GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Pseudomonas simiae WCS417

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate GFF3539 PS417_18125 polar amino acid ABC transporter permease

Query= reanno::acidovorax_3H11:Ac3H11_2554
         (222 letters)



>FitnessBrowser__WCS417:GFF3539
          Length = 258

 Score =  145 bits (365), Expect = 9e-40
 Identities = 80/211 (37%), Positives = 126/211 (59%), Gaps = 13/211 (6%)

Query: 16  LAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLFIL 75
           L G  +T  I  +++LLGCV+GL   + RL+ K  +++     YV  +RGTPLLVQ+  L
Sbjct: 20  LTGLWLTCLIAVSAMLLGCVLGLAAALLRLS-KNPLLHLPVRFYVWLMRGTPLLVQIVFL 78

Query: 76  FFGLPQ-----------FGILLPAFV-CGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAA 123
           +  L             FG+++P  +   +I LG+  GAY++E++R  I ++DKGQ EA 
Sbjct: 79  YTALAAGGIFRFEDIDLFGLVVPGNIQAAIIALGLNEGAYMAEIIRAGIGAVDKGQYEAG 138

Query: 124 RSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVS 183
           RS+GM     MR +VLPQA   ++PPLGNEF  ++KN+ LVS++ + +L+   Q + S +
Sbjct: 139 RSLGMGFAKLMRRIVLPQAFRVIVPPLGNEFNVMLKNTTLVSVIGVQELLLSTQMVTSAT 198

Query: 184 YRSLEVYLAIAVVYFILTGATTLVLRRIELR 214
           +R  E+YL +A+ + +LT       R +E R
Sbjct: 199 FRVFELYLVVAIYFLMLTTLWGFFQRWLEAR 229


Lambda     K      H
   0.328    0.143    0.412 

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: 138
Number of extensions: 6
Number of successful extensions: 2
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: 222
Length of database: 258
Length adjustment: 23
Effective length of query: 199
Effective length of database: 235
Effective search space:    46765
Effective search space used:    46765
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 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