GapMind for catabolism of small carbon sources

 

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

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate AO356_30355 AO356_30355 enoyl-CoA hydratase

Query= BRENDA::Q1D5Y4
         (258 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_30355
          Length = 264

 Score =  135 bits (339), Expect = 1e-36
 Identities = 81/265 (30%), Positives = 138/265 (52%), Gaps = 8/265 (3%)

Query: 1   MPEFKVDARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAF 60
           M + +V   G + +  ++   ++NA+S +ML  L   +     + D+   VITGAGD AF
Sbjct: 1   MSDLEVSTVGRVMVAKLNRPEKKNALSESMLDSLRTALLAADENDDIGCFVITGAGD-AF 59

Query: 61  CAGADLKERATMAEDEVRAFLDGLRRTFR-------AIEKSDCVFIAAINGAALGGGTEL 113
           C+G DL  RA  + +     L+   R  +       AIE  +   IAA+NGAA+G G +L
Sbjct: 60  CSGGDLGRRAAESAEGDPTPLERKIRLQKVTHQVALAIENFEKPLIAAVNGAAVGAGMDL 119

Query: 114 ALACDLRVAAPAAELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFS 173
           +L CD+R A+ +A      +++G+IPG GG   L R+VG  +A +L+ T   ++A EA +
Sbjct: 120 SLQCDMRFASESARFAEAYIRVGLIPGNGGCYLLPRIVGTAKALELLWTGDFVSAEEALA 179

Query: 174 VGLANRLAPEGHLLAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEE 233
           +G+ NR+  +  L+      A  + +  PI   + K  + +    +L  +L     +   
Sbjct: 180 LGIVNRVFSDDELMQQTLDFATRLADGPPIQQRSIKKLLYQSLRTDLRTSLESVAAQMAV 239

Query: 234 ILKTEDRLEGLRAFAEKRAPVYKGR 258
           +  T+D  E ++A+ EKR P + G+
Sbjct: 240 VQSTDDYKEAIKAYKEKRKPRFIGK 264


Lambda     K      H
   0.319    0.136    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: 124
Number of extensions: 5
Number of successful extensions: 3
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: 264
Length adjustment: 25
Effective length of query: 233
Effective length of database: 239
Effective search space:    55687
Effective search space used:    55687
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 (21.7 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