GapMind for catabolism of small carbon sources

 

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

Align BadK (characterized)
to candidate WP_067913773.1 AQZ52_RS17100 crotonase/enoyl-CoA hydratase family protein

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



>NCBI__GCF_001519075.1:WP_067913773.1
          Length = 255

 Score =  143 bits (360), Expect = 4e-39
 Identities = 92/256 (35%), Positives = 138/256 (53%), Gaps = 9/256 (3%)

Query: 1   MSSNP-ILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTR 59
           MS  P +LTE  G V I+T+NRP+  NA+  A  + +  A+   DA+  +   ++ G   
Sbjct: 1   MSEAPEVLTEVDGNVLIVTINRPEAKNAMTKAAAEGIAAAMDRLDAETDLRCAILTGAGG 60

Query: 60  AFAAGADIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDI 119
            F +G D+          V G  F   +  T +   KP++AA+ G A  GG ELAL+CD+
Sbjct: 61  TFCSGMDLKGFLRGERPSVPGRGFGGLSQWTPK---KPIIAAIDGYALAGGMELALSCDL 117

Query: 120 VIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSR 179
           ++A + +KF +PE K GL   AGG  +LPR I    AM++ L+   ++A  A   G ++ 
Sbjct: 118 IVASKGSKFGIPEAKRGLAAAAGGLIKLPRQIPPRIAMELALTGDFIDATRAYALGFINE 177

Query: 180 VVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHAR--FAS 237
           + +   L D   ALA  +AA    AL+A K  +  + E T AE  +++++E +    F S
Sbjct: 178 LTEGPAL-DAAKALAARVAANGPLALIASKAIVRDSHEWTEAE--MWDKQEAYIAPVFTS 234

Query: 238 ADAREGIQAFLEKRAP 253
           ADAREG  AF EKR P
Sbjct: 235 ADAREGALAFAEKRKP 250


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: 135
Number of extensions: 9
Number of successful extensions: 4
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: 255
Length adjustment: 24
Effective length of query: 234
Effective length of database: 231
Effective search space:    54054
Effective search space used:    54054
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.

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