Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_029131970.1 A3GO_RS0101980 citrate synthase
Query= reanno::pseudo6_N2E2:Pf6N2E2_6062 (375 letters) >NCBI__GCF_000428045.1:WP_029131970.1 Length = 430 Score = 184 bits (466), Expect = 5e-51 Identities = 120/364 (32%), Positives = 188/364 (51%), Gaps = 22/364 (6%) Query: 26 GQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYTGKLRQLRDLPQALKE 85 G+ G L YRG + L F EVA +L++GELP +AQ + ++ L +L + +K Sbjct: 61 GEKGI-LRYRGISLDALEHHPNFVEVALMLIFGELPNKAQYERFSTSLTNNANLDEDMKH 119 Query: 86 VLERIPADAHPMDVMRTGCSFLGNLEPE----QDFSQQHDKTDRLLAAFPAIMCYWYRFS 141 P A PM V+ S L PE +D +Q RL++ + Y YR S Sbjct: 120 HFAGFPRSAPPMAVLSAMISTLSCFHPEFLELEDATQVERAAARLISKVRTLAAYAYRRS 179 Query: 142 HQGQRIECVTDEVSIGGHFLHLLHGKKPSELHV-----KVMNVSLILYAEHEFNASTFTA 196 +G + +FLH++ + + + +N+ LIL+A+HE N ST T Sbjct: 180 -RGLPYNYPDPSLPYVSNFLHMMFSEPYRQYTIDDDVLSALNMVLILHADHEQNCSTSTV 238 Query: 197 RVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQEAIEGTLGMLARKD-- 254 R+ S+ ++LF+ A + +L GPLHGGAN A +EM+E + E + + KD Sbjct: 239 RMVGSSGANLFASCAAGVSALWGPLHGGANMAVIEMLEAIHNGNMTAEEYVALAKDKDSP 298 Query: 255 -KIMGFGHAIYKDNDPRNEVIKGWSKKLADEVG--DTVLFPVSE----AIDKTMWEQKKL 307 ++MGFGH +Y++ DPR +++ S+KL + +G D +L + A+ + + +KL Sbjct: 299 VRLMGFGHRVYRNFDPRATILREVSEKLLERMGKKDPLLSIARKLEEIALKDSYFIDRKL 358 Query: 308 FPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQR--ANNRIIRPSAEYTGVE 365 +PN DFY +GIPT +FT IF RL GW AH +EQ+ A+ +I RP Y G + Sbjct: 359 YPNVDFYSGIILRAIGIPTNMFTVIFAIGRLPGWIAHWYEQKRQADGKIWRPRQVYIGNK 418 Query: 366 QRKF 369 Q + Sbjct: 419 QSAY 422 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: 363 Number of extensions: 18 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: 375 Length of database: 430 Length adjustment: 31 Effective length of query: 344 Effective length of database: 399 Effective search space: 137256 Effective search space used: 137256 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 Apr 09 2024. 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