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_047212839.1 PATSB16_RS04610 aldo/keto reductase

Query= BRENDA::F2YCN5
         (340 letters)



>NCBI__GCF_001931675.1:WP_047212839.1
          Length = 328

 Score =  165 bits (417), Expect = 2e-45
 Identities = 107/312 (34%), Positives = 165/312 (52%), Gaps = 7/312 (2%)

Query: 27  ALGTWAIG-GWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRD 85
           ALG   +G    + G D+  SI TIHRA++LG+N  DTA  YG    E +VGKA+KG R+
Sbjct: 15  ALGLGCMGMSEFYSGRDEAESIATIHRALELGVNFFDTADMYGPFTNELLVGKALKGLRN 74

Query: 86  NLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIE 145
            +I+ATK G +     +    R   A  +K+  + SL+RLG D+IDLY  H  DP VPIE
Sbjct: 75  EVILATKFGNERGANGEFLGIRGDDAY-VKRACDASLQRLGVDHIDLYYQHRVDPKVPIE 133

Query: 146 ETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKDILPYAK 205
           ET   +  L K GK+R +G+S  + Q +        +   Q+ Y+L+ R+++ +ILP  +
Sbjct: 134 ETVGAMADLVKAGKVRYLGLSEAAAQTVRRAHAVHPITALQTEYSLWSRDVESEILPTLR 193

Query: 206 KNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAKE 265
           +  +  + Y  L RG L+G++        DD R+  P+FQ   F+  L    E++++A E
Sbjct: 194 ELGIGFVAYSPLGRGFLTGQIKRIDDLAADDYRRNSPRFQGDNFQRNLDLFAEIERMAAE 253

Query: 266 HYNKSVLALAIRWMLEQGPTLA-LWGACKPEQIDGIDEVFGWQISDEDLKQIDAILAKNI 324
               +   LA+ W+L QG  +  + G  +  +++         +SD DL++ID IL    
Sbjct: 254 K-GCTPAQLALAWVLAQGEDIVPIPGTKRRAKLEDNVGALEVTLSDADLQRIDGILP--- 309

Query: 325 PNPIGAEFMAPP 336
           P     E  A P
Sbjct: 310 PGAAAGERYAAP 321


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: 279
Number of extensions: 12
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: 328
Length adjustment: 28
Effective length of query: 312
Effective length of database: 300
Effective search space:    93600
Effective search space used:    93600
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