GapMind for catabolism of small carbon sources

 

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

Align BadK (characterized)
to candidate WP_156424864.1 AQZ52_RS04030 enoyl-CoA hydratase

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



>NCBI__GCF_001519075.1:WP_156424864.1
          Length = 277

 Score =  159 bits (401), Expect = 8e-44
 Identities = 103/262 (39%), Positives = 141/262 (53%), Gaps = 9/262 (3%)

Query: 2   SSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAF 61
           S   I  E +GRV  ITL RP VLNA+N  + + L  A  AF ADDG    V+ G  R F
Sbjct: 20  SMEHITVEQRGRVTRITLARPAVLNAINARMHEELEEAFNAFAADDGQWVAVVTGQGRGF 79

Query: 62  AAGADIASMAAWSYSD--VYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDI 119
            AG+D+ ++AA  +     +G   +   ++      KP++AAV GLA GGG E+ALACD+
Sbjct: 80  CAGSDLKAVAAEGFRSYPAHGYAGLIERFDC----DKPIIAAVNGLALGGGFEVALACDL 135

Query: 120 VIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSR 179
           +IA  SA+F LPE ++G +   GG  RL R IG  +AM M LSARP++A E +R G V+ 
Sbjct: 136 IIAAESARFGLPEPRVGAVALGGGLHRLARQIGLKRAMGMILSARPVDAAEGERLGFVTE 195

Query: 180 VVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFER---RELHARFA 236
           VV D  L          I   +  ++ A K+++ R  +       +  +       A  A
Sbjct: 196 VVPDTDLESAVERWVEAILLGAPLSIRASKQAVMRGLDEAGVAAAMAAQPGYPAFAAWSA 255

Query: 237 SADAREGIQAFLEKRAPCFSHR 258
           SAD REG  AF EKR P +  R
Sbjct: 256 SADLREGTTAFAEKRPPVWQGR 277


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: 146
Number of extensions: 6
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: 277
Length adjustment: 25
Effective length of query: 233
Effective length of database: 252
Effective search space:    58716
Effective search space used:    58716
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