GapMind for catabolism of small carbon sources

 

Alignments 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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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