GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Shewanella loihica PV-4

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 5208024 Shew_0540 enoyl-CoA hydratase/isomerase (RefSeq)

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__PV4:5208024
          Length = 245

 Score =  132 bits (331), Expect = 9e-36
 Identities = 80/247 (32%), Positives = 136/247 (55%), Gaps = 2/247 (0%)

Query: 1   MSELIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFA 60
           MS +    +Q V ++T+NRP  RNALN  +  +L   L    +D  I+  ++ G    F 
Sbjct: 1   MSNIQFQDEQGVRIITINRPDKRNALNLEMYARLTEYLIQGESDNGINAFLLKGEGDCFT 60

Query: 61  AGADLNEMAEKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAG 120
           +G D+ +  +       + T   L+  L    KPL+AAV G A+G G  L L CD+V A 
Sbjct: 61  SGNDVADFLKNSDLGQNHPTVRFLFTLLD-LTKPLVAAVAGPAVGIGTTLLLHCDLVYAD 119

Query: 121 ENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPS 180
             A+F LP + L ++P AG +  L R VG++ AS+++L GE   AQ A   GL++D+ PS
Sbjct: 120 NTAKFQLPFVNLALVPEAGASLLLPRLVGQTKASELLLLGEPFDAQSALSMGLINDLLPS 179

Query: 181 DLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEG 240
           D  + +A+  + K+A+  P AL+A+++ +R   E+ ++  + +E + F +   +++    
Sbjct: 180 DELMSHAMSQSIKLAKKPPQALRASRRLIRGDSEL-IREQMQKELEEFAVRLQSDEAKAQ 238

Query: 241 ISAFLQK 247
            +AFL +
Sbjct: 239 FNAFLSR 245


Lambda     K      H
   0.318    0.130    0.356 

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: 111
Number of extensions: 7
Number of successful extensions: 1
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: 255
Length of database: 245
Length adjustment: 24
Effective length of query: 231
Effective length of database: 221
Effective search space:    51051
Effective search space used:    51051
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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