GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Methanoculleus horonobensis T10

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_067078017.1 MCUHO_RS10540 ATP-binding cassette domain-containing protein

Query= TCDB::P21630
         (233 letters)



>NCBI__GCF_001602375.1:WP_067078017.1
          Length = 316

 Score =  113 bits (283), Expect = 4e-30
 Identities = 70/212 (33%), Positives = 118/212 (55%), Gaps = 5/212 (2%)

Query: 11  YGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGEELVGLPS 70
           +G   A+  +S  VKKGEI + +G NGAGKST +  L        G++R  G ++   P 
Sbjct: 16  FGDFTAVRGISFTVKKGEIFSFLGPNGAGKSTTINILTTLLPVQKGAVRVAGYDVAREPR 75

Query: 71  STIMRKSIAVVPEGRRVFSRLTVEENLAMGG--FFTDKDDYQVQMDKVLELFPRLKERYE 128
              +RK+I +V +   +   LTV E +   G  +   +++ + ++D +L +   L+ + +
Sbjct: 76  K--VRKAIGIVFQDDVLDRDLTVRETMEFHGRLYGIPREERRRRIDDLLRIV-ELEFKRD 132

Query: 129 QRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRREGVTVFL 188
           +R   +SGG ++ L I R LM++P +L LDEP+ GL P    +I++ I Q+   G T+FL
Sbjct: 133 ERTKNLSGGMKRRLQIARGLMTQPGVLFLDEPTQGLDPQTRMRIWDYIRQVNEAGTTIFL 192

Query: 189 VEQNANQALKLADRAYVLENGRIVMHDTGAAL 220
                 +A  L+DR  ++++GRIV+  T A L
Sbjct: 193 TTHYMEEADMLSDRISIIDHGRIVVSGTPAEL 224


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: 162
Number of extensions: 14
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: 233
Length of database: 316
Length adjustment: 25
Effective length of query: 208
Effective length of database: 291
Effective search space:    60528
Effective search space used:    60528
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 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