GapMind for catabolism of small carbon sources

 

Aligments for a candidate for badK in Pseudomonas fluorescens FW300-N2E2

Align BadK (characterized)
to candidate Pf6N2E2_1934 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= metacyc::MONOMER-943
         (258 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1934 Enoyl-CoA hydratase
           (EC 4.2.1.17)
          Length = 264

 Score =  145 bits (367), Expect = 6e-40
 Identities = 91/254 (35%), Positives = 139/254 (54%), Gaps = 8/254 (3%)

Query: 10  TQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIAS 69
           T GRV +  LNRP+  NAL+++++D+L  ALLA D +D IG  VI G   AF +G D+  
Sbjct: 8   TVGRVMVAKLNRPEKKNALSESMLDSLRTALLAADENDDIGCFVITGAGDAFCSGGDLGR 67

Query: 70  MAAWSYSD--------VYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVI 121
            AA S           +       +    I    KP++AAV G A G G +L+L CD+  
Sbjct: 68  RAAESAEGDPTPLERKIRLQKVTHQVALAIENFEKPLIAAVNGAAVGAGMDLSLQCDMRF 127

Query: 122 AGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVV 181
           A  SA+FA   I++GL+PG GG   LPR +G AKA+++  +   ++AEEA   G+V+RV 
Sbjct: 128 ASESARFAEAYIRVGLIPGNGGCYLLPRIVGTAKALELLWTGDFVSAEEALALGIVNRVF 187

Query: 182 DDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAR 241
            DD L  +T+  AT +A        ++K+ L ++  + L   +     ++    ++ D +
Sbjct: 188 SDDELMQQTLDFATRLADGPPIQQRSIKKLLYQSLRTDLRTSLESVAAQMAVVQSTDDYK 247

Query: 242 EGIQAFLEKRAPCF 255
           E I+A+ EKR P F
Sbjct: 248 EAIKAYKEKRKPRF 261


Lambda     K      H
   0.321    0.135    0.389 

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: 102
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: 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 (21.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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