Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011801696.1 PNAP_RS11555 homocitrate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000015505.1:WP_011801696.1 Length = 395 Score = 295 bits (756), Expect = 2e-84 Identities = 164/374 (43%), Positives = 228/374 (60%), Gaps = 8/374 (2%) Query: 11 PDEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRI 70 P + I DTTLRDGEQT GVA T +EK IA L GV +E G A E E+ I I Sbjct: 2 PLNLIINDTTLRDGEQTAGVAFTVDEKCAIACALAAAGVPEMEIGIPAMGEEEIDCINTI 61 Query: 71 AREELDAEVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERAREV 130 A EL A + R+ D+ +A+ +AD +H+ +P S++H++ KLR RE VL + V Sbjct: 62 AALELPAALMIWGRLTDADLASALRCQADIIHLSIPVSDIHLRHKLRQSREWVLAQVTRV 121 Query: 131 VEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAVK 190 +E A G + + ED +R + +L +V + GA R+ + DT+GV+ P + A+ Sbjct: 122 IEKAVASGRKISLGAEDASRADAGFLSQVARRAQDCGASRIRFADTLGVLDPFTTYEAIT 181 Query: 191 KLRERVGEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEVVVV 250 +LRE V D+ +H H+D G+ATANT+AA+RAGA + TVNG+GERAGNAALEEVV+ Sbjct: 182 RLREAVHLDI--EIHAHNDLGLATANTLAALRAGATHANTTVNGLGERAGNAALEEVVMG 239 Query: 251 LEELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILKDEST 310 + L+ TG+ T+ L +S+LV R +G +V NK++VGE FTHESGIH DG+LK+ ST Sbjct: 240 VRHLHHAQTGVSTQALVSISRLVARASGRQVAFNKSIVGEAVFTHESGIHIDGLLKNAST 299 Query: 311 YEPIPPEKVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRLGDRGKRI- 369 YE P ++G ERR VLGKH G+ +R+ MGV +DD+ L R L R+ D R+ Sbjct: 300 YESFDPSELGRERRTVLGKHSGSQSVRQAYGAMGVVLDDDALTG--RVLARIRDHAMRVK 357 Query: 370 ---TEADLRAIAED 380 T +LR D Sbjct: 358 QEATPDELRGFLRD 371 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: 474 Number of extensions: 15 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: 395 Length adjustment: 33 Effective length of query: 476 Effective length of database: 362 Effective search space: 172312 Effective search space used: 172312 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 10 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