GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Shewanella sp. ANA-3

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 7025598 Shewana3_2749 ABC transporter related (RefSeq)

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__ANA3:7025598
          Length = 346

 Score = 95.1 bits (235), Expect = 2e-24
 Identities = 67/237 (28%), Positives = 113/237 (47%), Gaps = 21/237 (8%)

Query: 6   LEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRLD 65
           +E  G+T  FGG+ AV  ++L + +  +   +GPNG GK+T    LTG   PT G IR+ 
Sbjct: 29  IETRGMTRAFGGINAVEDLDLAIPKGTIYGFLGPNGCGKSTSIRMLTGLLSPTSGDIRVL 88

Query: 66  GEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENL-LVAQHRHLNTNFLAGLFKTPAFR 124
           GE + G    +  R+ +    Q   L+  ++  ENL  VAQ   LN              
Sbjct: 89  GETLPG--AEEKLRRRIGYMTQKFSLYDNLSVRENLEFVAQIYGLN-------------- 132

Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184
              R+     A  L   +L     + AG+++ GQ++RL +A   +  P +L LDEP + +
Sbjct: 133 --RRQTKARLAELLSLYDLAGREKQMAGSMSGGQKQRLALAAATLHHPELLFLDEPTSAV 190

Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQI 241
           +P+   +    +  L ++   T+L+  H M         + ++ +G   ADG+P+Q+
Sbjct: 191 DPENRREFWERLFDLCAQ-GTTILVSTHYMDEAERCHG-LAILERGIKRADGSPQQL 245


Lambda     K      H
   0.320    0.137    0.391 

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: 172
Number of extensions: 11
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: 255
Length of database: 346
Length adjustment: 26
Effective length of query: 229
Effective length of database: 320
Effective search space:    73280
Effective search space used:    73280
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: 48 (23.1 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