GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pseudomonas fluorescens FW300-N2E3

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate AO353_04850 AO353_04850 bifunctional glyoxylate/hydroxypyruvate reductase B

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



>FitnessBrowser__pseudo3_N2E3:AO353_04850
          Length = 324

 Score =  314 bits (804), Expect = 2e-90
 Identities = 171/320 (53%), Positives = 217/320 (67%), Gaps = 4/320 (1%)

Query: 2   KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDA---FVAALKDADGGIGSSVKITPAMLE 58
           K ++A+  +  +++  L+   +V+       D    F  AL  A G IG   K+  A LE
Sbjct: 3   KTVLAFSRVSPEMVESLRHDFEVIVPTPKLGDINAQFNEALPHAHGLIGVGRKLGRAQLE 62

Query: 59  GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118
            A++L+ +S++SVG+D +D+A    RGI+L NTPDVLTESTAD  F+L+++SARRV EL 
Sbjct: 63  NASKLEVVSSVSVGYDNYDLAYFNERGIMLTNTPDVLTESTADLAFALLMSSARRVAELD 122

Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178
            W KAG WQ ++G  LFG DV GKTLGIVG+G IG A+ARR  LGFNM +LY+  S  PQ
Sbjct: 123 AWTKAGQWQATVGAPLFGCDVHGKTLGIVGMGNIGAAIARRGRLGFNMPILYSGNSRKPQ 182

Query: 179 AEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238
            E+  GA+   L +LLA ADFVCL VPL+ +T+HLI   EL  MK SAIL+N SRG  VD
Sbjct: 183 LEQELGAQFRSLDQLLAEADFVCLVVPLSDKTRHLISHRELALMKPSAILVNISRGPVVD 242

Query: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298
           E ALIEALQN  I GAGLDV+E EPL ++SPL +L N V LPHIGSATHETR AMA  A 
Sbjct: 243 EPALIEALQNNRIRGAGLDVYEKEPL-AESPLFQLKNAVTLPHIGSATHETREAMAHRAL 301

Query: 299 ENLVAALDGTLTSNIVNREV 318
            NL +AL G    ++VN +V
Sbjct: 302 ANLRSALLGKRPQDLVNPQV 321


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: 251
Number of extensions: 7
Number of successful extensions: 2
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: 324
Length adjustment: 28
Effective length of query: 293
Effective length of database: 296
Effective search space:    86728
Effective search space used:    86728
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: 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