GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Pseudomonas fluorescens FW300-N2C3

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AO356_30355 AO356_30355 enoyl-CoA hydratase

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_30355
          Length = 264

 Score =  150 bits (379), Expect = 3e-41
 Identities = 96/264 (36%), Positives = 145/264 (54%), Gaps = 9/264 (3%)

Query: 1   MSELIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFA 60
           MS+L VS   RV++  LNRP  +NAL+ ++L  L   L AA  +  I   VITG    F 
Sbjct: 1   MSDLEVSTVGRVMVAKLNRPEKKNALSESMLDSLRTALLAADENDDIGCFVITGAGDAFC 60

Query: 61  AGADLN----EMAEKDLAAT-----LNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELA 111
           +G DL     E AE D         L     Q+   ++ F KPLIAAVNG A+GAG +L+
Sbjct: 61  SGGDLGRRAAESAEGDPTPLERKIRLQKVTHQVALAIENFEKPLIAAVNGAAVGAGMDLS 120

Query: 112 LLCDVVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQA 171
           L CD+  A E+ARF    I +G++PG GG   L R VG + A +++ +G+ ++A++A   
Sbjct: 121 LQCDMRFASESARFAEAYIRVGLIPGNGGCYLLPRIVGTAKALELLWTGDFVSAEEALAL 180

Query: 172 GLVSDVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLL 231
           G+V+ VF  D  ++  L  A+++A   P+  ++ K+ L QS    L+  L        ++
Sbjct: 181 GIVNRVFSDDELMQQTLDFATRLADGPPIQQRSIKKLLYQSLRTDLRTSLESVAAQMAVV 240

Query: 232 AATEDRHEGISAFLQKRTPDFKGR 255
            +T+D  E I A+ +KR P F G+
Sbjct: 241 QSTDDYKEAIKAYKEKRKPRFIGK 264


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: 97
Number of extensions: 4
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: 255
Length of database: 264
Length adjustment: 24
Effective length of query: 231
Effective length of database: 240
Effective search space:    55440
Effective search space used:    55440
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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