Aligments for a candidate for braE in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for braE in Burkholderia phytofirmans PsJN

Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate BPHYT_RS15600 BPHYT_RS15600 ABC transporter ATP-binding protein

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__BFirm:BPHYT_RS15600
          Length = 389

 Score =  242 bits (617), Expect = 2e-68
 Identities = 154/351 (43%), Positives = 201/351 (57%), Gaps = 49/351 (13%)

Query: 95  VLALVVVAFVWPFFASRGA--VDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGA 152
           + A+ V+A      A+ G   V +    ++YVML +GLN+VVG AGLLDLGY+ FYAVGA
Sbjct: 28  ITAIFVIAAPMIIGAAGGNYWVRVLDFAMLYVMLALGLNVVVGFAGLLDLGYIAFYAVGA 87

Query: 153 YTYALL------------AEYAGFG----FWTALPIAGMMAALFGFLLGFPVLRLRGDYL 196
           YT ALL            A  A  G    F   +P A  +AA FG +LG P LRLRGDYL
Sbjct: 88  YTSALLSSPHLSSQFEWIAHLAPNGLHVPFLIIVPCAMAVAAFFGVILGAPTLRLRGDYL 147

Query: 197 AIVTLGFGEIIRILLRNM---TEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFG 253
           AIVTLGFGEI+RI L N+     IT GP GI  I  P   G          +   H  FG
Sbjct: 148 AIVTLGFGEIVRIFLNNLDRPVNITNGPKGITGID-PVHAG-------DFSLAQTHSLFG 199

Query: 254 IAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVK 313
           + + + Y    L+V+A LLV+   +V  RL    IGRAW A+REDE+A +A+G+N   VK
Sbjct: 200 LQFPSVYSYYYLFVLAALLVI---WVCTRLQHSRIGRAWAAIREDEIAAKAMGINTRNVK 256

Query: 314 LSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVM 373
           L AF +GASF G +G+ F + QG V+PESFT  ES ++LA VVLGGMG   GVIL AV++
Sbjct: 257 LLAFAMGASFGGLSGAMFGSFQGFVSPESFTLPESIVVLACVVLGGMGHIPGVILGAVLL 316

Query: 374 VLL-----------------QEMRGFNEYRMLIFGLTMIVMMIWRPQGLLP 407
            +L                  E+      R L++ L M+++M++R +GL P
Sbjct: 317 AVLPEFLRSTMGPLQNMVFGHEIVDTEVIRQLVYALAMVLIMLYRSEGLWP 367


Lambda     K      H
   0.330    0.146    0.439 

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: 462
Number of extensions: 23
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: 417
Length of database: 389
Length adjustment: 31
Effective length of query: 386
Effective length of database: 358
Effective search space:   138188
Effective search space used:   138188
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources