GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Phyllobacterium brassicacearum STM 196

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_106713529.1 CU102_RS23600 2-hydroxyacid dehydrogenase

Query= curated2:B1L765
         (332 letters)



>NCBI__GCF_003010955.1:WP_106713529.1
          Length = 315

 Score =  165 bits (417), Expect = 2e-45
 Identities = 94/252 (37%), Positives = 147/252 (58%), Gaps = 5/252 (1%)

Query: 61  VFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARRVV 120
           + EA P L I++ Y VGYD +D+    ++GI VTNTP VLT   AD   A+++  +R V+
Sbjct: 61  MIEACPNLEIISVYGVGYDAVDLSACQEKGIRVTNTPDVLTNDVADLGVAMMLCQSRGVI 120

Query: 121 EADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARRAKGFGMRILYYDSIR 180
            A+ +V++G W      +  +   V+GR  GI+G+GRIG  VA+R KGF M I Y D + 
Sbjct: 121 GAEGWVKDGSWSA--KGLYPVKRRVWGRRAGILGLGRIGFEVAKRLKGFDMEISYSD-VG 177

Query: 181 REDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNTSRGK 240
            + + + +     P+E L  + DF+ + +  + ET H++G + +  +    +L+N SR  
Sbjct: 178 AKSYAEGMRFVADPVE-LARDVDFLFVTLAASAETRHIVGPDVIAALGPQGMLINISRAS 236

Query: 241 VVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKLENVVLAPHAASASHETRSRMAE 300
            +D++AL  AL+ G +  A LDVFE EP   +   L L+NV+L PH AS + ETR  M +
Sbjct: 237 NIDEEALLDALESGALGSAALDVFEGEP-KLNPRFLALDNVLLQPHHASGTIETRKAMGK 295

Query: 301 MVAENLIAFKRG 312
           ++ +NL A   G
Sbjct: 296 LMRDNLAAHFSG 307


Lambda     K      H
   0.319    0.137    0.398 

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: 229
Number of extensions: 13
Number of successful extensions: 4
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: 332
Length of database: 315
Length adjustment: 28
Effective length of query: 304
Effective length of database: 287
Effective search space:    87248
Effective search space used:    87248
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 (21.8 bits)
S2: 48 (23.1 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