GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Synechococcus elongatus PCC 7942

Align BadK (characterized)
to candidate Synpcc7942_0597 Synpcc7942_0597 naphthoate synthase

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



>FitnessBrowser__SynE:Synpcc7942_0597
          Length = 279

 Score =  102 bits (255), Expect = 7e-27
 Identities = 84/248 (33%), Positives = 112/248 (45%), Gaps = 11/248 (4%)

Query: 17  ITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG------NTRAFAAGADIASM 70
           IT+NRP   NA     +  L  A      D  IG I++ G         AF AG D +  
Sbjct: 27  ITINRPHKRNAFRPKTVVELYDAFCDAREDIAIGVILLTGAGPHTDGRYAFCAGGDQSVR 86

Query: 71  AAWSYSDVYGS---NFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAK 127
            A  Y D  G    N +      IR I K V+A VAG A GGG  L + CD+ IA  +A 
Sbjct: 87  GAGGYIDEEGLPRLNVLDLQ-RLIRTIPKVVIALVAGYAIGGGHVLHILCDLTIAADNAV 145

Query: 128 FALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLR 187
           F     K+G   G  G   L R +G+ KA ++    R   A+EA + GLV+ VV  + L 
Sbjct: 146 FGQTGPKVGSFDGGFGASYLARLVGQKKAREIWFLCRQYGAKEALQMGLVNTVVPVEELE 205

Query: 188 DETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAF 247
            E +  A  I   S  A+  LK + N   +  +A          H  + + +  EG QAF
Sbjct: 206 AEGIRWALEILEKSPIAIRCLKAAFNAELDG-MAGIQELAGHATHLYYLTEEGSEGKQAF 264

Query: 248 LEKRAPCF 255
           LEKR+P F
Sbjct: 265 LEKRSPDF 272


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: 114
Number of extensions: 7
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: 279
Length adjustment: 25
Effective length of query: 233
Effective length of database: 254
Effective search space:    59182
Effective search space used:    59182
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 (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