Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate AO353_24260 AO353_24260 hypothetical protein
Query= curated2:A3CUF2 (503 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24260 Length = 309 Score = 173 bits (439), Expect = 7e-48 Identities = 107/302 (35%), Positives = 160/302 (52%), Gaps = 5/302 (1%) Query: 9 IRFFDTTLRDGEQTPGVSLTPAGKLEIATHLADVGVHVIEAGSAAASVGERESIRAIADA 68 I D+TLR+G Q PGV LT L IA LAD G+ IEAG AS E + + A+ + Sbjct: 4 ITLVDSTLREGNQAPGVKLTTKSTLTIAYALADAGIDFIEAGHPYASKQEFDRVTALVKS 63 Query: 69 GLAAECCTYVRALPGDIDLAADAGADSVHLVVPVSDLHIAKKLRKTREQVSEMAWSAVEY 128 +A + RA DID A GA+ + + +++ ++RK++ Q+ ++ +V Y Sbjct: 64 KIAKNILAHSRAHQDDIDAVAATGANWIGIFAGINETSQKYRIRKSKAQIQDLIKRSVLY 123 Query: 129 AKERGLVVELSGEDASRADQDFLAEVFREGVERGADRLCFCDTVGLLTPERAAAII---- 184 AK GL V + EDASR D L E F+ GADR+C+ D++G+ P + A I Sbjct: 124 AKSLGLKVRYTIEDASRTPSDDLIETFKIAKAAGADRICYADSLGVCDPFKVQATIKLIR 183 Query: 185 PPLLFAPLSIHCHDDLGFGLATTVAALRAGATCAHVTVNGLGERAGNTSLEELVMALEVL 244 L L +H HDD G +A T+A++ AGAT TVNG+GER G T L+ L Sbjct: 184 QSLSDIDLEVHFHDDRGLAMANTLASIEAGATFISCTVNGIGERCGITETCLLITNLHFN 243 Query: 245 YGVDTGIATEELYPLSTHVARLTGVPLATNKPIVGEMAFTHESGIHAHGVMRDASTYEPL 304 + +G A++ L LS+ V++ G +PI+GE +F H + +H R+ + Y + Sbjct: 244 SILCSGKASKVL-KLSSIVSKELGDAFDRRRPIIGEYSFVHTAKLHVTANSRNKNCYHWI 302 Query: 305 QP 306 P Sbjct: 303 DP 304 Lambda K H 0.318 0.134 0.376 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: 297 Number of extensions: 12 Number of successful extensions: 3 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: 503 Length of database: 309 Length adjustment: 31 Effective length of query: 472 Effective length of database: 278 Effective search space: 131216 Effective search space used: 131216 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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