GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Oceanisphaera arctica V1-41

Align BadK (characterized)
to candidate WP_104486761.1 UN63_RS10750 2,3-dehydroadipyl-CoA hydratase

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



>NCBI__GCF_002936955.1:WP_104486761.1
          Length = 258

 Score =  172 bits (436), Expect = 6e-48
 Identities = 104/239 (43%), Positives = 138/239 (57%), Gaps = 5/239 (2%)

Query: 17  ITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIASMAAWSYS 76
           ITLNRP+  NAL +  +  +G  L    A+  + A+VI GN R FAAGAD+  M    + 
Sbjct: 18  ITLNRPERRNALRNQTLAEIGEVLAGAAANPEVRAVVIGGNLRCFAAGADLEEMR---HL 74

Query: 77  DVYGSNFITRN--WETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALPEIK 134
           D  G     R   W+ I    KP++AAV G A G G EL L CD+V+AG  A   LPEIK
Sbjct: 75  DAVGLQQDIRPSLWKRIDDFNKPLIAAVNGYALGAGLELVLHCDLVVAGEGALLGLPEIK 134

Query: 135 LGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETVALA 194
           LG++PGAGGTQRL R IG+  AM M L+  P+ AE A   GLVS++       +  + LA
Sbjct: 135 LGIMPGAGGTQRLSRQIGQQTAMKMVLTGEPMTAERAYELGLVSQLCVPALTDEYALKLA 194

Query: 195 TTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEKRAP 253
             IAA +  A+ A K ++    E++L++G+  ER+       + D  EGI AFLEKRAP
Sbjct: 195 HQIAAQAPLAVQAAKGAIKACQETSLSQGLRQERQAFVWLAGTEDRNEGINAFLEKRAP 253


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: 141
Number of extensions: 4
Number of successful extensions: 2
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: 258
Length adjustment: 24
Effective length of query: 234
Effective length of database: 234
Effective search space:    54756
Effective search space used:    54756
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