GapMind for catabolism of small carbon sources

 

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

Align Short-chain dehydrogenase (characterized, see rationale)
to candidate AO353_01660 AO353_01660 short-chain dehydrogenase

Query= uniprot:A0A2E7P8M8
         (258 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_01660
          Length = 253

 Score = 99.8 bits (247), Expect = 5e-26
 Identities = 81/255 (31%), Positives = 122/255 (47%), Gaps = 8/255 (3%)

Query: 1   MDLNLQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALF 60
           M +    +V +VTG A+GIG A +   AAEG   VV        +  A L       A+F
Sbjct: 1   MSMTFSGQVALVTGAAAGIGRATAQAFAAEGLKVVVADLDVAGGEGTAELIRAAGGEAVF 60

Query: 61  -QLELQDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVG--LDAGRNEFVASLERNLIHY 117
            Q  +  E+     +A+ V  +GRLD   NNAG+    G   +   +EF A +  N+   
Sbjct: 61  VQCNVTQESDVQNLMAKAVSTYGRLDYAFNNAGIEIEKGKLAEGTLDEFDAIMGVNVKGV 120

Query: 118 YVMAHYCVPHLKATRG-AILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGV 176
           ++   Y +P + A  G AI+N +S   L      S Y ASK A + LT+  A       +
Sbjct: 121 WLCMKYQLPLMLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIGLTKSAAIEYAKKKI 180

Query: 177 RVNALIPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRS 236
           RVNA+ PA + T ++ +    +E   +K D   +  P+G R    EE+A   ++L S  +
Sbjct: 181 RVNAVCPAVIDTDMFRR---AYEADPKKADFAAAMHPVG-RIGKVEEIASAVLYLCSDGA 236

Query: 237 SHTTGQWVFVDGGYT 251
           + TTG  + VDGG T
Sbjct: 237 AFTTGHSLAVDGGVT 251


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: 121
Number of extensions: 7
Number of successful extensions: 4
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: 253
Length adjustment: 24
Effective length of query: 234
Effective length of database: 229
Effective search space:    53586
Effective search space used:    53586
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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