GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Stutzerimonas stutzeri A1501

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate WP_011913471.1 PST_RS11845 cystine ABC transporter permease

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



>NCBI__GCF_000013785.1:WP_011913471.1
          Length = 222

 Score =  145 bits (366), Expect = 6e-40
 Identities = 78/204 (38%), Positives = 122/204 (59%), Gaps = 1/204 (0%)

Query: 12  VPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQ 71
           +P LL GA  TV ++ + +  G ++G  + + RL     + + L   YV+  RGTPLLVQ
Sbjct: 13  LPFLLKGAWWTVVLSLSGMFFGLLLGFGLALLRLYAFWPLQW-LARVYVSFFRGTPLLVQ 71

Query: 72  LFILFFGLPQFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSSG 131
           LF++++GLPQ GI L      +IG  +   AY +E++R AI SID+GQ EAA SIGM   
Sbjct: 72  LFMIYYGLPQLGIQLDPLPAALIGFSLNMAAYTAEILRAAIASIDRGQWEAAASIGMGRA 131

Query: 132 LAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRSLEVYL 191
             +   +LPQA    +PPLGN FI+L+K++AL + + + +L  + Q I + ++    +YL
Sbjct: 132 QTLYRAILPQAARTALPPLGNSFISLVKDTALAATIQVPELFRQAQLITARTFEIFTMYL 191

Query: 192 AIAVVYFILTGATTLVLRRIELRL 215
           A A++Y++L         R+E R+
Sbjct: 192 AAALIYWLLASVLAYFQGRLEHRV 215


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: 143
Number of extensions: 4
Number of successful extensions: 1
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: 222
Length adjustment: 22
Effective length of query: 200
Effective length of database: 200
Effective search space:    40000
Effective search space used:    40000
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: 45 (21.9 bits)

This GapMind analysis is from Apr 09 2024. 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