GapMind for catabolism of small carbon sources

 

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

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate AO353_03780 AO353_03780 enoyl-CoA hydratase

Query= reanno::psRCH2:GFF2389
         (257 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03780
          Length = 249

 Score =  115 bits (287), Expect = 1e-30
 Identities = 80/252 (31%), Positives = 122/252 (48%), Gaps = 23/252 (9%)

Query: 6   LLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAAGA 65
           +L++ +  +  + LNRP   NAL   + S+L  AL Q +ADP+I  I++TG+ + F AG 
Sbjct: 5   ILLERERGLLTLRLNRPDKKNALTRAMYSQLADALLQADADPEINAILITGTRECFTAGN 64

Query: 66  DIKEMAELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMIFAADNA 125
           DI +  E   P       F     +   RKP+IAAVAG A+G G  L L CD+++ + +A
Sbjct: 65  DIADFLEEP-PSDLTSPVFQFMRNLLECRKPVIAAVAGAAVGIGTTLLLHCDLVYISADA 123

Query: 126 RFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFPAESL 185
           +   P VNLG+ P  G +  L R +G+AKA ++ L G   +  +A   G+  +  P    
Sbjct: 124 KLRMPFVNLGLCPEFGSSLILPRLLGQAKAAELLLLGEGFNGEQAAAWGIATQALPTG-- 181

Query: 186 LEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHA----VFATADQKE 241
            E  L  AR +A +               FET   E +R  +++  A        A ++E
Sbjct: 182 -EAALAKAREMALR---------------FETLAPEAVRISKQLMKAPDREQLRKAIEEE 225

Query: 242 GMAAFSEKRKPE 253
           G       R PE
Sbjct: 226 GNLFVQRLRSPE 237


Lambda     K      H
   0.321    0.135    0.375 

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: 145
Number of extensions: 10
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: 257
Length of database: 249
Length adjustment: 24
Effective length of query: 233
Effective length of database: 225
Effective search space:    52425
Effective search space used:    52425
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: 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 (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