GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Pseudomonas putida KT2440

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate PP_1946 PP_1946 Oxidoreductase, short chain dehydrogenase/reductase family

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__Putida:PP_1946
          Length = 262

 Score =  134 bits (336), Expect = 3e-36
 Identities = 80/250 (32%), Positives = 132/250 (52%), Gaps = 11/250 (4%)

Query: 22  KVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKADVSN 81
           KVVL+TGA  GIG A   AFA   A + ++DI  +         +  G +      DV +
Sbjct: 10  KVVLVTGAGSGIGRATALAFAQSGASVAVADISTDHGLKTVELVKAEGGEATFFHVDVGS 69

Query: 82  QQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPL-EMTEEDWRRCFAIDLDGAWYGCKAV 140
           +  + +M    V  +G +D+  N AG+     PL E+  ++WRR   ++L   +Y  K  
Sbjct: 70  EPSVQSMLAGVVAHYGGLDIAHNNAGIEANIVPLAELDSDNWRRVIDVNLSSVFYCLKGE 129

Query: 141 LPQMIEQGVGSIINIASTHSSHIIPG--CFPYPVAKHGLLGLTRALGIEYAPKGVRVNAI 198
           +P M+++G G+I+N AS  +S +I G     Y   KHG++GLT+A  I+YA + +R+NA+
Sbjct: 130 IPLMLKRGGGAIVNTAS--ASGLIGGYRLSGYTATKHGVVGLTKAAAIDYANQNIRINAV 187

Query: 199 APGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINAS 258
            PG +++    D       P   R R L   P  R+    E+A + ++L SD+A ++   
Sbjct: 188 CPGPVDSPFLADM------PQPMRDRLLFGTPIGRLATAEEIARSVLWLCSDDAKYVVGH 241

Query: 259 CITIDGGRSV 268
            +++DGG +V
Sbjct: 242 SMSVDGGVAV 251


Lambda     K      H
   0.321    0.137    0.419 

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: 147
Number of extensions: 9
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: 272
Length of database: 262
Length adjustment: 25
Effective length of query: 247
Effective length of database: 237
Effective search space:    58539
Effective search space used:    58539
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 (21.8 bits)
S2: 47 (22.7 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