GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fdh in Pseudomonas stutzeri RCH2

Align L-fucose dehydrogenase (EC 1.1.1.122) (characterized)
to candidate GFF2306 Psest_2353 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases)

Query= reanno::BFirm:BPHYT_RS34225
         (346 letters)



>FitnessBrowser__psRCH2:GFF2306
          Length = 323

 Score =  236 bits (603), Expect = 5e-67
 Identities = 132/321 (41%), Positives = 185/321 (57%), Gaps = 7/321 (2%)

Query: 25  LGLGTAPLGGLYRDLSDEEAHATIAAAWDAGVRYFDTAPHYGNTKAEHRLGDALRRYPRA 84
           +GLG APLG ++  LS+E A AT+ AAWDAG RY+D +PHYG   AE R G  L   PR 
Sbjct: 8   IGLGGAPLGNMFHPLSEETADATLNAAWDAGFRYYDVSPHYGAGLAEQRFGRLLSGKPRD 67

Query: 85  DYVLSTKVGRRFVPRTTPFDDKEGWQNPLPFEAIYDYTHDGILRSFEDSQQRLGIVDIDI 144
           +YVLSTKVGR       P ++ + + + LP + + DY+ DG  RS EDS +R+G+  +D+
Sbjct: 68  EYVLSTKVGRLLQSAGQP-ENAKPFVDELPNKRVPDYSADGARRSIEDSLERMGVDHLDV 126

Query: 145 LLVHDIGRVTHGDNHPHYWRQLTEGGGFRALDALRSSGAIKAVGLGVNEGAAILDAMAEF 204
           + +HD+     G     Y++Q   G   +AL  LR  G I+  GLGVN       A+ + 
Sbjct: 127 VFIHDVSEDQWGPQWKEYFQQAMNGAA-KALTQLRDEGVIRGWGLGVNLVEPCRMALEQS 185

Query: 205 DIDCALLAGRYTLLE-QTTLDDLLPACEKRGVSILLGGAFNSGILARGVQGDLKFNYGEA 263
           D +  LLAGRY+LLE    LD L P C+ R V +++GG FNSG+LA G      + Y + 
Sbjct: 186 DPNVFLLAGRYSLLEHDEALDTLFPTCQARDVGVVVGGPFNSGVLAGGDH----YEYDQI 241

Query: 264 PPEVIERVARLEAVCRTHGVPLAAAALQFPYAHPTVATVLTGARSADELRENAASFELPI 323
           PP++ +R  +L+A     GV L AAAL F  A+P VA+V+ G  + +  ++    F   +
Sbjct: 242 PPQIAQRREQLKAAAERCGVDLRAAALHFCLANPVVASVIPGTANPERPKQYMDYFNTQV 301

Query: 324 PAALWFALREEGLLDSRAPAP 344
           P   W  L+ EGLL   AP P
Sbjct: 302 PREFWQTLKREGLLREDAPVP 322


Lambda     K      H
   0.320    0.139    0.421 

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: 304
Number of extensions: 17
Number of successful extensions: 5
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: 346
Length of database: 323
Length adjustment: 28
Effective length of query: 318
Effective length of database: 295
Effective search space:    93810
Effective search space used:    93810
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: 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