GapMind for catabolism of small carbon sources

 

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

Align BadK (characterized)
to candidate WP_058860026.1 AS188_RS15825 hypothetical protein

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



>NCBI__GCF_001482365.1:WP_058860026.1
          Length = 267

 Score =  127 bits (320), Expect = 2e-34
 Identities = 86/255 (33%), Positives = 123/255 (48%), Gaps = 14/255 (5%)

Query: 9   ETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIA 68
           E  G V ++TL+     N L   L   L   L     D  +GA+V+ G    F+ G D+A
Sbjct: 18  ERTGAVAVVTLDDERRRNVLGAELRTRLRAVLAELAVDPAVGAVVLTGAGGCFSGGGDLA 77

Query: 69  SM-------AAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVI 121
           SM       +A   ++V G          +  + KPV+AAV G A G    L   CD+V+
Sbjct: 78  SMPPAGPAESAARMAEVAGLVL------ELASLEKPVVAAVTGPAAGVAVGLVCCCDVVV 131

Query: 122 AGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVV 181
           AG SA+F  P  +LGL P  G    L +  G A+A  + L A P++A  A   GL   VV
Sbjct: 132 AGESARFLFPFTRLGLAPDGGLVHSLTQRTGAARARRILLEAAPVDAATALETGLADHVV 191

Query: 182 DDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAR 241
            D  + D  VA A  +A  +  A+ A+K  +  A   +L + + FER    A F ++D  
Sbjct: 192 PDREVLDAAVARAGELAGRAPLAVAAVKRGIREA-SGSLEDALAFEREHQPALFGTSDFL 250

Query: 242 EGIQAFLEKRAPCFS 256
           EG Q+F ++R P FS
Sbjct: 251 EGKQSFFDRRVPSFS 265


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: 109
Number of extensions: 7
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: 267
Length adjustment: 25
Effective length of query: 233
Effective length of database: 242
Effective search space:    56386
Effective search space used:    56386
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