Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_002719494.1 RSPH17029_RS05125 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000015985.1:WP_002719494.1 Length = 529 Score = 355 bits (910), Expect = e-102 Identities = 206/518 (39%), Positives = 305/518 (58%), Gaps = 16/518 (3%) Query: 1 MREANADADPPDEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAAS 60 M + A D V IFDTTLRDGEQ+PG +T +EKL IA LDE+GVD IEAGF AS Sbjct: 1 MTDTTKTASEQDRVLIFDTTLRDGEQSPGATMTHDEKLEIAALLDEMGVDIIEAGFPIAS 60 Query: 61 EGELKAIRRIAREELDAEVCSMARMVKGDVD----AAVEAEADAVHIVVPTSEVHVKKKL 116 EG+ +A+ IAR+ +A +C +AR D+D A A++ +H + TS +H + Sbjct: 61 EGDFEAVSAIARQSKNATICGLARANYKDIDRCWEAVRHAKSPRIHTFIGTSPLH-RAIP 119 Query: 117 RMDREEVLERAREVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDT 176 +D +++ ER + V +AR+ V+ S D TRTE +YL V + ++AGA + DT Sbjct: 120 NLDMDQMAERIHDTVSHARNLCDNVQWSPMDATRTEHDYLCRVVEIAIKAGATTINIPDT 179 Query: 177 VGVMAPEGMFLAVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNG 234 VG AP ++ L ERV + ++ + HCH+D GMATAN +AAV AGARQ+ T+NG Sbjct: 180 VGYTAPRESADLIRMLVERVPGADTIVFATHCHNDLGMATANALAAVEAGARQIECTING 239 Query: 235 IGERAGNAALEEVVVVLE---ELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGEN 291 +GERAGN ALEEVV+ L+ ++ TGI T ++ +S+ V ++G V NKA+VG+N Sbjct: 240 LGERAGNTALEEVVMALKVRNDIMPFRTGIDTTKIMNISRKVATVSGFPVQFNKAIVGKN 299 Query: 292 AFTHESGIHADGILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDE 350 AF HESGIH DG+LK+ T+E + P VG + V+GKH G + +R KLK +G D+ D Sbjct: 300 AFAHESGIHQDGMLKNAQTFEIMRPADVGLADTSLVMGKHSGRAALRAKLKDLGYDLADN 359 Query: 351 QLLEILRRLKRLGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIV 410 QL ++ R K L DR K + + D+ A+ +D + ++++ V G A + Sbjct: 360 QLNDVFVRFKALADRKKEVYDDDIVALIQDQVTSAEHDTLQLKRLRVVCGTDGPQEAEMT 419 Query: 411 VKIDGTRKEAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKL 470 + ++G +TG GPVDA A++ +L Y+ A+T GTDA V V+L Sbjct: 420 LSVEGVDHAIDATGDGPVDAAFNAVKMIYPHHA---KLHLYQVHAVTEGTDAQATVSVRL 476 Query: 471 RDPETGDIVHSGSSREDIVVASLEAFIDGINSLMARKR 508 E G I ++ D VVAS++A+++ +N L+ R++ Sbjct: 477 E--EDGKIATGQAADTDTVVASVKAYVNALNRLIHRRQ 512 Lambda K H 0.315 0.134 0.367 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: 662 Number of extensions: 31 Number of successful extensions: 5 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: 509 Length of database: 529 Length adjustment: 35 Effective length of query: 474 Effective length of database: 494 Effective search space: 234156 Effective search space used: 234156 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 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 16 2024. The underlying query database was built on Apr 09 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