Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate BWI76_RS18860 BWI76_RS18860 homocitrate synthase
Query= curated2:Q8TYM1 (509 letters) >FitnessBrowser__Koxy:BWI76_RS18860 Length = 380 Score = 232 bits (591), Expect = 2e-65 Identities = 140/378 (37%), Positives = 204/378 (53%), Gaps = 3/378 (0%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 + V I DTTLRDGEQ+PGVA EK+ IA L G+ +E G A + E+ I+ + Sbjct: 2 ERVLINDTTLRDGEQSPGVAFRTSEKVAIAEALYAAGITAMEVGTPAMGDEEIARIQLVR 61 Query: 72 REELDAEVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERAREVV 131 R+ DA + + RM ++ + + D V I +P S+ + KLR +LER + Sbjct: 62 RQLPDATLMTWCRMNALEIRQSADLGIDWVDISIPASDKLRQYKLREPLAVLLERLAMFI 121 Query: 132 EYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAVKK 191 A GL V I ED +R + L + + + A RL Y DTVG++ P + Sbjct: 122 HLAHTLGLKVCIGCEDASRASGQTLRAIAEVAQQCAAARLRYADTVGLLDPFTTAAQISA 181 Query: 192 LRERVGEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEVVVVL 251 LR+ ++ +H H+D GMATANT+AAV AGA V+ TV G+GERAGNAALE V + L Sbjct: 182 LRDVWSGEI--EMHAHNDLGMATANTLAAVSAGATSVNTTVLGLGERAGNAALETVALGL 239 Query: 252 EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILKDESTY 311 E GV+TG+ L L + V + P + +VGE FTHESG+H +L+D +Y Sbjct: 240 ERCLGVETGVHFSALPALCQRVAEAAQRAIDPQQPLVGELVFTHESGVHVAALLRDSESY 299 Query: 312 EPIPPEKVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRLGDRGKRI-T 370 + I P +G R VLGKH G + QMG ++ Q+ ++L ++R + KR Sbjct: 300 QSIAPSLMGRSYRLVLGKHSGRQAVNGVFDQMGYHLNAAQINQLLPAIRRFAENWKRSPK 359 Query: 371 EADLRAIAEDVLGRPAER 388 + +L AI +++ G A R Sbjct: 360 DYELVAIYDELCGESALR 377 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: 407 Number of extensions: 19 Number of successful extensions: 2 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: 380 Length adjustment: 32 Effective length of query: 477 Effective length of database: 348 Effective search space: 165996 Effective search space used: 165996 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: 51 (24.3 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