GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lldE in Burkholderia phytofirmans PsJN

Align Uncharacterized protein (characterized, see rationale)
to candidate BPHYT_RS12810 BPHYT_RS12810 Fe-S oxidoreductase

Query= uniprot:B2TBW0
         (256 letters)



>FitnessBrowser__BFirm:BPHYT_RS12810
          Length = 240

 Score =  141 bits (356), Expect = 1e-38
 Identities = 90/250 (36%), Positives = 127/250 (50%), Gaps = 18/250 (7%)

Query: 10  MKVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTER 69
           M+V LF+ C ID   PE+G + ++L E  G +V  P  QTCCGQP  NSG    A     
Sbjct: 1   MRVGLFVTCLIDLMRPEIGFSVIKLTEGAGFEVMVPPAQTCCGQPAYNSGERRIARDLAE 60

Query: 70  VFARNFAGYDYIVGPSASCIHHVREHLTAL-----EQTDEVKKVRANAYELVEFLHDVVG 124
              R F  +DY+V PS SC   +R H   L     E  +   ++RA  +EL +FL +V  
Sbjct: 61  KTLREFEQFDYVVVPSGSCGGMIRAHYGDLFADDPELMNRFGRLRAKVFELTDFLVNVAK 120

Query: 125 AREFPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPD 184
            +  P  EF  +V  H+SCS LR L             ++PR LL  V G+   +    +
Sbjct: 121 VQLQP-GEFAGQVTYHDSCSGLREL----------GVKAQPRALLAQV-GVTVNEMKDCE 168

Query: 185 ECCGFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERM-KADAR 243
            CCGFGGTF+V    +S  +  +K  +   +G   +V GD+ C+++ +G   R   A  R
Sbjct: 169 HCCGFGGTFAVKYGDISTAIVDEKCANIRASGTGAVVLGDLGCMLNIEGRLRRTGDATTR 228

Query: 244 FIHIAQVLNG 253
            +HIAQVL G
Sbjct: 229 VLHIAQVLAG 238


Lambda     K      H
   0.323    0.137    0.422 

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: 192
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: 256
Length of database: 240
Length adjustment: 24
Effective length of query: 232
Effective length of database: 216
Effective search space:    50112
Effective search space used:    50112
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 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