GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Pedobacter sp. GW460-11-11-14-LB5

Align Glyoxylate reductase 1; EC 1.1.1.26 (characterized)
to candidate CA265_RS09010 CA265_RS09010 3-phosphoglycerate dehydrogenase

Query= SwissProt::P53839
         (350 letters)



>FitnessBrowser__Pedo557:CA265_RS09010
          Length = 315

 Score =  119 bits (299), Expect = 8e-32
 Identities = 92/292 (31%), Positives = 144/292 (49%), Gaps = 24/292 (8%)

Query: 48  PQNKLSQVQVITRTARSVKNTGRFDEELALALPSSVVAVCHTGAGYDQIDVEPFKKRHIQ 107
           PQ++L++  +    A +V++  +  +EL  A+P+ +  +   G G D IDVE  + + I 
Sbjct: 30  PQDQLAEA-LKNYDAITVRSATKVRKELIDAVPN-IKLIGRGGVGMDNIDVEYARSQGIN 87

Query: 108 VANVPDLVSNATADTHVFLLLGALRNFGIGNRRL-IEGNWPEAGPACGSPFGYDPEGKTV 166
           V N P   S + A+     L   +R     NR++ +EG+            G +  GKT+
Sbjct: 88  VVNTPAASSLSVAELVFSHLFTGIRFLQDANRKMPVEGSTQFNNLKKAYAKGTELSGKTI 147

Query: 167 GILGLGRIGRCILERLKPFGFENFIYHNRHQLPSEEEHGCEYVG------------FEEF 214
           GI+G GRIGR   +     G     Y      PSE E   E+ G             +E 
Sbjct: 148 GIIGFGRIGRATAKVALGLGMNVLAYD---LYPSESEITLEFQGGKSVSIPIKTVSLDEV 204

Query: 215 LKRSDIVSVNVPLNHNTHHLINAETIEKMKDGVVIVNTARGAVIDEQAMTDALRSGKIRS 274
           +  SD  S++ P       ++ AE   KMK+GV IVN +RG  IDE A+ DAL SGK+  
Sbjct: 205 ITGSDFFSLHTPFADKP--ILGAEEFAKMKNGVGIVNCSRGGTIDELALIDALNSGKVSF 262

Query: 275 AGLDVFEYEPKISKELLSMSQVLGLPHMGTHSVETRKK----MEELVVENAK 322
           AGLDVF+ EP    E+L+  ++   PH+G  + E +++    +  L++E+ K
Sbjct: 263 AGLDVFDNEPTPLAEILTHPKISLTPHIGASTNEAQERIGTELATLIIEHFK 314


Lambda     K      H
   0.317    0.136    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: 269
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: 350
Length of database: 315
Length adjustment: 28
Effective length of query: 322
Effective length of database: 287
Effective search space:    92414
Effective search space used:    92414
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: 49 (23.5 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