GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaM in Sinorhizobium medicae WSM419

Align L-rhamnose mutarotase; EC 5.1.3.32; Rhamnose 1-epimerase; Type-3 mutarotase (uncharacterized)
to candidate YP_001313688.1 Smed_4974 hypothetical protein

Query= curated2:A5FC30
         (107 letters)



>NCBI__GCF_000017145.1:YP_001313688.1
          Length = 109

 Score = 57.4 bits (137), Expect = 5e-14
 Identities = 28/79 (35%), Positives = 47/79 (59%), Gaps = 3/79 (3%)

Query: 6  RNAFTMKVKSGFETEYKIRHDQIWPELTALLSESGICDYSIFLDEETGILFGV-QKLSSG 64
          R    + ++S    EYK  H  +WP++ AL+SE  I +YSIFL E   +LFG  + +   
Sbjct: 3  RMGMVIGLESAKLAEYKRLHAAVWPDILALISECNITNYSIFLKEPENLLFGYWEYVGQD 62

Query: 65 F--DRSQLSSHPLMRKWWN 81
          F  D +++++HP  ++WW+
Sbjct: 63 FDADMAKMAAHPKNQEWWS 81


Lambda     K      H
   0.317    0.132    0.401 

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: 45
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: 107
Length of database: 109
Length adjustment: 12
Effective length of query: 95
Effective length of database: 97
Effective search space:     9215
Effective search space used:     9215
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: 40 (21.2 bits)
S2: 40 (20.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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