GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloB in Desulfovibrio vulgaris Miyazaki F

Align Hydroxyacylglutathione hydrolase GloC; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2; EC 3.1.2.6 (characterized)
to candidate 8502142 DvMF_2853 beta-lactamase domain protein (RefSeq)

Query= SwissProt::P75849
         (215 letters)



>FitnessBrowser__Miya:8502142
          Length = 210

 Score =  124 bits (311), Expect = 1e-33
 Identities = 68/185 (36%), Positives = 100/185 (54%), Gaps = 3/185 (1%)

Query: 26  AALVDPGGDAEKIKQEVDDSGLTLMQILLTHGHLDHVGAAAELAQHYGVPVFGPEKEDEF 85
           A  VDPGG    + Q  + +GL L  IL+TH H DH+  AA L +  G PV      D F
Sbjct: 26  AVAVDPGGTPRPMLQYAEKNGLALTHILITHLHFDHIYGAAALVEASGAPVLA-SAADAF 84

Query: 86  WLQGLPAQSRMFGLEECQPLTPDRWLNEGDTISIGNVTLQVLHCPGHTPGHVVFFDDRAK 145
            ++    +   FG     P +    + EGD + +G +T + L  PGHTPG + F   +  
Sbjct: 85  LMETELGRGGAFGFPRVTPFSYQP-VEEGD-LDLGAITCRALATPGHTPGSLSFHFPQVG 142

Query: 146 LLISGDVIFKGGVGRSDFPRGDHNQLISSIKDKLLPLGDDVIFIPGHGPLSTLGYERLHN 205
            +I GD++F   +GR+DFP GD + L  S+  K+  L DD +  PGHG  +T+G E+L+N
Sbjct: 143 AVIVGDLLFHRSIGRTDFPGGDLDALRRSVVQKIFTLPDDTVVYPGHGRETTVGSEKLNN 202

Query: 206 PFLQD 210
           P+  +
Sbjct: 203 PYFTE 207


Lambda     K      H
   0.321    0.142    0.453 

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: 183
Number of extensions: 12
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: 215
Length of database: 210
Length adjustment: 21
Effective length of query: 194
Effective length of database: 189
Effective search space:    36666
Effective search space used:    36666
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: 45 (21.9 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