GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xyrA in Pandoraea thiooxydans ATSB16

Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate WP_047212629.1 PATSB16_RS03325 aldo/keto reductase

Query= BRENDA::F2YCN5
         (340 letters)



>NCBI__GCF_001931675.1:WP_047212629.1
          Length = 331

 Score =  139 bits (350), Expect = 1e-37
 Identities = 101/300 (33%), Positives = 154/300 (51%), Gaps = 29/300 (9%)

Query: 18  GIDKSATRVALGTWAIGGWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYG-------RG 70
           G   + +R+ LGT   G      T++ AS   + +A D G+N IDTA  Y         G
Sbjct: 8   GTGLTVSRLCLGTMTFGLQ----TEEAASHAILDKAADAGVNFIDTADVYPLGGTEQLAG 63

Query: 71  HAEEVVGKAIKGQRDNLIIATK-VGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDY 129
             EE+VGK +KG+R+  I+ATK VG       DQ     +S   +   I+ SLRRLGTDY
Sbjct: 64  RTEEIVGKWLKGKRERFILATKAVGKVGPSLWDQG----ASRKHLLDAIDVSLRRLGTDY 119

Query: 130 IDLYQVHWPDPLVPIEETATILEALRKEGKIRSIGVSNYSVQQM------DEFKKYAELA 183
           +DLYQ+H  D   P++ET   L+ + ++GK R IGVSN+   ++       +  + A   
Sbjct: 120 VDLYQLHADDAQTPLDETLEALDTIVRQGKARYIGVSNFLAYRLARALGRADVLRVARFV 179

Query: 184 VSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTAD-----RAFTGDDLR 238
             Q  YNL  R+I++++LP A++  L V+ Y  L  GLL+G+   D       FT    +
Sbjct: 180 SVQPRYNLLFRQIERELLPLAQEEQLAVIPYNPLAGGLLTGKHRHDVTPTEGRFTATVGK 239

Query: 239 KTDPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLALAIRWMLEQGP-TLALWGACKPEQI 297
             +   Q+   E     +E+LK++A +   K +   A+ W+L     T A+ GA + EQ+
Sbjct: 240 AGEMYTQRYWHEREFHTIEKLKEIAAQ-TGKPLTQTALAWVLANPTVTSAIIGASRAEQL 298


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: 276
Number of extensions: 16
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: 340
Length of database: 331
Length adjustment: 28
Effective length of query: 312
Effective length of database: 303
Effective search space:    94536
Effective search space used:    94536
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 24 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