GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12640 in Methylocystis bryophila S285

Align D-lactate transporter, ATP-binding component (characterized)
to candidate WP_085770502.1 B1812_RS04380 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF1248
         (251 letters)



>NCBI__GCF_002117405.1:WP_085770502.1
          Length = 293

 Score =  141 bits (356), Expect = 1e-38
 Identities = 83/249 (33%), Positives = 133/249 (53%), Gaps = 5/249 (2%)

Query: 4   LEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMFD 63
           L + N+   FGG+QALS+++ SV    + +IIGPNGAGKS+L+N + G   PD G +  D
Sbjct: 35  LALTNISLSFGGIQALSEIDFSVAAGEICSIIGPNGAGKSSLINVITGLYRPDWGRIQLD 94

Query: 64  GKSVLGRAPYE-INQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQ 122
            K+   R P E +  +G++R FQ   +F  LSV +N+ +   +     +          +
Sbjct: 95  -KNSFSRMPTERLASLGVARTFQNLALFRGLSVFDNIAVGRVSATRSHWLEQVFGLPRAR 153

Query: 123 RDILEK---AEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGM 179
            D L      E ML  + +   R+  A ++  G ++R+E+   L+  PRLLLLDEP AGM
Sbjct: 154 ADRLATEIIVEEMLVFLGLGQVRNRIAGTLPYGMQKRVELARALAIRPRLLLLDEPMAGM 213

Query: 180 ARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGN 239
              +     + ++  +     +I +IEHD+ VV  L+DR+ VL  G  + +  P ++  +
Sbjct: 214 TAGEKAEMGEFIQLTRDRFGASIVLIEHDIGVVMELSDRVAVLDYGRKIADGPPSDVMND 273

Query: 240 PKVREAYLG 248
             V +AYLG
Sbjct: 274 EAVIDAYLG 282


Lambda     K      H
   0.318    0.135    0.379 

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: 175
Number of extensions: 5
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: 251
Length of database: 293
Length adjustment: 25
Effective length of query: 226
Effective length of database: 268
Effective search space:    60568
Effective search space used:    60568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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