GapMind for catabolism of small carbon sources

 

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

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Echvi_2909 Echvi_2909 ABC-type antimicrobial peptide transport system, ATPase component

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__Cola:Echvi_2909
          Length = 218

 Score = 96.7 bits (239), Expect = 3e-25
 Identities = 64/217 (29%), Positives = 110/217 (50%), Gaps = 7/217 (3%)

Query: 11  LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70
           +L+  G+  YYG++  L GVDV +  GEIVS++GA+GAGKSTL+  +     A  G V  
Sbjct: 1   MLRAKGIHKYYGDLHVLKGVDVEIAAGEIVSIVGASGAGKSTLLHILGTLDDADKGLVSI 60

Query: 71  EGRDITRMPTHEIARLR---IAQSPEGRRIFPRMTVLENLQMGA--GLDNLKHFAEDVEK 125
           + + +T +   ++A  R   +    +   + P  T  EN+ +       + K+  E  ++
Sbjct: 61  DDKSLTALKGDKLAAYRNQEVGFIFQFHNLLPEFTAEENIIIPGLIAKKDEKYLTEKAKE 120

Query: 126 IFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEA 185
           +  L   + +R   +   LSGGEQQ +++ RAL+  PK++  DEPS  L     + + E 
Sbjct: 121 LARLL-GIMDRLGHKPSELSGGEQQRVAVARALINDPKIIFADEPSGNLDTQSAESLHEL 179

Query: 186 IRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKV 222
              L +  G +  +V  N   A +++ R   M +G +
Sbjct: 180 FFTLRDRFGQSFVIVTHNQQLA-QMADRMLTMQDGVI 215


Lambda     K      H
   0.320    0.137    0.387 

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: 118
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: 247
Length of database: 218
Length adjustment: 23
Effective length of query: 224
Effective length of database: 195
Effective search space:    43680
Effective search space used:    43680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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