GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Shewanella oneidensis MR-1

Align BadI (characterized)
to candidate 203808 SO4739 naphthoate synthase (NCBI ptt file)

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



>FitnessBrowser__MR1:203808
          Length = 300

 Score =  179 bits (454), Expect = 6e-50
 Identities = 112/275 (40%), Positives = 154/275 (56%), Gaps = 19/275 (6%)

Query: 3   FEDLIYEIR--NGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60
           F D+ Y     +G   I INRPD +NAFR  T DEL  AL  A    DVG  +L G G  
Sbjct: 22  FTDITYHRAKAHGTVRIAINRPDCLNAFRPKTVDELYIALDHARQWSDVGCALLTGNGPS 81

Query: 61  A-----FCTGGDQST-------HDGNYDGRGTVG----LPMEELHTAIRDVPKPVIARVQ 104
           A     F +GGDQ         ++G  +G+  +     L + E+   IR +PK VIA V 
Sbjct: 82  AKGQYSFSSGGDQRIRGKDGYKYEGAEEGKADLARMGRLHILEVQRLIRFMPKVVIAVVP 141

Query: 105 GYAIGGGNVLATICDLTICS-EKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYM 163
           G+A+GGG+ L  +CDLT+ S E AIF Q  P + S D GYG+A+LA+++G+K+AREI++ 
Sbjct: 142 GWAVGGGHSLHVVCDLTLASKEHAIFKQTDPDVASFDSGYGSAYLAKMIGQKRAREIFFC 201

Query: 164 CKRYSGKEAEAMGLANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGI 223
              YS  EA AMG+ N  VPH EL+ E  +W +E+  +SPTA+ + K  FNM      G 
Sbjct: 202 GFNYSADEAFAMGMVNKSVPHAELEVEALRWAKEINSKSPTAMRMLKYGFNMTDDGMVGQ 261

Query: 224 AGMGMYALKLYYDTDESREGVKALQEKRKPEFRKY 258
                 A +L Y + E++EG  A  EKR  +F  +
Sbjct: 262 QLFAGEATRLAYASAEAQEGRDAFLEKRDQDFSAF 296


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: 220
Number of extensions: 11
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: 300
Length adjustment: 26
Effective length of query: 234
Effective length of database: 274
Effective search space:    64116
Effective search space used:    64116
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