GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Frischella perrara PEB0191

Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate WP_039103631.1 FPB0191_RS01985 ADP-glyceromanno-heptose 6-epimerase

Query= BRENDA::Q9WYX9
         (309 letters)



>NCBI__GCF_000807275.1:WP_039103631.1
          Length = 308

 Score = 89.7 bits (221), Expect = 8e-23
 Identities = 73/245 (29%), Positives = 121/245 (49%), Gaps = 17/245 (6%)

Query: 3   ILVTGGAGFIGSHVVDKLIENGY-GVIVVDNLSSGKVENLNRNALFYEQSIEDEEMMERI 61
           I+VTGGAGFIGS++V  L   G   ++VVD+L+ G  +  N   L     ++ +E +  I
Sbjct: 2   IIVTGGAGFIGSNIVKGLNAIGRTDILVVDDLTDG-TKFANLADLDIADYMDKDEFISLI 60

Query: 62  FSLHRP--EYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKK---FIFSS 116
            S      E +FH  A +S          D K  +  +    +  + Y + +   F+++S
Sbjct: 61  VSDEDLDIEVIFHEGACSSTT------EWDGKFMMENNYSYSKDLLHYCLDRRIPFLYAS 114

Query: 117 TGGAIYGENVKVFPTPETEIPHPISPYGIAKYSTEMYLEFFAREYGLKYTVLRYANVYGP 176
           +  A YG   + F   + +   P++ YG +K+  + Y+     +   +    RY NVYGP
Sbjct: 115 SA-ATYGGCSENF-IEDRQFEKPLNVYGYSKFLFDQYVRTILPKAKSQVCGFRYFNVYGP 172

Query: 177 RQDPYGEAGVVAI-FTERMLRGEEVHIF-GDGEYVRDYVYVDDVVRANLLAMEKGDNEVF 234
           R+   G    VA     ++++GE+  +F G   + RD++YVDDVV  N+   E   + +F
Sbjct: 173 REQHKGSMASVAFHLNSQLIKGEKPKLFEGSDNFQRDFIYVDDVVAVNIWFWENNQSGIF 232

Query: 235 NIGTG 239
           N GTG
Sbjct: 233 NCGTG 237


Lambda     K      H
   0.318    0.139    0.396 

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: 235
Number of extensions: 11
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: 309
Length of database: 308
Length adjustment: 27
Effective length of query: 282
Effective length of database: 281
Effective search space:    79242
Effective search space used:    79242
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 (21.6 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