GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcrC in Rhizobium etli CFN 42

Align 4-hydroxybenzoyl-CoA reductase subunit gamma; 4-HBCR subunit gamma; EC 1.3.7.9 (characterized)
to candidate WP_011426360.1 RHE_RS15975 xanthine dehydrogenase small subunit

Query= SwissProt::O33818
         (161 letters)



>NCBI__GCF_000092045.1:WP_011426360.1
          Length = 488

 Score =  109 bits (272), Expect = 7e-29
 Identities = 73/168 (43%), Positives = 91/168 (54%), Gaps = 18/168 (10%)

Query: 1   MKNILRLTLNGR--AREDLVPDNMLLLDYLRETVGLTGTKQGCDGGECGACTVLVDDRPR 58
           M + +R  LNG   A  D+ P   LL D+LR    LTGTK+GC  G+CGACTVLV    R
Sbjct: 1   MNDSIRFILNGEDIALTDVGPTETLL-DFLRLKRRLTGTKEGCAEGDCGACTVLVG---R 56

Query: 59  LACSTLAHQ-----------VAGKKVETVESLATQ-GTLSKLQAAFHEKLGTQCGFCTPG 106
           LA   LA++           +    V TVE LA + G L  +Q A  +  G+QCGFCTPG
Sbjct: 57  LADGKLAYESVNACIRFLGSLHATHVVTVEHLAGRDGALHPVQQALVDCHGSQCGFCTPG 116

Query: 107 MIMASEALLRKNPSPSRDEIKAALAGNLCRCTGYVRSSKSVETAAAAR 154
            +M+   L      P R EI+ AL GNLCRCTGY    K+ E  +  R
Sbjct: 117 FVMSLYGLWLTKEKPGRREIEKALQGNLCRCTGYEPIVKAAEQVSLMR 164


Lambda     K      H
   0.318    0.132    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: 190
Number of extensions: 13
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: 161
Length of database: 488
Length adjustment: 25
Effective length of query: 136
Effective length of database: 463
Effective search space:    62968
Effective search space used:    62968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 Apr 09 2024. 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