GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Crocosphaera subtropica ATCC 51142

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

Query= metacyc::MONOMER-892
         (260 letters)



>NCBI__GCF_000017845.1:WP_009546068.1
          Length = 277

 Score =  241 bits (616), Expect = 9e-69
 Identities = 125/263 (47%), Positives = 168/263 (63%), Gaps = 7/263 (2%)

Query: 3   FEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR-- 60
           +ED++Y   +G+A I INRP K NAFR  T  EL  A   A  D  +G I+L GAG    
Sbjct: 11  YEDILYHKADGIAKITINRPHKRNAFRPKTVFELYDAFCDAREDSSIGVILLTGAGPHTD 70

Query: 61  ---AFCTGGDQSTHD--GNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLA 115
              AFC+GGDQS     G  D  G   L + +L   IR +PK VIA V GYAIGGG+VL 
Sbjct: 71  GKYAFCSGGDQSVRGQAGYVDDAGIPRLNVLDLQRLIRSMPKVVIALVAGYAIGGGHVLH 130

Query: 116 TICDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAM 175
            ICDLTI ++ A+FGQ GPK+GS D G+G ++LAR++G+KKAREIW++C++Y+ ++A  M
Sbjct: 131 VICDLTIAADNAVFGQTGPKVGSFDGGFGASYLARIIGQKKAREIWFLCRQYNAEQALEM 190

Query: 176 GLANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKLYY 235
           GL N  VP ++L+ E  +W +E+  +SP A+   K +FN D   QAG+  +   A  LYY
Sbjct: 191 GLVNCVVPVEQLETEGVQWAKEILSKSPIAIRCLKAAFNADCDGQAGLQELAGNATLLYY 250

Query: 236 DTDESREGVKALQEKRKPEFRKY 258
            T+E  EG +A  EKR P FR+Y
Sbjct: 251 MTEEGAEGKQAFLEKRPPNFRQY 273


Lambda     K      H
   0.319    0.138    0.418 

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: 264
Number of extensions: 15
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: 260
Length of database: 277
Length adjustment: 25
Effective length of query: 235
Effective length of database: 252
Effective search space:    59220
Effective search space used:    59220
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 (21.7 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