GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fdh in Pseudomonas fluorescens FW300-N1B4

Align Short-chain dehydrogenase (characterized, see rationale)
to candidate Pf1N1B4_4954 Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10)

Query= uniprot:A0A2E7P8M8
         (258 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4954
           Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC
           1.3.1.10)
          Length = 248

 Score = 94.0 bits (232), Expect = 3e-24
 Identities = 77/247 (31%), Positives = 118/247 (47%), Gaps = 7/247 (2%)

Query: 5   LQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLEL 64
           LQ K  ++TGG SGIG   + Q  AEGA  +V   +  +P+  A    +     L     
Sbjct: 4   LQGKRTLITGGTSGIGLETAKQFLAEGARVIV---TGVNPESMANAQAILGSEVLVLRAD 60

Query: 65  QDEARCGEAVAETVR-RFGRLDGLVNNAGVNDSVGLDAGRNE-FVASLERNLIHYYVMAH 122
                  + +A+ V+  +G+LD    NAGV+  + ++    E F  S + N+   Y +  
Sbjct: 61  SASVAAQKELAQAVQSHYGQLDVAFLNAGVSVWMPIEDWNEEMFDRSFDINVKGPYFLLQ 120

Query: 123 YCVPHLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNALI 182
             +P        +LN S    L G   +S Y A+K A L++++  ++ L   GVRVNA+ 
Sbjct: 121 ALLPVFSNPASVVLNTSVSAHL-GAARSSIYAATKAAFLNMSKTLSSELLPRGVRVNAVS 179

Query: 183 PAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTGQ 242
           P  + TPLY+K        ++    I + IP G RF T EE+A   ++L S  S  T G 
Sbjct: 180 PGPIDTPLYDKAGIPDAYREQVNKDIAATIPFG-RFGTPEEVAKAVLYLASDESRWTVGT 238

Query: 243 WVFVDGG 249
            + VDGG
Sbjct: 239 EIIVDGG 245


Lambda     K      H
   0.318    0.134    0.394 

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: 146
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: 258
Length of database: 248
Length adjustment: 24
Effective length of query: 234
Effective length of database: 224
Effective search space:    52416
Effective search space used:    52416
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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