GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34240 in Burkholderia phytofirmans PsJN

Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate BPHYT_RS28210 BPHYT_RS28210 ATPase

Query= uniprot:B2T9V8
         (351 letters)



>FitnessBrowser__BFirm:BPHYT_RS28210
          Length = 352

 Score =  171 bits (432), Expect = 3e-47
 Identities = 112/310 (36%), Positives = 160/310 (51%), Gaps = 10/310 (3%)

Query: 33  SELARLRELALLPALALLIVIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGK 92
           + +A+ RE  L   L LLIV      P FL   NL  VL   + ++L+    ++++L   
Sbjct: 29  ASIAKSRETTLFVVLVLLIVGTGLAKPQFLNLQNLRDVLLNVSIISLLTAGMTVVILMRH 88

Query: 93  FDLSLESTVGI-APAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRL 151
            DLS+ STVGI A AVG++ V            P    L A + +G V G IN  LV   
Sbjct: 89  IDLSVGSTVGISAYAVGSLYVAFP-------HMPVIVALAAGLAIGLVAGTINALLVGVG 141

Query: 152 RLNAFIVTLAMLIVLRGMLVGATKGGTL--FDMPTSFFALATTIVLGLPLSVWLAAAAFA 209
           R+ + + TL+ L + RG       GG +    +P +F  LAT  +LG+P    +A     
Sbjct: 142 RVPSLVATLSTLYIFRGADYAWVHGGQINATSLPDAFSRLATGTLLGIPTLALIAVVVLI 201

Query: 210 IAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGA 269
             A  L+  R GR  YAIG NPEAAR AG+ VER     F+L   +A   G +     G 
Sbjct: 202 GLAVYLKQFRGGREHYAIGSNPEAARLAGVNVERRVMAGFLLSGAIAGFAGALWLARFGT 261

Query: 270 INANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQA 329
           ++A+   G+   V AAAV+G +++ GG GT+ GA  G L+LGV+   L +  V  FW QA
Sbjct: 262 VDASTAKGIELQVVAAAVVGSVAITGGVGTILGATLGALVLGVISIALVVLHVSPFWEQA 321

Query: 330 IYGAIILGSL 339
           I GA+I+ ++
Sbjct: 322 IEGALIVAAI 331


Lambda     K      H
   0.326    0.140    0.397 

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: 290
Number of extensions: 11
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: 351
Length of database: 352
Length adjustment: 29
Effective length of query: 322
Effective length of database: 323
Effective search space:   104006
Effective search space used:   104006
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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