GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pseudomonas fluorescens FW300-N1B4

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Pf1N1B4_2954 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2954
          Length = 321

 Score =  142 bits (357), Expect = 1e-38
 Identities = 92/276 (33%), Positives = 134/276 (48%), Gaps = 11/276 (3%)

Query: 30  TQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLA 89
           T  D  +  LK A   I + + I  A +  +  LK +   + G +  D+A     GI + 
Sbjct: 38  TMPDQVIERLKGASVAISNKIVIDAAAMAASPELKLILITATGTNNVDLAAARAHGITVC 97

Query: 90  NTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFG---VDVQGKTLGI 146
           N     T S A     L+L  A R+ +  + V  G WQ +    L     V+++GKTLG+
Sbjct: 98  NCQGYGTPSVAQHTIMLLLNLATRLADYQKAVAEGRWQQAKQFCLLDYPIVELEGKTLGL 157

Query: 147 VGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPL 206
           +G G +G AVAR A   F M+V+       P   +     R+ L ELL   D + L  PL
Sbjct: 158 LGHGELGSAVARLAE-AFGMRVMLGQIPGRPARPD-----RLPLDELLPQIDALTLHCPL 211

Query: 207 TPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPS 266
              T+H IGA EL SMK  A ++N +RG  +DE+AL +AL+NG + GA  DV   EP  +
Sbjct: 212 NEHTRHFIGARELASMKPGAFVVNTARGGLIDEQALADALRNGHLGGAATDVLSVEPPTA 271

Query: 267 DSPLL--KLANVVALPHIGSATHETRHAMARNAAEN 300
            +PLL   +  ++  PH    + E R  +     EN
Sbjct: 272 GNPLLAQDIPRLIVTPHNAWGSREARQRIVGQLTEN 307


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: 204
Number of extensions: 8
Number of successful extensions: 1
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: 321
Length adjustment: 28
Effective length of query: 293
Effective length of database: 293
Effective search space:    85849
Effective search space used:    85849
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