GapMind for catabolism of small carbon sources

 

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

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

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



>NCBI__GCF_001482365.1:WP_058860024.1
          Length = 264

 Score =  181 bits (459), Expect = 1e-50
 Identities = 104/255 (40%), Positives = 151/255 (59%), Gaps = 2/255 (0%)

Query: 2   SSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRA 60
           S+  + T  + R+ ++T+NRP+V NALN  ++D +  AL AF+  + + A+V  G   +A
Sbjct: 7   SATTVTTTVRDRIAVVTVNRPEVRNALNFGVLDGIEAALDAFERREDVDAVVFTGAGEKA 66

Query: 61  FAAGADIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIV 120
           F AGADI+ +  ++  D   +  + R ++ I+ +  P +AAV G A GGG ELA++CDI 
Sbjct: 67  FVAGADISQLIGYTLQDGLRAR-MQRLYDRIQDLELPTIAAVNGFALGGGNELAMSCDIR 125

Query: 121 IAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRV 180
           IA  +A+F LPE  LG+LPGAGGTQRL R +G  +A +M L+ R ++AEEA R GLV+ V
Sbjct: 126 IAAANARFGLPETNLGILPGAGGTQRLSRLVGLGRAQEMILTGRIIDAEEALRIGLVTSV 185

Query: 181 VDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADA 240
           V  + L D   A A TI A    A+   K  +    E+    G+L ER      +A+ + 
Sbjct: 186 VPAEELMDTAHATARTILAKGPLAVRLAKLVVRNGAETDQRTGLLLERLAQSLLYAADEK 245

Query: 241 REGIQAFLEKRAPCF 255
            EG  AFLEKR   F
Sbjct: 246 AEGASAFLEKRPARF 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: 124
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: 264
Length adjustment: 25
Effective length of query: 233
Effective length of database: 239
Effective search space:    55687
Effective search space used:    55687
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