GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_2909 Echvi_2909 ABC-type antimicrobial peptide transport system, ATPase component

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__Cola:Echvi_2909
          Length = 218

 Score =  109 bits (273), Expect = 4e-29
 Identities = 67/216 (31%), Positives = 108/216 (50%), Gaps = 4/216 (1%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           ML    +  YYG +  L  V VE+  GEIV+++GA+GAGKSTLL  L     A  G +  
Sbjct: 1   MLRAKGIHKYYGDLHVLKGVDVEIAAGEIVSIVGASGAGKSTLLHILGTLDDADKGLVSI 60

Query: 61  EGEELVGLPSSTIM---RKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDD-YQVQMDKV 116
           + + L  L    +     + +  + +   +    T EEN+ + G    KD+ Y  +  K 
Sbjct: 61  DDKSLTALKGDKLAAYRNQEVGFIFQFHNLLPEFTAEENIIIPGLIAKKDEKYLTEKAKE 120

Query: 117 LELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEII 176
           L     + +R   +   +SGGEQQ +A+ RAL++ PK++  DEPS  L     + + E+ 
Sbjct: 121 LARLLGIMDRLGHKPSELSGGEQQRVAVARALINDPKIIFADEPSGNLDTQSAESLHELF 180

Query: 177 EQLRREGVTVFLVEQNANQALKLADRAYVLENGRIV 212
             LR      F++  +  Q  ++ADR   +++G IV
Sbjct: 181 FTLRDRFGQSFVIVTHNQQLAQMADRMLTMQDGVIV 216


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: 107
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: 233
Length of database: 218
Length adjustment: 22
Effective length of query: 211
Effective length of database: 196
Effective search space:    41356
Effective search space used:    41356
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 17 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