GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Novosphingobium fuchskuhlense FNE08-7

Align BadK (characterized)
to candidate WP_067911092.1 AQZ52_RS12330 enoyl-CoA hydratase

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



>NCBI__GCF_001519075.1:WP_067911092.1
          Length = 260

 Score =  150 bits (378), Expect = 3e-41
 Identities = 97/260 (37%), Positives = 142/260 (54%), Gaps = 8/260 (3%)

Query: 1   MSSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRA 60
           MS   I  ET G V  I LNRP+ LNA    +   +G AL   +   G  A+VI G  RA
Sbjct: 1   MSYETIRVETVGLVRSIVLNRPERLNACPPNMAVEIGDALYDLE---GARAVVITGEGRA 57

Query: 61  FAAGADIASMAAWSYSDVYGS-NFITRNWET----IRQIRKPVLAAVAGLAYGGGCELAL 115
           F +GAD+A     S +   GS   +T ++      + ++  P++ AV G A G GC +AL
Sbjct: 58  FCSGADLAVSGKRSVAGGAGSYKALTESYNPMIAKLSRLSVPIVTAVNGPAAGVGCSIAL 117

Query: 116 ACDIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYG 175
             D V+A +SA F    + +GL+P  G +  LPR IGK++A+ M +    + AE+A+ +G
Sbjct: 118 MGDFVLAAKSAYFLQAFVNIGLVPDGGASWVLPRLIGKSRALQMMMLGERVGAEKAEEWG 177

Query: 176 LVSRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARF 235
           ++ + VDD  L DE +ALA  +A     AL  +++++ RA E+ L   +L E        
Sbjct: 178 MIYKAVDDAALADEAMALAERLANGPTVALGVMRQNVARALETDLPAALLIEAEGQWKAG 237

Query: 236 ASADAREGIQAFLEKRAPCF 255
            S+DA+EGI AFLEKR   F
Sbjct: 238 DSSDAKEGISAFLEKRKADF 257


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: 127
Number of extensions: 5
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: 260
Length adjustment: 24
Effective length of query: 234
Effective length of database: 236
Effective search space:    55224
Effective search space used:    55224
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 24 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