GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Burkholderia phytofirmans PsJN

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 BPHYT_RS31750 BPHYT_RS31750 ABC transporter

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__BFirm:BPHYT_RS31750
          Length = 258

 Score =  222 bits (565), Expect = 7e-63
 Identities = 110/248 (44%), Positives = 163/248 (65%), Gaps = 1/248 (0%)

Query: 6   LEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRLD 65
           L V G++ RFGGL A++ V L+++E  +  +IGPNGAGKTT FN +TG Y P  G   LD
Sbjct: 8   LSVKGVSKRFGGLQALSDVGLQIDEGSIYGLIGPNGAGKTTFFNVITGLYSPDSGEFELD 67

Query: 66  GEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFRR 125
            +       HK+A+ G+ RTFQN+RLF  MTA+EN++V QH       +  + +T + RR
Sbjct: 68  NKPYTPTAVHKVAKTGIARTFQNIRLFGGMTALENVMVGQHVRTKQGLIGAVLQTLSERR 127

Query: 126 SEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGLN 185
            ER   E A   L+ V + ++A+ +A  L+YG QRRLEIAR + T P++L LDEPAAG+N
Sbjct: 128 EERAIRERAIELLDYVGIAQYADYTARNLSYGHQRRLEIARALATDPKLLALDEPAAGMN 187

Query: 186 PKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDNP 245
             E  +L  L+ ++R++   T+LLIEHD+KL+M + + + V++ G  +A+G P  ++ +P
Sbjct: 188 ATEKLELTGLLKQIRADGR-TILLIEHDVKLMMGVCNGMTVLDYGKVIAEGLPRDVQRDP 246

Query: 246 DVIKAYLG 253
            VI+AYLG
Sbjct: 247 KVIEAYLG 254


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: 183
Number of extensions: 8
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: 255
Length of database: 258
Length adjustment: 24
Effective length of query: 231
Effective length of database: 234
Effective search space:    54054
Effective search space used:    54054
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: 47 (22.7 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