GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Escherichia coli BW25113

Align BadI (characterized)
to candidate 16369 b2262 naphthoate synthase (NCBI)

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



>FitnessBrowser__Keio:16369
          Length = 285

 Score =  245 bits (626), Expect = 6e-70
 Identities = 124/260 (47%), Positives = 170/260 (65%), Gaps = 4/260 (1%)

Query: 3   FEDLIYE-IRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRA 61
           FED+ YE   +G+A I INRP   NAFR  T  E+I+AL  A YD ++G I+L GAGD+A
Sbjct: 22  FEDIRYEKSTDGIAKITINRPQVRNAFRPLTVKEMIQALADARYDDNIGVIILTGAGDKA 81

Query: 62  FCTGGDQST---HDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATIC 118
           FC+GGDQ     + G  D  G   L + +    IR  PKPV+A V GY+IGGG+VL  +C
Sbjct: 82  FCSGGDQKVRGDYGGYKDDSGVHHLNVLDFQRQIRTCPKPVVAMVAGYSIGGGHVLHMMC 141

Query: 119 DLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLA 178
           DLTI ++ AIFGQ GPK+GS D G+G +++AR+VG+KKAREIW++C++Y  K+A  MGL 
Sbjct: 142 DLTIAADNAIFGQTGPKVGSFDGGWGASYMARIVGQKKAREIWFLCRQYDAKQALDMGLV 201

Query: 179 NLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKLYYDTD 238
           N  VP  +L+ E  +W  E+ + SP AL   K + N D   QAG+  +   A  L+Y T+
Sbjct: 202 NTVVPLADLEKETVRWCREMLQNSPMALRCLKAALNADCDGQAGLQELAGNATMLFYMTE 261

Query: 239 ESREGVKALQEKRKPEFRKY 258
           E +EG  A  +KR+P+F K+
Sbjct: 262 EGQEGRNAFNQKRQPDFSKF 281


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: 266
Number of extensions: 13
Number of successful extensions: 2
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: 285
Length adjustment: 25
Effective length of query: 235
Effective length of database: 260
Effective search space:    61100
Effective search space used:    61100
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 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