GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Collimonas arenae Ter10

Align Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate WP_061533332.1 CAter10_RS10280 amino acid ABC transporter permease

Query= TCDB::Q9HU30
         (231 letters)



>NCBI__GCF_001584165.1:WP_061533332.1
          Length = 250

 Score =  116 bits (290), Expect = 5e-31
 Identities = 78/233 (33%), Positives = 122/233 (52%), Gaps = 17/233 (7%)

Query: 13  LAGTWMTLKLSLAAVCVGLLLGLL---GAIAKTSKYAALRFLGGT-------YTTIVRGV 62
           + GT MTLK+++  V  G  LGLL   G +A+    A   FL          Y +  RG 
Sbjct: 18  IEGTLMTLKVAVICVVTGTFLGLLLGVGRVAEARHGAMKYFLRYAVQWPVRFYVSFFRGT 77

Query: 63  PETLWVLMIYFGTV-------SGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVF 115
           P  + +L+I+F  +        GL   GD+  +       F +  LA+ L  GAY +E+F
Sbjct: 78  PLFVQILLIHFALMPLLINPNGGLLLSGDIAREVRSQYGAFLSAVLAITLNSGAYVSEIF 137

Query: 116 RGALLSIPRGHREAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLIT 175
           R  + SI RG  EA ++LG++  +   ++VLPQ +R  LP LGN  + ++KD++L S I 
Sbjct: 138 RAGIQSIDRGQSEASRSLGMTYLQTLRKVVLPQAFRRMLPPLGNNAIAIVKDSSLASAIG 197

Query: 176 LDEIMRKAQVASNATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRGFVR 228
           L E+   A+  S A    +  Y+T + IY  +T+++ V +  LE+R G+G  R
Sbjct: 198 LAELAYAARTVSGAYARYWEPYLTISLIYWGITLLLSVFVQHLEKRYGKGDTR 250


Lambda     K      H
   0.327    0.143    0.431 

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: 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: 231
Length of database: 250
Length adjustment: 23
Effective length of query: 208
Effective length of database: 227
Effective search space:    47216
Effective search space used:    47216
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. 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