Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate HSERO_RS06380 HSERO_RS06380 excisionase
Query= BRENDA::Q9I5E3 (375 letters) >FitnessBrowser__HerbieS:HSERO_RS06380 Length = 431 Score = 89.0 bits (219), Expect = 2e-22 Identities = 58/189 (30%), Positives = 92/189 (48%), Gaps = 10/189 (5%) Query: 175 KVMNVSLILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIE 234 +++ ++L+L A+HE NAS+FT+R AST + L + V + L G H GA +E + Sbjct: 211 ELIRMALVLCADHELNASSFTSRCVASTDASLRAVVIAGLAGLSGGRH-GATTGRVEALW 269 Query: 235 RFSSPQEATAELLKMLERKDKIMGFGHAIYKDSDPRNEVIKGWSKQLADEVGDKVLFAVS 294 ++ ++ + L R D + GFGH +Y D DPR + L+ + +A Sbjct: 270 DELGTRDVDRKMRERLSRGDDLPGFGHTLYPDGDPRASYL------LSQILPRHSPWAAM 323 Query: 295 EAIDKTMWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRANNRI 354 T+ QK P+ DF + + +P +F R+ GW AH EQR + + Sbjct: 324 IDAGITLTGQK---PSVDFALVALRRHLRLPVGAAFGLFALGRSIGWIAHGLEQREQHHL 380 Query: 355 IRPSAEYTG 363 IRP A Y G Sbjct: 381 IRPRAVYIG 389 Score = 25.4 bits (54), Expect = 0.003 Identities = 13/25 (52%), Positives = 14/25 (56%) Query: 28 EGAGLTYRGYDVRDLAAAAIFEEVA 52 +G L YRG D LA A EEVA Sbjct: 84 DGGRLFYRGVDALSLAEHASLEEVA 108 Lambda K H 0.319 0.134 0.396 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: 355 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 431 Length adjustment: 31 Effective length of query: 344 Effective length of database: 400 Effective search space: 137600 Effective search space used: 137600 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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