GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Phaeobacter inhibens BS107

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF3560 PGA1_c36140 D-3-phosphoglycerate dehydrogenase SerA

Query= reanno::BFirm:BPHYT_RS11290
         (321 letters)



>FitnessBrowser__Phaeo:GFF3560
          Length = 531

 Score =  181 bits (459), Expect = 4e-50
 Identities = 106/284 (37%), Positives = 158/284 (55%), Gaps = 6/284 (2%)

Query: 33  DAFVAALKDADG-GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANT 91
           D   A + D DG  I S+ K+T  +L+ AT LK ++   +G D  D    +++G+++ NT
Sbjct: 37  DKLAAIIGDYDGLAIRSATKVTQKILDNATNLKVIARAGIGTDNIDKDAASQKGVIVMNT 96

Query: 92  PDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGR 151
           P     +TA+   +++ A AR++ E +    AG W+ S      GV++  KTLG++G G 
Sbjct: 97  PFGNMITTAEHAIAMMFAVARQIPEASASTHAGKWEKS---KFMGVELTNKTLGVIGAGN 153

Query: 152 IGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETK 211
           IGG V  RA  G  MKV+  +   + +  +  G  +VEL ELLA ADF+ L VPLT +T+
Sbjct: 154 IGGIVCDRAR-GLKMKVVAYDPFLSQEKADKIGVEKVELDELLARADFITLHVPLTDQTR 212

Query: 212 HLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLL 271
           +++    L+  KK   +IN +RG  VDE AL E L +G + GA  DVF  EP  + +PL 
Sbjct: 213 NILSKENLEKTKKGVRIINCARGGLVDEAALAELLTSGHVAGAAFDVFSEEPAKT-NPLF 271

Query: 272 KLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315
            L NVV  PH+G+AT E +  +A   AE +   L      N +N
Sbjct: 272 GLPNVVCTPHLGAATSEAQENVALQVAEQMSNYLLDGAVENALN 315


Lambda     K      H
   0.317    0.131    0.366 

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: 330
Number of extensions: 19
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: 321
Length of database: 531
Length adjustment: 31
Effective length of query: 290
Effective length of database: 500
Effective search space:   145000
Effective search space used:   145000
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: 50 (23.9 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