Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate AZOBR_RS05495 AZOBR_RS05495 homocitrate synthase
Query= curated2:Q8TYM1 (509 letters) >FitnessBrowser__azobra:AZOBR_RS05495 Length = 381 Score = 299 bits (766), Expect = 1e-85 Identities = 162/366 (44%), Positives = 223/366 (60%), Gaps = 3/366 (0%) Query: 16 IFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIAREEL 75 I DTTLRDGEQT GVA T +EK+ IAR LDE GV +E G A E + IR +A L Sbjct: 9 INDTTLRDGEQTAGVAFTLDEKIAIARALDEAGVPELEIGIPAMGPEEREGIRAVAALGL 68 Query: 76 DAEVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERAREVVEYAR 135 A + RM D+ AA++ + V++ +P S++H+ KKL+ R L V+ AR Sbjct: 69 KARLMVWCRMHDTDLKAALDCKVGTVNLSMPVSDIHITKKLKRSRAWALAEIERKVKTAR 128 Query: 136 DHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAVKKLRER 195 DHGL V + ED +R ++++L EAGA R + DT+GV+ P +++LR Sbjct: 129 DHGLEVSLGGEDSSRADMDFLIAAATVAQEAGARRFRFADTLGVLDPFQTRACIERLRRA 188 Query: 196 VGEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEVVVVLEELY 255 D+ + +H HDD G+A AN++AAV GA V+ TVNG+GERAGNA LEEVVV L+ LY Sbjct: 189 T--DLEIEIHAHDDLGLANANSLAAVLGGATHVNTTVNGLGERAGNAPLEEVVVSLKVLY 246 Query: 256 GVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILKDESTYEPIP 315 G D G+ T L +S LVER + V NK++VG+ FTHE+GIH DG+L+D +TY+ Sbjct: 247 GQDCGVDTRALGAISDLVERASNRPVAVNKSIVGDAVFTHEAGIHVDGLLRDRATYQNFD 306 Query: 316 PEKVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRLGDRGKRI-TEADL 374 P +VG E R VLGKH GT+ ++ Q+G+ DD +L R++ L R KR T +L Sbjct: 307 PAEVGREHRIVLGKHSGTAGVKMAYGQLGIPCDDATAQAVLPRVRALATRAKRAPTAEEL 366 Query: 375 RAIAED 380 RA +D Sbjct: 367 RAFHDD 372 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: 480 Number of extensions: 18 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: 381 Length adjustment: 32 Effective length of query: 477 Effective length of database: 349 Effective search space: 166473 Effective search space used: 166473 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