GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ady2 in Flavobacterium sp. LM5

Align Accumulation of dyads protein 2; Ammonia transport outward protein 1 (characterized)
to candidate WP_078212752.1 BXU11_RS12425 hypothetical protein

Query= SwissProt::P25613
         (283 letters)



>NCBI__GCF_002017945.1:WP_078212752.1
          Length = 185

 Score = 97.1 bits (240), Expect = 3e-25
 Identities = 59/173 (34%), Positives = 88/173 (50%), Gaps = 5/173 (2%)

Query: 86  KFANPAPLGLSAFALTTFVLSMFNARAQGITVPNVVVGCAMFYGGLVQLIAGIWEIALEN 145
           K AN APLGL  F +TT +L++ N       V +V++   +FYGG+ Q+IAGI+ +    
Sbjct: 4   KQANVAPLGLLGFGMTTILLNIHNMGF--FPVSSVIISMGLFYGGMAQIIAGIFSLHQGK 61

Query: 146 TFGGTALCSYGGFWLSFAAIYIPWFGILEAYEDNESDLNNALGFYLLGWAIFTFGLTVCT 205
           TF GTA  SYG FW+S   I   W      +E   +      G YL+ W +FT  +   T
Sbjct: 62  TFAGTAFTSYGFFWISLVGI---WLFPNTGFELAGTTPAPFFGCYLVLWGLFTAFMWWGT 118

Query: 206 MKSTVMFFLLFFLLALTFLLLSIGHFANRLGVTRAGGVLGVVVAFIAWYNAYA 258
              + +   +F  L + F +L++  F N   +    GV+GV+    A+Y A A
Sbjct: 119 WGGSKVQQFVFLSLTILFFVLALSKFLNSEAINEIAGVIGVICGGSAFYLAMA 171


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: 200
Number of extensions: 19
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: 185
Length adjustment: 23
Effective length of query: 260
Effective length of database: 162
Effective search space:    42120
Effective search space used:    42120
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 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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