GapMind for catabolism of small carbon sources

 

Alignments for a candidate for snatA in Rhodobacter maris JA276

Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate WP_097069106.1 CRO22_RS05425 MarC family protein

Query= TCDB::Q8J305
         (216 letters)



>NCBI__GCF_900217815.1:WP_097069106.1
          Length = 208

 Score =  103 bits (256), Expect = 3e-27
 Identities = 63/196 (32%), Positives = 107/196 (54%), Gaps = 13/196 (6%)

Query: 18  LFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQWIFKFFGSSTD 77
           L+ + +P+G +PVFL+VT  LS  +RR +A++        LV+F L GQ + +  G +  
Sbjct: 14  LWVVIDPIGTLPVFLAVTTGLSAAQRRAVATRAVAVAFGVLVLFLLAGQMVLEALGLALP 73

Query: 78  AFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEEVAIIPLAIPLISGPGA 137
           +F IAGGI+LF  AL M+ G        + + EE       +   ++ P+AIP I+ PGA
Sbjct: 74  SFQIAGGIILFLFALTMIFG--------HSKPEEEIAAAERVSRTSVFPVAIPSIASPGA 125

Query: 138 ITTVMLYMAKSTTNLQRLAVILTIILIGITV---WFVLCSANRIKARLGRVGIKVMTRMM 194
           +  V++       +L   A  +T  L+G+ +     +L +A  +   LG  G  V++R+M
Sbjct: 126 MLAVVVLTDNDRFSLAHQA--MTGALMGVVLLCTLVILLAAAPLHRVLGATGEAVISRVM 183

Query: 195 GLILTSMAVQMIINGI 210
           G+IL ++AV  ++ G+
Sbjct: 184 GMILAAVAVDAVLRGL 199


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: 100
Number of extensions: 6
Number of successful extensions: 3
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: 208
Length adjustment: 21
Effective length of query: 195
Effective length of database: 187
Effective search space:    36465
Effective search space used:    36465
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.

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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