GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Methanospirillum lacunae Ki8-1

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_109969962.1 DK846_RS15735 amino acid ABC transporter permease

Query= TCDB::Q9HU30
         (231 letters)



>NCBI__GCF_003173355.1:WP_109969962.1
          Length = 225

 Score =  102 bits (253), Expect = 8e-27
 Identities = 62/210 (29%), Positives = 107/210 (50%), Gaps = 10/210 (4%)

Query: 12  LLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLWVLMI 71
           LL+G ++T+ L   A+ +G++LGL  A+ +      +R +   Y    RG+P  + + + 
Sbjct: 14  LLSGIFITVGLVAVALLIGIILGLPMALGQVYGKHLIRSVISIYVWFFRGLPVLVLLFLF 73

Query: 72  YFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHREAGQ 131
           YFG   GL           L L  F  G + LGL   AY +++FRGA+ SI  G   A +
Sbjct: 74  YFGIFPGLG----------LDLPAFVVGAVVLGLRGAAYQSQIFRGAIQSIAEGQMTAAR 123

Query: 132 ALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVASNATK 191
           +LG+S  +    I+LPQ  R+ALPG  N Y  +L ++++   I + E++ ++    + T 
Sbjct: 124 SLGMSRAQAIRSIILPQAMRIALPGWSNEYPEILTESSICYAIGVAELLTRSSQIVSQTY 183

Query: 192 EPFTFYMTAAAIYLSLTVVIMVALHFLERR 221
                Y+  A +++ L+      +  LE+R
Sbjct: 184 VTMPIYLACAVMFILLSYAGTHLIQRLEKR 213


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: 130
Number of extensions: 7
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: 225
Length adjustment: 23
Effective length of query: 208
Effective length of database: 202
Effective search space:    42016
Effective search space used:    42016
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