Align Accumulation of dyads protein 2; Ammonia transport outward protein 1 (characterized)
to candidate BWI76_RS04285 BWI76_RS04285 hypothetical protein
Query= SwissProt::P25613 (283 letters) >FitnessBrowser__Koxy:BWI76_RS04285 Length = 188 Score = 116 bits (291), Expect = 3e-31 Identities = 71/180 (39%), Positives = 98/180 (54%), Gaps = 9/180 (5%) Query: 86 KFANPAPLGLSAFALTTFVLSMFNARAQGITVPNVVVGCAMFYGGLVQLIAGIWEIALEN 145 K ANPAPLGL F +TT +L++ N+ V + +G +FYGG+ Q+ AG+ E N Sbjct: 5 KLANPAPLGLMGFGMTTILLNLANSGLFAFDVAILAMG--IFYGGIAQIFAGLLEFKKGN 62 Query: 146 TFGGTALCSYGGFWLSFAAIYI-PWFGILEAYEDNESDLNNALGFYLLGWAIFTFGLTVC 204 TFG TA SYG FWL+ AI + P G+ EA + LG YL W IFT + Sbjct: 63 TFGLTAFTSYGAFWLTLVAILLMPKMGLAEAPN------AHFLGMYLGLWGIFTLFMFFG 116 Query: 205 TMKSTVMFFLLFFLLALTFLLLSIGHFANRLGVTRAGGVLGVVVAFIAWYNAYAGVATKQ 264 T+K+ M +F L + F LL+IGH A+ G+ + G +G+V A Y A V +Q Sbjct: 117 TLKAARMLQFVFLSLTVLFALLAIGHLADNEGIVKIAGWVGLVCGGSAIYLAMGEVLNEQ 176 Lambda K H 0.323 0.140 0.436 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: 194 Number of extensions: 9 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: 283 Length of database: 188 Length adjustment: 23 Effective length of query: 260 Effective length of database: 165 Effective search space: 42900 Effective search space used: 42900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 46 (22.3 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