GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1D in Stutzerimonas stutzeri A1501

Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate WP_011913471.1 PST_RS11845 cystine ABC transporter permease

Query= uniprot:A0A0H3PA28
         (219 letters)



>NCBI__GCF_000013785.1:WP_011913471.1
          Length = 222

 Score =  102 bits (253), Expect = 7e-27
 Identities = 66/197 (33%), Positives = 106/197 (53%), Gaps = 3/197 (1%)

Query: 9   NIEFLMQGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLLW 68
           ++ FL++G + T+ ++L+     ++ G  LA+ + Y     ++LA  Y+  FR TPLL+ 
Sbjct: 12  SLPFLLKGAWWTVVLSLSGMFFGLLLGFGLALLRLYAFWPLQWLARVYVSFFRGTPLLVQ 71

Query: 69  MLAACFVLPVFFGQFPQAFWGTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYSQGFGKF 128
           +    + LP    Q        IGFSL  ++  AEI+R  + SI +GQ+EAA S G G+ 
Sbjct: 72  LFMIYYGLPQLGIQLDPLPAALIGFSLNMAAYTAEILRAAIASIDRGQWEAAASIGMGRA 131

Query: 129 FTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKLTSFEEILA 188
            TL+  ILPQ  R  +P L +  ++ VKDTA  A + + EL   ++ I A+     EI  
Sbjct: 132 QTLYRAILPQAARTALPPLGNSFISLVKDTALAATIQVPELFRQAQLITARTF---EIFT 188

Query: 189 MIGVVAGIYFIICFSLS 205
           M    A IY+++   L+
Sbjct: 189 MYLAAALIYWLLASVLA 205


Lambda     K      H
   0.331    0.144    0.428 

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: 146
Number of extensions: 4
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: 219
Length of database: 222
Length adjustment: 22
Effective length of query: 197
Effective length of database: 200
Effective search space:    39400
Effective search space used:    39400
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 (21.9 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