GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxaB in Burkholderia phytofirmans PsJN

Align Altronate oxidoreductase; EC 1.1.1.58; Tagaturonate dehydrogenase; Tagaturonate reductase (uncharacterized)
to candidate BPHYT_RS27215 BPHYT_RS27215 D-mannonate oxidoreductase

Query= curated2:Q9KFI7
         (512 letters)



>FitnessBrowser__BFirm:BPHYT_RS27215
          Length = 386

 Score =  125 bits (313), Expect = 4e-33
 Identities = 114/373 (30%), Positives = 165/373 (44%), Gaps = 37/373 (9%)

Query: 22  LPERVLQFGEGNFLRGFIDWMIQQMNKQNVFNGRVVAIQPT--PHGKVVPKLQEQDSLYT 79
           + E +LQFG   FL+  +   + Q  ++    G +  +Q T  P  +       Q + Y 
Sbjct: 1   MSEPILQFGTSRFLQAHVALFVSQALERGDAIGGICVVQTTDNPSSQARIAALAQAASYP 60

Query: 80  VWLRGIADGETVDHHEVITSISRGLNPYTNWQDVLEVAASPDISVVFSNTTEAGLTYLEE 139
           V +RG   G  VD      +I        +W  +   AA  D+ V+ SNT + G    E 
Sbjct: 61  VKIRGREGGAIVDTVVDCRAIRAAWIANRDWATIRH-AAIHDVRVIVSNTGDMGYRLDER 119

Query: 140 GYD-----KEKAPLSFPGKLAACLWHRYETLGWGE--GSGLVIIPCELVEQNGKVLKELV 192
                   + +AP S+P KL   L  R     W E   SG+ I PCELV  NG  L++LV
Sbjct: 120 DSPALLAREGQAPHSYPAKLLTLLHAR-----WRERPDSGISIFPCELVASNGDTLRDLV 174

Query: 193 CRYAKAWNFPQEFFTWLERENEFCHTLVDRIVPGFPSDTADECFERLGYEDILLTVAEPY 252
              A+ W  P  F  +L +   + ++LVDRIV         E  E +G       VAEPY
Sbjct: 175 TGLARQWVLPTPFVAYLSQRCIWVNSLVDRIV--------SEPIEPVG------AVAEPY 220

Query: 253 HLFIIEGSERVRKLLPFNEAGLHVRWNHLEKHRNMKVRVLNGTHTFM---FALSYLSGVD 309
            L+ IE   R    LP     + V  + L  +  +K+  LN  HT++   +     S  +
Sbjct: 221 ALWAIE--RRAGMELPCTHEHIVVT-DDLSSYEQLKLFFLNLGHTWLADQWLAQRRSATE 277

Query: 310 TVGEAMADEQLCSFIRKGLFEEIIPCVDAPEQEVTA--FAETVLERFENPFLQHRLTDIG 367
           TV +AM D  L   I      E++P   A      A  +  +V ERF NP+L HR+ DI 
Sbjct: 278 TVFDAMNDGPLRDGIEAVWDNEVLPVFSAMGLRARAVQYVASVRERFLNPYLDHRIADIA 337

Query: 368 LNAVNKFRTRLMP 380
            + V K R R++P
Sbjct: 338 NHHVEKVRRRILP 350


Lambda     K      H
   0.321    0.138    0.419 

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: 451
Number of extensions: 21
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: 512
Length of database: 386
Length adjustment: 32
Effective length of query: 480
Effective length of database: 354
Effective search space:   169920
Effective search space used:   169920
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: 51 (24.3 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