GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaF in Pseudomonas fluorescens FW300-N2E3

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AO353_03780 AO353_03780 enoyl-CoA hydratase

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



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_03780 AO353_03780 enoyl-CoA
           hydratase
          Length = 249

 Score =  108 bits (271), Expect = 8e-29
 Identities = 76/252 (30%), Positives = 129/252 (51%), Gaps = 15/252 (5%)

Query: 6   ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGA 65
           IL+E    +  + LNRP   NAL  A+  +L  AL + DAD  I AI++TG+ + F AG 
Sbjct: 5   ILLERERGLLTLRLNRPDKKNALTRAMYSQLADALLQADADPEINAILITGTRECFTAGN 64

Query: 66  DIGMMSTYTYMDVYKGDYITRNWETVRSI---RKPIIAAVAGFALGGGCELAMMCDIIFA 122
           DI       +++    D  +  ++ +R++   RKP+IAAVAG A+G G  L + CD+++ 
Sbjct: 65  DIA-----DFLEEPPSDLTSPVFQFMRNLLECRKPVIAAVAGAAVGIGTTLLLHCDLVYI 119

Query: 123 ADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIP 182
           +  AK   P + LG+ P  G +  LPR + +AKA +L L     +  +A   G+ ++ +P
Sbjct: 120 SADAKLRMPFVNLGLCPEFGSSLILPRLLGQAKAAELLLLGEGFNGEQAAAWGIATQALP 179

Query: 183 AASLVDEAIAAAATIA---EFPSP-AVMMVKESVNRAYETTLAEGVHFERRLFHSLFATE 238
                + A+A A  +A   E  +P AV + K+ +       L + +  E  LF     + 
Sbjct: 180 TG---EAALAKAREMALRFETLAPEAVRISKQLMKAPDREQLRKAIEEEGNLFVQRLRSP 236

Query: 239 DQKEGMAAFVEK 250
           +    ++ F+ +
Sbjct: 237 EAIAALSGFINR 248


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: 123
Number of extensions: 5
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: 249
Length adjustment: 24
Effective length of query: 234
Effective length of database: 225
Effective search space:    52650
Effective search space used:    52650
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 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