GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Crocosphaera subtropica ATCC 51142

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_009546068.1 CCE_RS03960 1,4-dihydroxy-2-naphthoyl-CoA synthase

Query= BRENDA::Q5SLK3
         (254 letters)



>NCBI__GCF_000017845.1:WP_009546068.1
          Length = 277

 Score =  108 bits (270), Expect = 1e-28
 Identities = 84/260 (32%), Positives = 128/260 (49%), Gaps = 11/260 (4%)

Query: 2   VLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGR------ 55
           +L  + DG+  +T+NRP K NA   + +  LY A  +  ED  +  +LLTGAG       
Sbjct: 14  ILYHKADGIAKITINRPHKRNAFRPKTVFELYDAFCDAREDSSIGVILLTGAGPHTDGKY 73

Query: 56  AFSAGQDLTEFGDRKPDYEAHLRRYN--RVVEALSGLEKPLVVAVNGVAAGAGMSLALWG 113
           AF +G D +  G      +A + R N   +   +  + K ++  V G A G G  L +  
Sbjct: 74  AFCSGGDQSVRGQAGYVDDAGIPRLNVLDLQRLIRSMPKVVIALVAGYAIGGGHVLHVIC 133

Query: 114 DLRLAAVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLV 173
           DL +AA  A F     ++G       +  L R++G  KA+E+  L  + +AE+AL +GLV
Sbjct: 134 DLTIAADNAVFGQTGPKVGSFDGGFGASYLARIIGQKKAREIWFLCRQYNAEQALEMGLV 193

Query: 174 HRVVPAEKLMEEALSLAKE-LAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQ 232
           + VVP E+L  E +  AKE L++ P     L      +    +  + LA  A L      
Sbjct: 194 NCVVPVEQLETEGVQWAKEILSKSPIAIRCLKAAFNADCDGQAGLQELAGNATLLYY--M 251

Query: 233 TQDHEEGVRAFREKRPPRFQ 252
           T++  EG +AF EKRPP F+
Sbjct: 252 TEEGAEGKQAFLEKRPPNFR 271


Lambda     K      H
   0.318    0.135    0.371 

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: 151
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: 254
Length of database: 277
Length adjustment: 25
Effective length of query: 229
Effective length of database: 252
Effective search space:    57708
Effective search space used:    57708
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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