GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12640 in Herbaspirillum autotrophicum IAM 14942

Align D-lactate transporter, ATP-binding component (characterized)
to candidate WP_050461644.1 AKL27_RS04810 ABC transporter ATP-binding protein

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



>NCBI__GCF_001189915.1:WP_050461644.1
          Length = 256

 Score =  189 bits (480), Expect = 5e-53
 Identities = 106/253 (41%), Positives = 152/253 (60%), Gaps = 12/253 (4%)

Query: 3   ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62
           IL++ +V KRFGGLQALS V+L + +  ++ +IGPNGAGK+T  N + G   PDTG+   
Sbjct: 5   ILKIADVSKRFGGLQALSGVSLKIDQGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64

Query: 63  DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAV--- 119
            GK     AP+E+ + GI+R FQ   +FGD++VLEN+M+ C  +     + N   AV   
Sbjct: 65  AGKPYSPSAPHEVAKAGIARTFQNIRLFGDMTVLENVMVGCHVRT----KQNVFGAVFRH 120

Query: 120 SGQRD----ILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEP 175
              RD    I  K++ +L+ + +       A  +S GD+RRLEI   L+ +P+LL LDEP
Sbjct: 121 KAARDEEAGIRSKSQQLLDFVGIGKFASRTARHLSYGDQRRLEIARALATDPQLLALDEP 180

Query: 176 TAGMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQN 235
            AGM   +     +LL +I++E   TI +IEHD+ ++  L DR+TVL  G P+ E  P  
Sbjct: 181 AAGMNATEKLGLRELLVKIRAEGK-TILLIEHDVKLMMGLCDRLTVLDYGKPIAEGTPVE 239

Query: 236 IKGNPKVREAYLG 248
           +K NP V EAYLG
Sbjct: 240 VKTNPAVIEAYLG 252


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: 183
Number of extensions: 8
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: 251
Length of database: 256
Length adjustment: 24
Effective length of query: 227
Effective length of database: 232
Effective search space:    52664
Effective search space used:    52664
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