GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Crocosphaera subtropica ATCC 51142

Align BadK (characterized)
to candidate WP_009546068.1 CCE_RS03960 1,4-dihydroxy-2-naphthoyl-CoA synthase

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



>NCBI__GCF_000017845.1:WP_009546068.1
          Length = 277

 Score = 99.4 bits (246), Expect = 7e-26
 Identities = 86/259 (33%), Positives = 114/259 (44%), Gaps = 11/259 (4%)

Query: 6   ILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG------NTR 59
           IL      +  IT+NRP   NA     +  L  A      D  IG I++ G         
Sbjct: 14  ILYHKADGIAKITINRPHKRNAFRPKTVFELYDAFCDAREDSSIGVILLTGAGPHTDGKY 73

Query: 60  AFAAGADIASMAAWSYSDVYGS---NFITRNWETIRQIRKPVLAAVAGLAYGGGCELALA 116
           AF +G D +      Y D  G    N +      IR + K V+A VAG A GGG  L + 
Sbjct: 74  AFCSGGDQSVRGQAGYVDDAGIPRLNVLDLQ-RLIRSMPKVVIALVAGYAIGGGHVLHVI 132

Query: 117 CDIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGL 176
           CD+ IA  +A F     K+G   G  G   L R IG+ KA ++    R  NAE+A   GL
Sbjct: 133 CDLTIAADNAVFGQTGPKVGSFDGGFGASYLARIIGQKKAREIWFLCRQYNAEQALEMGL 192

Query: 177 VSRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFA 236
           V+ VV  ++L  E V  A  I + S  A+  LK + N   +       L     L   + 
Sbjct: 193 VNCVVPVEQLETEGVQWAKEILSKSPIAIRCLKAAFNADCDGQAGLQELAGNATL-LYYM 251

Query: 237 SADAREGIQAFLEKRAPCF 255
           + +  EG QAFLEKR P F
Sbjct: 252 TEEGAEGKQAFLEKRPPNF 270


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: 116
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 Apr 09 2024. 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