GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Kocuria flava HO-9041

Align BadI (characterized)
to candidate WP_058860024.1 AS188_RS15810 enoyl-CoA hydratase

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



>NCBI__GCF_001482365.1:WP_058860024.1
          Length = 264

 Score =  119 bits (298), Expect = 6e-32
 Identities = 82/249 (32%), Positives = 122/249 (48%), Gaps = 4/249 (1%)

Query: 10  IRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFCTGGDQS 69
           +R+ +A + +NRP+  NA      D +  AL      +DV A+V  GAG++AF  G D S
Sbjct: 15  VRDRIAVVTVNRPEVRNALNFGVLDGIEAALDAFERREDVDAVVFTGAGEKAFVAGADIS 74

Query: 70  THDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICDLTICSEKAIF 129
              G Y  +  +   M+ L+  I+D+  P IA V G+A+GGGN LA  CD+ I +  A F
Sbjct: 75  QLIG-YTLQDGLRARMQRLYDRIQDLELPTIAAVNGFALGGGNELAMSCDIRIAAANARF 133

Query: 130 GQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANLCVPHDELDA 189
           G     +G +    GT  L+R+VG  +A+E+    +    +EA  +GL    VP +EL  
Sbjct: 134 GLPETNLGILPGAGGTQRLSRLVGLGRAQEMILTGRIIDAEEALRIGLVTSVVPAEELMD 193

Query: 190 EVQKWGEELCERSPTALAIAKRSF--NMDTAHQAGIAGMGMYALKLYYDTDESREGVKAL 247
                   +  + P A+ +AK       +T  + G+  +   A  L Y  DE  EG  A 
Sbjct: 194 TAHATARTILAKGPLAVRLAKLVVRNGAETDQRTGLL-LERLAQSLLYAADEKAEGASAF 252

Query: 248 QEKRKPEFR 256
            EKR   FR
Sbjct: 253 LEKRPARFR 261


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: 157
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: 264
Length adjustment: 25
Effective length of query: 235
Effective length of database: 239
Effective search space:    56165
Effective search space used:    56165
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 24 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