Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate Dsui_0578 Dsui_0578 homocitrate synthase NifV
Query= curated2:Q8TYM1 (509 letters) >FitnessBrowser__PS:Dsui_0578 Length = 384 Score = 274 bits (700), Expect = 5e-78 Identities = 149/355 (41%), Positives = 208/355 (58%), Gaps = 2/355 (0%) Query: 14 VRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIARE 73 + I DTTLRDGEQT GVA T EKL IA+ L GV +E G A E E + IR IA Sbjct: 4 ITINDTTLRDGEQTAGVAFTAAEKLAIAQALAAAGVPEMEVGIPAMGEQEQEVIRAIAGL 63 Query: 74 ELDAEVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERAREVVEY 133 L + + RM D++ A V++ +P S+ ++ KL D VL+ R V Sbjct: 64 GLSSRLMVWGRMCAADLEVTRRCNAHIVNLSIPVSDQQIRHKLNKDHRWVLDSIRRFVPE 123 Query: 134 ARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAVKKLR 193 AR GL V + ED +R +L++L+ V +A AGA R + DT+GV+ P + LR Sbjct: 124 ARAAGLEVCVGGEDSSRADLDFLHRVMEAAQAAGARRFRFADTLGVLDPFITHQRIAALR 183 Query: 194 ERVGEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEVVVVLEE 253 R D+ + +H HDD G+ATANT+AAV AGA ++ TVNG+GERAGNA LEE V+ L Sbjct: 184 AR--SDLEIEIHAHDDLGLATANTLAAVTAGATHINTTVNGLGERAGNAPLEESVIALRH 241 Query: 254 LYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILKDESTYEP 313 LY +D+G+ +L +S LV + +G V NK++VG N FTHE+GIH DG+ K+ + Y+ Sbjct: 242 LYDIDSGVDPLQLPAISDLVAKASGRPVAVNKSIVGANVFTHEAGIHVDGLAKNPANYQA 301 Query: 314 IPPEKVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRLGDRGKR 368 P +VG R VLGKH G++ + K +G+D+D+ IL R++ KR Sbjct: 302 FDPAEVGKGHRIVLGKHSGSTAVIHAYKDLGIDIDEGMARRILSRVRSYAMAFKR 356 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: 445 Number of extensions: 12 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: 384 Length adjustment: 32 Effective length of query: 477 Effective length of database: 352 Effective search space: 167904 Effective search space used: 167904 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