Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_010960169.1 MCA_RS04175 citrate synthase
Query= reanno::pseudo6_N2E2:Pf6N2E2_6062 (375 letters) >NCBI__GCF_000008325.1:WP_010960169.1 Length = 429 Score = 203 bits (517), Expect = 6e-57 Identities = 125/371 (33%), Positives = 198/371 (53%), Gaps = 23/371 (6%) Query: 26 GQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYTGKLRQLRDLPQALKE 85 G+ G L YRG D+ +L + F EV+YLL+YG+LPT Q + K+ + + +K Sbjct: 61 GEQGI-LRYRGIDIAELCEKSTFVEVSYLLIYGQLPTVEQYARFKEKIHHHSLIHEDMKS 119 Query: 86 VLERIPADAHPMDVMRTGCSFLGN-----LEPEQDFSQQHDKTDRLLAAFPAIMCYWYRF 140 P AHPM ++ + L L+P+Q ++ + RLL+ + + Y+ Sbjct: 120 FFTSYPGHAHPMAILSSMVCSLSVYHPELLKPDQTIDERDETISRLLSKVRVLAAFAYKR 179 Query: 141 SHQGQRIECVTDEVSIGGHFLHLL-----HGKKPSELHVKVMNVSLILYAEHEFNASTFT 195 S G+ E+ +FLH++ G P EL KV++V IL+A+HE N ST T Sbjct: 180 S-VGEAFVYTRPELDYISNFLHMMFTRPMRGYVPDELIRKVLDVLFILHADHEQNCSTST 238 Query: 196 ARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQEAIEGTLGMLARKD- 254 R+ S+ ++LF+ I+A I +L GPLHGGAN+A +EM+E + + K+ Sbjct: 239 VRMVGSSKANLFAAISAGICALWGPLHGGANQAVIEMLEEIHRAGGCYKKYIERAKDKND 298 Query: 255 --KIMGFGHAIYKDNDPRNEVIKGWSKKLADEVG-DTVLFPVSEAIDKT-----MWEQKK 306 ++MGFGH +YK DPR +++K + ++ + +G D + +++ +++ + ++K Sbjct: 299 PYRLMGFGHRVYKSYDPRAQILKKYCDEVLNYLGIDDPILEIAKGLEEVALTDPYFIERK 358 Query: 307 LFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFE--QRANNRIIRPSAEYTGV 364 L+PN DFY Y + IPT +FT +F RL GW AH E + RI RP Y G Sbjct: 359 LYPNVDFYSGIIYRALKIPTNMFTVMFALGRLPGWIAHWKEMLEDPGMRIARPRQIYIGE 418 Query: 365 EQRKFVPIEQR 375 QR +VPI QR Sbjct: 419 RQRPYVPIAQR 429 Lambda K H 0.321 0.135 0.406 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: 385 Number of extensions: 23 Number of successful extensions: 6 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: 375 Length of database: 429 Length adjustment: 31 Effective length of query: 344 Effective length of database: 398 Effective search space: 136912 Effective search space used: 136912 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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