GapMind for catabolism of small carbon sources

 

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

Align BadK (characterized)
to candidate WP_058857482.1 AS188_RS02285 enoyl-CoA hydratase

Query= metacyc::MONOMER-943
         (258 letters)



>NCBI__GCF_001482365.1:WP_058857482.1
          Length = 262

 Score =  172 bits (435), Expect = 8e-48
 Identities = 100/244 (40%), Positives = 142/244 (58%), Gaps = 2/244 (0%)

Query: 13  RVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRAFAAGADIASMA 71
           +V ++T++RP+V NALN A++D L  AL   +    + A+V+ G   +AF AGADI+ + 
Sbjct: 18  QVAVVTVDRPEVRNALNAAVLDGLEAALDECERRTDVRAVVLTGAGEKAFVAGADISQLV 77

Query: 72  AWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALP 131
            ++  D   +  + R W+ I  +  P +AAV G A GGG ELA+ACDI IA   A+F LP
Sbjct: 78  GYTLRDGLRAR-MQRLWDRIEDLELPTIAAVNGFALGGGTELAMACDIRIAAGGARFGLP 136

Query: 132 EIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETV 191
           E  LG++PGAGGTQRL R +G  +A ++ L+ R ++AEEA R GLV+ VV    L D  +
Sbjct: 137 EANLGIIPGAGGTQRLSRLVGLGRAQELILTGRLVDAEEALRIGLVTSVVPGPELLDAAL 196

Query: 192 ALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEKR 251
             A TI A    A+   K  +    E+    G+L ER      +A+ +  EG  AFLEKR
Sbjct: 197 GTAATILAKGPLAVRMAKLVVRHGAETDQRTGLLLERLAQSLLYAADEKAEGAAAFLEKR 256

Query: 252 APCF 255
              F
Sbjct: 257 PARF 260


Lambda     K      H
   0.321    0.135    0.389 

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: 127
Number of extensions: 9
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: 258
Length of database: 262
Length adjustment: 24
Effective length of query: 234
Effective length of database: 238
Effective search space:    55692
Effective search space used:    55692
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 (21.9 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