Align 2-aminomucoate semialdehyde dehydrogenase subunit (EC 1.2.1.32) (characterized)
to candidate WP_015446956.1 R2APBS1_RS03885 aldehyde dehydrogenase
Query= metacyc::MONOMER-13321 (542 letters) >NCBI__GCF_000230695.2:WP_015446956.1 Length = 527 Score = 142 bits (358), Expect = 3e-38 Identities = 95/281 (33%), Positives = 137/281 (48%), Gaps = 6/281 (2%) Query: 43 EAVKSGHQALSGEWGRTTATQRVALLRRIADEMERRQGDFLAAEMADTGKPHSMASSIDV 102 +A QA W +R LL R+ + +E R D AA + + GK + M + + Sbjct: 75 QAAMCAAQAAGPAWRAMPVAERTRLLHRVGELLEERVYDIAAAMVLEVGK-NRMEALGEA 133 Query: 103 PRGIANFRTFADILATAPVDSHRL--DLADGAYALNYSARKPLGVVGVISPWNLPLLLMT 160 + F +AD + +H L D G + N S +P GV VI+P+N PL L Sbjct: 134 QETVDFFHHYADDFESHAGYNHVLPDDPVTGFASHNASVMRPYGVWVVIAPFNFPLALAG 193 Query: 161 WKVAPALACGNTVVVKPSEDTPGTATLLAEVMEAAGVPPGVFNLVHGFGPNSAGEFISSH 220 VA AL GNTVV+K + DTP LLA+ + AG+PPGVFN + G G GE ++ H Sbjct: 194 GPVAAALVTGNTVVLKGASDTPWAGRLLADCIRDAGLPPGVFNYLSGAG-REIGEALAQH 252 Query: 221 PDISAITFTGESRTGTTIMRAAAEGV--KPVSFELGGKNAAIIFADCDFDKMLDTMMRAL 278 P + ITFTG G +MR A G +P E+GGKN I+ D D+ ++R+ Sbjct: 253 PLTAGITFTGSVPVGRHLMRQMAGGAYPRPCIAEMGGKNPCIVTERADLDRAAAGIVRSA 312 Query: 279 FLNSGQVCLCSERVYVERPLYDRFCAALVERIKGMKIDWPQ 319 + GQ C R+YV + D L + ++I P+ Sbjct: 313 YGMGGQKCSALSRLYVHESVADALIGRLHAQATAIRIGDPR 353 Lambda K H 0.319 0.135 0.423 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: 533 Number of extensions: 30 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: 542 Length of database: 527 Length adjustment: 35 Effective length of query: 507 Effective length of database: 492 Effective search space: 249444 Effective search space used: 249444 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 (21.7 bits) S2: 52 (24.6 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