GapMind for catabolism of small carbon sources

 

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

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 7024442 Shewana3_1620 ABC transporter related (RefSeq)

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__ANA3:7024442
          Length = 302

 Score =  103 bits (258), Expect = 3e-27
 Identities = 66/207 (31%), Positives = 112/207 (54%), Gaps = 8/207 (3%)

Query: 7   VSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGEELV 66
           +S +YG  +AL++V++ ++ G  + L+G NGAGK+TL   LCG    ++G++R  GE   
Sbjct: 9   LSKHYGSKKALNNVNLTLEAGAPIALVGPNGAGKTTLFSLLCGYLTPSAGTVRILGE--- 65

Query: 67  GLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMD--KVLELFPRLK 124
             P+S  +   IA +P+   +   LT+   L+        D  Q   +  +VL L   L 
Sbjct: 66  -APNSPALLGQIAALPQDATLDPNLTIISQLSFFARIQGMDSKQANQEALRVLNLVD-LA 123

Query: 125 ERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRREGV 184
           E  +Q+  ++S G  + +AI +AL+  PKL+LLDEP+ GL P   ++I E++  L    +
Sbjct: 124 EVAQQKPPSLSHGMSKRVAIAQALIGSPKLVLLDEPTAGLDPANAKKIRELVRTL-SPSI 182

Query: 185 TVFLVEQNANQALKLADRAYVLENGRI 211
           T  +   N ++  KL D+   L+ G +
Sbjct: 183 TFVISSHNLDELEKLCDQVLYLDKGEL 209


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: 135
Number of extensions: 7
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: 302
Length adjustment: 25
Effective length of query: 208
Effective length of database: 277
Effective search space:    57616
Effective search space used:    57616
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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