GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artQ in Halomonas xinjiangensis TRM 0175

Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate WP_043532177.1 JH15_RS16055 ABC transporter permease subunit

Query= reanno::pseudo3_N2E3:AO353_03050
         (229 letters)



>NCBI__GCF_000759345.1:WP_043532177.1
          Length = 234

 Score =  191 bits (486), Expect = 8e-54
 Identities = 90/205 (43%), Positives = 138/205 (67%)

Query: 2   LKGYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPD 61
           L  +   IL GA +T+++AL +  + + LGL+G A RLSP R +  L   YST++R +P+
Sbjct: 9   LMDWAGPILQGALVTIEIALLAYVIGLGLGLVGAAARLSPYRPIQALAAFYSTLVRAVPE 68

Query: 62  LVLILLIFYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAIP 121
           L+LI+L++Y G   LN V   LG+   ++++  ++ +G L F+ GAY++E FRGA +AIP
Sbjct: 69  LLLIILLYYAGTQALNMVLGALGWQSQLEISGFISAVGVLAFVQGAYMTEVFRGAILAIP 128

Query: 122 KGQAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKA 181
           +GQ EA  AYG S +  F R+++P M+  A+PG +N WL+L K TALISV+G +++ F A
Sbjct: 129 RGQLEAADAYGFSRWARFHRIVIPAMLPNALPGMSNLWLILVKDTALISVIGFEELFFTA 188

Query: 182 KQAADATREPFTFFLAVAAMYLVIT 206
           +QAA +TR  F F+    A+YLV+T
Sbjct: 189 QQAAASTRSYFLFYAVAGALYLVMT 213


Lambda     K      H
   0.329    0.144    0.421 

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: 176
Number of extensions: 16
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: 229
Length of database: 234
Length adjustment: 23
Effective length of query: 206
Effective length of database: 211
Effective search space:    43466
Effective search space used:    43466
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 24 2021. 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