Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011841500.1 RSPH17029_RS10985 homocitrate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000015985.1:WP_011841500.1 Length = 391 Score = 230 bits (586), Expect = 8e-65 Identities = 148/363 (40%), Positives = 193/363 (53%), Gaps = 9/363 (2%) Query: 10 PPDEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRR 69 P V + DTTLRDGEQT GVA T EK IA L GV +E G A E E IR Sbjct: 15 PLAPVALCDTTLRDGEQTAGVAFTRAEKRAIAEALQAAGVAEVEVGVPAMGEEERADIRA 74 Query: 70 IAREELDAEVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERARE 129 +A A R+ D+ AA +HI VP SE + KL D V ++ + Sbjct: 75 VAAVLKTAAPVVWCRLRAEDLAAAQRTGVVRLHIGVPVSERQISAKLGKDAAWVRDKVEK 134 Query: 130 VVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAV 189 +V A G V + ED +R + +L E+ EAGA R +DT+GV+ P A Sbjct: 135 LVRAASWAGHKVSVGAEDASRADPFFLAEIAHVAAEAGAIRFRISDTLGVLDP----FAA 190 Query: 190 KKLRERVGEDVILSV--HCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEV 247 +L RV L V H H+D GMATAN++AA RAGA + VTVNG+GERAGNAALEEV Sbjct: 191 HELVGRVVTRCPLPVEFHGHNDLGMATANSLAAARAGASHLSVTVNGLGERAGNAALEEV 250 Query: 248 VVVLEELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILKD 307 LE G TG+ +L LS+LV R +G + P K +VGE FTHE GIH DG++KD Sbjct: 251 AAALEAA-GRATGVALGQLCALSELVARASGRPLSPQKPIVGEGVFTHECGIHVDGLMKD 309 Query: 308 ESTYE--PIPPEKVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRLGDR 365 +TYE + PE+ G R +GKH + + + L + G+ D L ++ L+ Sbjct: 310 RATYESADLRPERFGRSHRIAIGKHSSAAGLARALAEAGLPADAATLAALMPALRDWAAT 369 Query: 366 GKR 368 KR Sbjct: 370 AKR 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: 452 Number of extensions: 20 Number of successful extensions: 4 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: 391 Length adjustment: 32 Effective length of query: 477 Effective length of database: 359 Effective search space: 171243 Effective search space used: 171243 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 16 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