Query: 274 VGENAFAHESGIHADGVLKKAETYEPITPEMVG-HGRGFVMGKHIGTHALRKRLDELGMK 332 VG NAFAHESGIH DGVLK TYE + +++G V+GKH G +A R RL ELG + Sbjct: 305 VGANAFAHESGIHQDGVLKNKLTYEIMDAQLIGLTDNQIVLGKHSGRNAFRTRLKELGFE 364 Query: 333 VADDKLMEIFRRVKTLGDMGKCVTDVDLQAIAEDVLGVMEDKVVDLQEVTIVSGNRVTPT 392 +++ +L + F + K + D K ++D DL+AI D + D + ++ V + G+ PT Sbjct: 365 LSETELNKAFVKFKEVADKKKEISDWDLEAIVNDEIQQAPD-LFRVELVQVSCGSNARPT 423 Query: 393 ASVKLRV-DDREVLEAGTGVGPVDAAIVAIKKSLEDFADITLEEYHVDAITGGTDALIDV 451 A+V LR D E+ +A G GPVDA AI + + L E+ V ++T G DA+ +V Sbjct: 424 ATVTLRTPDGEELTDAAIGTGPVDAVYKAINRVVN--VPNQLIEFSVQSVTAGIDAIGEV 481 Query: 452 VIKLRHGDRIISARSTQPDIIMASVEAFLSGVNRLLANEKSE 493 I+LR+ R+ S + DII+AS +A+++ +NRL A+ +++ Sbjct: 482 TIRLRYESRVFSGHAANTDIIVASAQAYVNALNRLYASLQTQ 523 Lambda K H 0.317 0.135 0.373 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 641 Number of extensions: 37 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 496 Length of database: 531 Length adjustment: 35 Effective length of query: 461 Effective length of database: 496 Effective search space: 228656 Effective search space used: 228656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory