Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011764286.1 AZO_RS02775 homocitrate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000061505.1:WP_011764286.1 Length = 396 Score = 259 bits (663), Expect = 9e-74 Identities = 157/386 (40%), Positives = 215/386 (55%), Gaps = 7/386 (1%) Query: 14 VRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIARE 73 V I DTTLRDGEQ+ GVA T EK IAR L EIGV +E G A E IR IA Sbjct: 5 VTIDDTTLRDGEQSAGVAFTRAEKCGIARILAEIGVPELEIGIPAMGSEECGDIRAIADT 64 Query: 74 ELDA----EVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERARE 129 D + R+ D+DA + + VP S+ ++ KL R+EVL R Sbjct: 65 LADGGHDTRLIVWGRLTSADIDACRSLPVQMLELSVPVSDQQIRHKLGATRDEVLARIAR 124 Query: 130 VVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAV 189 V AR+ G V + ED +R + +L EV A AGA R + DT+G++ P F A+ Sbjct: 125 WVPVAREAGFDVGVGGEDASRADPAFLAEVIQAAEAAGARRFRFADTLGILDPFATFEAI 184 Query: 190 KKLRERVGEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEVVV 249 + LR + + +H HDD G+ATANT+AAVRAGA V+ TVNG+GERAGNAALEEV + Sbjct: 185 RALR--AASKLEIEMHAHDDLGLATANTLAAVRAGASHVNTTVNGLGERAGNAALEEVAL 242 Query: 250 VLEELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILKDES 309 L + +G+ I RL + S+ V R +G V +K+VVGE FTHE+GIH DG+LKD + Sbjct: 243 GLRQFHGMGEIIDFTRLLDTSEAVARASGRPVGWHKSVVGEGVFTHEAGIHVDGLLKDPA 302 Query: 310 TYEPIPPEKVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRLGDRGKRI 369 Y+ I P +G R +LGKH G + +G+++D + +L R++ R KR Sbjct: 303 NYQGIDPALLGRSHRMLLGKHSGGRGVAAAYAGLGIELDAARTACLLARIREFTSRTKRT 362 Query: 370 TE-ADLRAIAEDVLGRPAERDIEVED 394 + DL A E++ A+ D + D Sbjct: 363 PQREDLLAFWEELEAGSAQCDDLLHD 388 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: 512 Number of extensions: 20 Number of successful extensions: 3 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: 396 Length adjustment: 33 Effective length of query: 476 Effective length of database: 363 Effective search space: 172788 Effective search space used: 172788 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 Jul 25 2024. The underlying query database was built on Jul 25 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