GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17600 in Stutzerimonas stutzeri A1501

Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate WP_011913471.1 PST_RS11845 cystine ABC transporter permease

Query= uniprot:A0A1N7U128
         (237 letters)



>NCBI__GCF_000013785.1:WP_011913471.1
          Length = 222

 Score =  104 bits (260), Expect = 1e-27
 Identities = 71/198 (35%), Positives = 96/198 (48%), Gaps = 10/198 (5%)

Query: 20  LSGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFRGTPLYIQLLICY 79
           L G   T+ L +  +  G  L   LAL R+     L+W   VY   FRGTPL +QL + Y
Sbjct: 17  LKGAWWTVVLSLSGMFFGLLLGFGLALLRLYAFWPLQWLARVYVSFFRGTPLLVQLFMIY 76

Query: 80  TGLYSLEIVQDNALLNQFFRNALNCTLLAFVLNTCAYTVEIFAGAIRNIPHGEIEAARAY 139
            GL  L I  D           L   L+ F LN  AYT EI   AI +I  G+ EAA + 
Sbjct: 77  YGLPQLGIQLD----------PLPAALIGFSLNMAAYTAEILRAAIASIDRGQWEAAASI 126

Query: 140 GLHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATVADILKVARDANAETFLT 199
           G+   +     ++P A R ALP   N  I ++  T+LA T  V ++ + A+   A TF  
Sbjct: 127 GMGRAQTLYRAILPQAARTALPPLGNSFISLVKDTALAATIQVPELFRQAQLITARTFEI 186

Query: 200 FQAFGIAALLYMLLSFAL 217
           F  +  AAL+Y LL+  L
Sbjct: 187 FTMYLAAALIYWLLASVL 204


Lambda     K      H
   0.332    0.143    0.443 

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: 168
Number of extensions: 8
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: 237
Length of database: 222
Length adjustment: 23
Effective length of query: 214
Effective length of database: 199
Effective search space:    42586
Effective search space used:    42586
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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