GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Marivita geojedonensis DPG-138

Align ABC transporter permease (characterized, see rationale)
to candidate WP_085638900.1 MGEO_RS13915 sugar ABC transporter permease

Query= uniprot:A0A165KPZ4
         (293 letters)



>NCBI__GCF_002115805.1:WP_085638900.1
          Length = 339

 Score =  110 bits (274), Expect = 6e-29
 Identities = 88/288 (30%), Positives = 140/288 (48%), Gaps = 19/288 (6%)

Query: 11  PKLVVAPAFVLGFAFIYGLMVWNGV-LSLTVSRMLPN----YEWAGLAQYERLWEMDRWW 65
           P L + PA +L         V+  + LSLT  + L +    Y + GLA Y ++ E  ++W
Sbjct: 53  PWLFLLPA-ILALGLYLAYPVFETIRLSLTERQTLSDGTTVYNFVGLANYAQMSEDPKFW 111

Query: 66  VALKNLGIFGVGYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWKWL 125
            AL N   + +     S   G++ A L D +I      +++   PMA+SFV     WK +
Sbjct: 112 EALVNNMFWLIVVPAASTAFGLLAAQLTD-RISWGNLAKSLIFMPMAISFVGAAVIWKLV 170

Query: 126 LN---PG---LGIEKMVRDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGL 179
            +   PG   +G+   +  W   N    WL       + ++I  IW   GFAM +  A L
Sbjct: 171 YDARPPGTEQIGVLNAIYVWLTGNDPQQWLTTPFWNSFLLMIVLIWIQTGFAMVILSAAL 230

Query: 180 RGIDDSIIKAAQVDGASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAGGP 239
           RGI +  I+AA VDGA+  +I+++I +P +          ++ + +K FD+V A+T G  
Sbjct: 231 RGIPEETIEAAIVDGANPFQIFFKIKMPQIAGTIVVVWTTITLVVLKVFDIVFAMTNGQW 290

Query: 240 GFATDVPATFMYTMSFSRGQIGLGAASATMMLATVAALVIPYLYSELR 287
           G  T V A +M+   F     G+G+ASA +++     LV P LY  +R
Sbjct: 291 G--TQVLANYMFNQLFVARDWGVGSASAMIIM----LLVTPILYWNVR 332


Lambda     K      H
   0.327    0.141    0.451 

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: 327
Number of extensions: 27
Number of successful extensions: 4
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: 293
Length of database: 339
Length adjustment: 27
Effective length of query: 266
Effective length of database: 312
Effective search space:    82992
Effective search space used:    82992
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: 48 (23.1 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