GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Pseudomonas putida KT2440

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate PP_2784 PP_2784 Oxidoreductase, short-chain dehydrogenase/reductase family

Query= reanno::Burk376:H281DRAFT_00644
         (263 letters)



>FitnessBrowser__Putida:PP_2784
          Length = 254

 Score =  134 bits (338), Expect = 1e-36
 Identities = 92/255 (36%), Positives = 137/255 (53%), Gaps = 19/255 (7%)

Query: 13  LRVFVSAGAA-GIGLAIAEAFIEAQAE--VYICDVNQAAID------EATSRFPKLHAGI 63
           LR  V  GAA GIG A+AE+F  AQAE  + + D + A +       E  +R     A I
Sbjct: 4   LRTIVITGAANGIGRAVAESFA-AQAEHLLILLDRDLATLQGWVTEGEFAARIETHQANI 62

Query: 64  ADVSKQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFY 123
           AD+   A +  +      ++G +DVLVN+AG+       E+LD   W   +S NLN  FY
Sbjct: 63  ADL---ASLQLLFKGLADRVGFVDVLVNSAGVCDENEP-EDLD--NWHKVISINLNGTFY 116

Query: 124 FLRKAVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVR 183
                +P++   +D   I+ MSS+ GR G    T Y ++K  I+G+ K+LA +L P  + 
Sbjct: 117 VTSLCLPLM---ADGGRIVNMSSILGRAGKVRNTAYCASKHGIIGMTKALALDLAPRRIT 173

Query: 184 VNAILPGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLAS 243
           VNAILP  ++   +   ++A+A   GI    +     KK+ LRR +  D++AAM  +LAS
Sbjct: 174 VNAILPAWIDTPMLQGELAAQARIAGITHEQILRNAKKKLPLRRFIQGDEVAAMVRYLAS 233

Query: 244 PAGSNVTGQAISVDG 258
           P  S VT Q++ +DG
Sbjct: 234 PQASGVTAQSLMIDG 248


Lambda     K      H
   0.318    0.134    0.375 

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: 111
Number of extensions: 5
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: 254
Length adjustment: 24
Effective length of query: 239
Effective length of database: 230
Effective search space:    54970
Effective search space used:    54970
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 (21.7 bits)
S2: 47 (22.7 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