GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcrC in Sinorhizobium meliloti 1021

Align 4-hydroxybenzoyl-CoA reductase subunit gamma; 4-HBCR subunit gamma; EC 1.3.7.9 (characterized)
to candidate SM_b21558 SM_b21558 aldehyde or xanthine dehydrogenase, iron-sulfur subunit protein

Query= SwissProt::O33818
         (161 letters)



>FitnessBrowser__Smeli:SM_b21558
          Length = 207

 Score =  119 bits (298), Expect = 3e-32
 Identities = 62/147 (42%), Positives = 86/147 (58%)

Query: 5   LRLTLNGRAREDLVPDNMLLLDYLRETVGLTGTKQGCDGGECGACTVLVDDRPRLACSTL 64
           L +T+NGR  + +V   + +LD LRE + LTGTK+GC+ G CGACTVL+D +   AC  L
Sbjct: 56  LEVTVNGRVHQLVVDPRLSVLDMLRERLSLTGTKKGCNQGACGACTVLIDGQRVNACLAL 115

Query: 65  AHQVAGKKVETVESLATQGTLSKLQAAFHEKLGTQCGFCTPGMIMASEALLRKNPSPSRD 124
           A    G K+ T+E +A    L  LQ AF E    QCG+CT G IM+    + +  + S +
Sbjct: 116 AVMYDGAKITTIEGVAEGEALHPLQVAFIEHDAFQCGYCTSGQIMSGLGCISEGHASSAE 175

Query: 125 EIKAALAGNLCRCTGYVRSSKSVETAA 151
           EI   ++GN+CRC  Y     +V  AA
Sbjct: 176 EISYWMSGNICRCGAYPGIVAAVAQAA 202


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: 122
Number of extensions: 4
Number of successful extensions: 1
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: 207
Length adjustment: 19
Effective length of query: 142
Effective length of database: 188
Effective search space:    26696
Effective search space used:    26696
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: 44 (21.6 bits)

This GapMind analysis is from Sep 17 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