GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Acidovorax sp. GW101-3H11

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Ac3H11_4989 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4989
          Length = 266

 Score =  115 bits (288), Expect = 9e-31
 Identities = 77/256 (30%), Positives = 124/256 (48%), Gaps = 5/256 (1%)

Query: 6   ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGA 65
           +L+E  G +  +  NRP+ALNA++  + +   AA++   AD A+ A+V+ G+ + F AG 
Sbjct: 13  LLLEREGAIATLRFNRPEALNAIDVPMANAFLAAVQTVAADPAVRAVVLCGNGRGFMAGG 72

Query: 66  DIGMMSTYTYMDVYKGDYIT---RNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFA 122
           D+  +           D +T        +  +  P++A V G A G G  L +M D + A
Sbjct: 73  DLATLRADPVQSAI--DILTPLNAALLLLAQMNAPVVAQVHGVAAGAGLSLLLMADYVIA 130

Query: 123 ADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIP 182
           A+  +     I LG     G +  LPR V   +A+++ L      A +A R GLV+RV+P
Sbjct: 131 AEGTRLNLAYINLGTSCDVGASWALPRIVGVRQALEIALLGDAFTADDALRLGLVNRVVP 190

Query: 183 AASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKE 242
           AA L     A A  +A  P+ A   +K  +  + + TL E +  E+  F     TED + 
Sbjct: 191 AAELDSATAALAQRLASGPTLAYGAMKRLMRASMDHTLPEQLAAEKDAFVHCAGTEDFRA 250

Query: 243 GMAAFVEKRKPVFKHR 258
           G+ AF  ++   F  R
Sbjct: 251 GVEAFHLRQSASFAGR 266


Lambda     K      H
   0.321    0.134    0.380 

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: 150
Number of extensions: 9
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: 266
Length adjustment: 25
Effective length of query: 233
Effective length of database: 241
Effective search space:    56153
Effective search space used:    56153
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 (21.9 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