GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xyrA in Dyella japonica UNC79MFTsu3.2

Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate N515DRAFT_4192 N515DRAFT_4192 Predicted oxidoreductase

Query= BRENDA::F2YCN5
         (340 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4192
          Length = 314

 Score =  122 bits (306), Expect = 1e-32
 Identities = 96/318 (30%), Positives = 154/318 (48%), Gaps = 36/318 (11%)

Query: 26  VALGTWAIGGWMWG-GTDDDASIKTIHRAIDLGINIIDTAPAYGR-------GHAEEVVG 77
           +++   A GG ++G   D+  S + + + +D G N+IDTA  Y         G +E ++G
Sbjct: 11  LSIAPLAFGGNVFGWSVDEKRSFELLDQFVDAGFNLIDTADVYSAWAPGNRGGESETIIG 70

Query: 78  KAIK--GQRDNLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQV 135
           K +K  G+RD ++IATKV   W         +  +   I++ +E SL+RL TD+IDLYQ 
Sbjct: 71  KWLKQSGKRDRVLIATKVA-KWV------EHKGLAPLNIQQAVEGSLKRLQTDHIDLYQA 123

Query: 136 HWPDPLVPIEETATILEALRKEGKIRSIGVSNYSVQQMDE---------FKKYAELAVSQ 186
           H  D  VP+ ET      L ++GK+R IG SNY   +  E           +Y  L   Q
Sbjct: 124 HEDDASVPLHETLGAFARLIEQGKVRVIGASNYGADRFAEALDVSARHNLPRYESL---Q 180

Query: 187 SPYNLFER-EIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTD-PKF 244
             YNL  R + +K + P   K  + V+ Y AL  G LSG+  ++        R     KF
Sbjct: 181 PEYNLMVRGDYEKYLEPLVTKEQVGVINYYALASGFLSGKYRSETDLGKSAARAAAVRKF 240

Query: 245 QKPRFEHYLAAVEELKKLAKEHYNKSVLALAIRWMLEQ-GPTLALWGACKPEQIDGIDEV 303
             PR    LAA++++ K     +  +   +A+ W++ +   T  +  A   EQ++ +   
Sbjct: 241 LNPRGMGVLAALDDVAKT----HRATPSQVALAWLMARPSITAPIASATSAEQLNDLIGA 296

Query: 304 FGWQISDEDLKQIDAILA 321
              Q+S  ++ Q+DA  A
Sbjct: 297 ARLQLSATEIAQLDAASA 314


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: 263
Number of extensions: 20
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: 314
Length adjustment: 28
Effective length of query: 312
Effective length of database: 286
Effective search space:    89232
Effective search space used:    89232
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: 48 (23.1 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