GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Methanococcus maripaludis C5

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_011869254.1 MMARC5_RS07655 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein

Query= TCDB::P21630
         (233 letters)



>NCBI__GCF_000016125.1:WP_011869254.1
          Length = 323

 Score =  109 bits (272), Expect = 7e-29
 Identities = 73/209 (34%), Positives = 118/209 (56%), Gaps = 6/209 (2%)

Query: 11  YGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGEELVGLPS 70
           + K  A+++VS  VKKGEI   +G NGAGKST +  L    +A SGS    G +    P 
Sbjct: 13  FDKNVAVNNVSFNVKKGEIFAFLGPNGAGKSTTINMLTTLLKATSGSAIISGFDASKDPK 72

Query: 71  STIMRKSIAVVPEGRRVFSRLTVEENLAMGG--FFTDKDDYQVQMDKVLELFPRLKERYE 128
              +RK+I +V +   + ++LT  ENL + G  +    +  + ++D++LE F  L E  +
Sbjct: 73  K--VRKTIGIVFQDSTLDNQLTAYENLYIHGKIYGYKGEALKTRIDELLE-FVELLEVKD 129

Query: 129 QRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLR-REGVTVF 187
                 SGG  + L I R+L+ +P++L LDEP++GL P     I+E I+ +R R  +T+F
Sbjct: 130 TVVKNFSGGMVRRLEIARSLIHEPEVLFLDEPTIGLDPQTRSHIWEYIQNMRKRNNMTIF 189

Query: 188 LVEQNANQALKLADRAYVLENGRIVMHDT 216
           L     ++A  LAD+  +++NG+I+   T
Sbjct: 190 LTTHYMDEAELLADKVAIIDNGKIIAEGT 218


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: 176
Number of extensions: 11
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: 233
Length of database: 323
Length adjustment: 25
Effective length of query: 208
Effective length of database: 298
Effective search space:    61984
Effective search space used:    61984
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