GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5403 in Stutzerimonas stutzeri A1501

Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate WP_011913471.1 PST_RS11845 cystine ABC transporter permease

Query= reanno::pseudo6_N2E2:Pf6N2E2_5403
         (375 letters)



>NCBI__GCF_000013785.1:WP_011913471.1
          Length = 222

 Score = 71.2 bits (173), Expect = 2e-17
 Identities = 35/89 (39%), Positives = 57/89 (64%)

Query: 238 VLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQAL 297
           + +  L A  +  ++  AA+ AEI+R+ I S+  GQ EAA S+G+    TL + I+PQA 
Sbjct: 84  IQLDPLPAALIGFSLNMAAYTAEILRAAIASIDRGQWEAAASIGMGRAQTLYRAILPQAA 143

Query: 298 RVIIPPLTSQYLNLAKNSSLAAGIGYPEM 326
           R  +PPL + +++L K+++LAA I  PE+
Sbjct: 144 RTALPPLGNSFISLVKDTALAATIQVPEL 172



 Score = 40.8 bits (94), Expect = 4e-08
 Identities = 19/57 (33%), Positives = 32/57 (56%)

Query: 73  TLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQILFWYFAV 129
           T++++  G+    +LGF + + RL   W +  LA VYV  FR  P L+Q+   Y+ +
Sbjct: 23  TVVLSLSGMFFGLLLGFGLALLRLYAFWPLQWLARVYVSFFRGTPLLVQLFMIYYGL 79


Lambda     K      H
   0.328    0.141    0.430 

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: 209
Number of extensions: 19
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 375
Length of database: 222
Length adjustment: 26
Effective length of query: 349
Effective length of database: 196
Effective search space:    68404
Effective search space used:    68404
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: 47 (22.7 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