GapMind for catabolism of small carbon sources

 

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

Align Histidine transport system permease protein HisQ (characterized)
to candidate WP_109969949.1 DK846_RS15745 amino acid ABC transporter permease

Query= SwissProt::P52094
         (228 letters)



>NCBI__GCF_003173355.1:WP_109969949.1
          Length = 218

 Score =  102 bits (254), Expect = 6e-27
 Identities = 62/212 (29%), Positives = 110/212 (51%), Gaps = 15/212 (7%)

Query: 12  GALVTLELAISSVVLAVIIGLIGAGGKLSQNRLSGLIFEGYTTLIRGVPDLVLMLLIFYG 71
           G LVTL L   +  +   +G+I A G++   ++   IF+GYT   +G P L+L+ ++++G
Sbjct: 18  GLLVTLSLIAVTAPIGFALGIIIACGRVYGGKVVSKIFQGYTIFFKGCPLLLLLFILYFG 77

Query: 72  LQIALNTVTEAMGVGQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPKGHIEAATAFG 131
           L               I + P VA +I       AY +E  RGA ++V +G I AA A G
Sbjct: 78  LPPY-----------GITLSPFVASVIGFILCNSAYNSEYVRGAILSVKEGQITAAKALG 126

Query: 132 FTRGQVFRRIMFPSMMRYALPGIGNNWQVILKSTALVSLLGLEDVVKATQLAGKS--TWE 189
            TR Q  R ++ P  +R A+PGI N +  ++K ++L  ++ + ++  A +L       + 
Sbjct: 127 MTRNQAIRFVVLPQALRRAIPGISNEFIYLIKYSSLAYMITVIELTGAGKLIATKYFAYN 186

Query: 190 PFYFAIVCGVIYLVFTTVSNGVLLFLERRYSV 221
             +FA+   ++YL   T++      +ER++S+
Sbjct: 187 ETFFAL--AIVYLALVTITTFGANAIERKFSI 216


Lambda     K      H
   0.328    0.145    0.422 

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: 148
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: 228
Length of database: 218
Length adjustment: 22
Effective length of query: 206
Effective length of database: 196
Effective search space:    40376
Effective search space used:    40376
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