GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xyrA in Burkholderia phytofirmans PsJN

Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate BPHYT_RS22485 BPHYT_RS22485 NADP-dependent aryl-alcohol dehydrogenase

Query= BRENDA::F2YCN5
         (340 letters)



>FitnessBrowser__BFirm:BPHYT_RS22485
          Length = 326

 Score =  131 bits (329), Expect = 3e-35
 Identities = 103/324 (31%), Positives = 160/324 (49%), Gaps = 29/324 (8%)

Query: 13  KISIKGIDKSATRVALGTWAIG----GWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYG 68
           K+   G+D S  R+ LG  + G    G      DD+A+   I +A+D GIN  DTA  Y 
Sbjct: 5   KLGRTGLDVS--RLCLGCMSYGVPSRGTHPWSLDDEAARPFIKQALDHGINFFDTANVYS 62

Query: 69  RGHAEEVVGKAIK--GQRDNLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLG 126
            G +EE+VG+A+K   +RD +++ATKV       P+ +     S   I  EI+ SLRRLG
Sbjct: 63  DGTSEEIVGRALKDFAKRDEIVLATKVNSRMHPGPNGA---GLSRKAIMSEIDHSLRRLG 119

Query: 127 TDYIDLYQVHWPDPLVPIEETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAE----- 181
           TDY+DLYQ+H  D   PIEET   L  + K GK R IG S+    Q  +    AE     
Sbjct: 120 TDYVDLYQIHRWDYGTPIEETMEALHDVVKAGKARYIGASSMYAWQFAKALHVAEKNGWT 179

Query: 182 -LAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKT 240
                Q+  NL  RE ++++LP  +   + V+ +  L RG L+      R +  +  R  
Sbjct: 180 RFVTMQNYVNLLYREEEREMLPLCESEGIGVIPWSPLARGRLT------RDWNTESARSE 233

Query: 241 DPKFQKPRFEHYLAA----VEELKKLAKEHYNKSVLALAIRWMLEQGP-TLALWGACKPE 295
             +F +  +     A    VE + ++AKE        +A+ W+L++ P T  + GA K  
Sbjct: 234 TDEFGQTLYAQTEDADRRVVERVSQIAKER-GVPRAQVALAWVLQKKPITAPIVGATKLH 292

Query: 296 QIDGIDEVFGWQISDEDLKQIDAI 319
            +D         +S ++++Q++ +
Sbjct: 293 HLDDAVAALSLSLSADEIRQLEEL 316


Lambda     K      H
   0.317    0.136    0.407 

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: 267
Number of extensions: 16
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: 340
Length of database: 326
Length adjustment: 28
Effective length of query: 312
Effective length of database: 298
Effective search space:    92976
Effective search space used:    92976
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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