GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Pseudomonas fluorescens FW300-N1B4

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate Pf1N1B4_4556 D-beta-hydroxybutyrate dehydrogenase (EC 1.1.1.30)

Query= reanno::BFirm:BPHYT_RS04775
         (263 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4556
          Length = 235

 Score =  126 bits (316), Expect = 5e-34
 Identities = 70/197 (35%), Positives = 111/197 (56%), Gaps = 6/197 (3%)

Query: 64  ADVSDCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFY 123
           AD++D A +  +     ++LG +D+L+N+AG+       EDLD   W + I  NLN  FY
Sbjct: 41  ADIADLASLQVLFKTLATRLGYVDVLVNSAGVCDENEP-EDLD--NWHKVISVNLNGTFY 97

Query: 124 FLRKAVPLLKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVR 183
                +PL+ +      II M+S+ GR G    T Y ASK  I+G+ K+LA++L P  + 
Sbjct: 98  VTSLCLPLMADRGR---IINMSSILGRAGKVRNTAYCASKHGIIGLTKALAMDLAPRQIT 154

Query: 184 VNAILPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLAS 243
           VNAILP  ++   +   ++A+A   GI  +Q+     +K+ LRR +   +VAAM  +LAS
Sbjct: 155 VNAILPAWIDTPMLQGELAAQARIAGISQEQILRNAKKKLPLRRFIQGDEVAAMVRYLAS 214

Query: 244 PAGQNISGQAISVDGNV 260
           P    ++ Q++ +DG V
Sbjct: 215 PEAGGVTAQSLMIDGGV 231


Lambda     K      H
   0.320    0.136    0.391 

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: 137
Number of extensions: 8
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: 263
Length of database: 235
Length adjustment: 24
Effective length of query: 239
Effective length of database: 211
Effective search space:    50429
Effective search space used:    50429
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: 46 (22.3 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