GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Algiphilus aromaticivorans DG1253

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_043772228.1 U743_RS13640 urea ABC transporter ATP-binding subunit UrtE

Query= TCDB::P21630
         (233 letters)



>NCBI__GCF_000733765.1:WP_043772228.1
          Length = 229

 Score =  151 bits (382), Expect = 9e-42
 Identities = 90/212 (42%), Positives = 129/212 (60%), Gaps = 3/212 (1%)

Query: 2   LSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYE 61
           +S   ++ +YG    L DV + V +G I  L+G NG GK+TLL  + G   AA G IR+ 
Sbjct: 1   MSIRGLNQFYGGSHTLWDVDMTVPEGAITCLMGRNGMGKTTLLKCVMGL-LAARGEIRFG 59

Query: 62  GEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLELFP 121
             EL  L +       I  VP+GR +F +LTV ENL +G  +  +D     +++V ELFP
Sbjct: 60  DTELTKLAADRRAGIGIGYVPQGREIFPQLTVAENLQLG-VYVRRDRSTQALERVYELFP 118

Query: 122 RLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRR 181
            LK+   +R G +SGG+QQ LAIGR L+ +P+LL+LDEP  G+ P I+ +I + + +L R
Sbjct: 119 VLKQMRGRRGGDLSGGQQQQLAIGRTLVFEPRLLILDEPCEGIQPNIVAEIGDTLLKLNR 178

Query: 182 -EGVTVFLVEQNANQALKLADRAYVLENGRIV 212
            EG+TV LVEQ    A ++AD   +LE GR+V
Sbjct: 179 DEGLTVLLVEQKLPFARRVADAFRILEKGRLV 210


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: 138
Number of extensions: 10
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: 229
Length adjustment: 23
Effective length of query: 210
Effective length of database: 206
Effective search space:    43260
Effective search space used:    43260
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 24 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