GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Lactobacillus silagei IWT126

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_089137323.1 CES79_RS11830 phosphate ABC transporter ATP-binding protein

Query= TCDB::P21630
         (233 letters)



>NCBI__GCF_002217945.1:WP_089137323.1
          Length = 251

 Score =  101 bits (251), Expect = 2e-26
 Identities = 75/247 (30%), Positives = 124/247 (50%), Gaps = 16/247 (6%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCG-----SPQAAS 55
           +L    V   YG  +ALH ++++     I  LIG +G GKST L  L       +    +
Sbjct: 4   ILQTKNVHLSYGSKEALHGINLDFDDHSITALIGPSGCGKSTFLRCLNRMNDLIANTTIT 63

Query: 56  GSIRYEGEELVGLPSSTI-MRKSIAVVPEGRRVFSRLTVEENLAMG----GFFTDK--DD 108
           GS ++ G++L    ++ + +RK I +V +    F   +V EN+  G    G    K  D+
Sbjct: 64  GSFQFHGQDLYAPTTNLVELRKQIGMVFQQPNPFP-FSVYENVTYGLKLAGHHERKFLDE 122

Query: 109 YQVQMDKVLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPII 168
              +  K   ++  +K+   + A + SGG+QQ + I R L  +P ++LLDEP+  L PI 
Sbjct: 123 QVERALKQAAVWDEVKDNLNKSAMSFSGGQQQRICIARLLAVQPDIILLDEPTSALDPIS 182

Query: 169 IQQIFEIIEQLRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRD 228
             QI E +  L+++   + +V  N  QA ++ADR   + NG +V +D  + + T P  +D
Sbjct: 183 SAQIEETLITLKKD-YCIIIVTHNLQQASRIADRTAFMLNGNLVEYDLTSKMFTQPAKQD 241

Query: 229 A--YLGG 233
              YL G
Sbjct: 242 TSDYLNG 248


Lambda     K      H
   0.318    0.136    0.374 

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: 101
Number of extensions: 3
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: 233
Length of database: 251
Length adjustment: 23
Effective length of query: 210
Effective length of database: 228
Effective search space:    47880
Effective search space used:    47880
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: 46 (22.3 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