GapMind for catabolism of small carbon sources

 

Alignments for a candidate for snatA in Gallaecimonas xiamenensis 3-C-1

Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate WP_008485442.1 B3C1_RS13330 YchE family NAAT transporter

Query= TCDB::Q8J305
         (216 letters)



>NCBI__GCF_000299915.1:WP_008485442.1
          Length = 210

 Score =  138 bits (348), Expect = 7e-38
 Identities = 76/197 (38%), Positives = 113/197 (57%), Gaps = 4/197 (2%)

Query: 18  LFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQWIFKFFGSSTD 77
           + AI NP G +PVF+ +T      ERR  A   A +    L V  LLG+ + KFF  S  
Sbjct: 13  MLAIVNPFGLLPVFMGLTSHQDQAERRRTAMMAAFASAVILWVVLLLGEDLLKFFSISVA 72

Query: 78  AFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEEVAIIPLAIPLISGPGA 137
           +F +AGG+LL   AL ML GKL   + + EE      E   +E V ++PLA+PLI+GP A
Sbjct: 73  SFQVAGGVLLSFTALSMLQGKLGETRRTTEE----GREAARMESVTLVPLALPLIAGPAA 128

Query: 138 ITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKARLGRVGIKVMTRMMGLI 197
           ITTV+++     + + + A+ L I ++ +  W V   A  +   LG  GI ++TR+MGLI
Sbjct: 129 ITTVIVFTQAHHSLVDKGALGLAIGILALVTWGVFLCAPMLARWLGTTGINLITRVMGLI 188

Query: 198 LTSMAVQMIINGIKGAF 214
           + ++AV+ +  G+KG F
Sbjct: 189 MMALAVEFMAKGVKGLF 205


Lambda     K      H
   0.327    0.141    0.396 

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: 119
Number of extensions: 4
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: 216
Length of database: 210
Length adjustment: 22
Effective length of query: 194
Effective length of database: 188
Effective search space:    36472
Effective search space used:    36472
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: 45 (21.9 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