GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Pseudomonas putida KT2440

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate PP_3376 PP_3376 putative phosphonate dehydrogenase

Query= curated2:B1L765
         (332 letters)



>FitnessBrowser__Putida:PP_3376
          Length = 320

 Score =  263 bits (671), Expect = 6e-75
 Identities = 147/324 (45%), Positives = 207/324 (63%), Gaps = 9/324 (2%)

Query: 1   MKPRVFVTREIPERGLSKIEEHFELDLWKDEAPPSKKVIIERVKDCDALVSLLTDP---I 57
           MK R+ + + + +  ++++++  E+  W D   P     + R++D       L      +
Sbjct: 1   MKKRIVLYKRLSDDLMARLQDRVEVT-WVDTTQPDA---LARLRDALPGAHGLLGASLRL 56

Query: 58  DAEVFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAAR 117
           DA + + AP+L +V+  +VG DN D+ E ++RG+ +TNTP VLTETTAD  FAL++A AR
Sbjct: 57  DASLLDLAPQLEVVSSVSVGVDNYDIAELSRRGVMLTNTPDVLTETTADTGFALILATAR 116

Query: 118 RVVEADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARRAK-GFGMRILYY 176
           RVVE   +VR+G+W+    P    G DV+G+TLGIVGMGRIG A+ARRA  GFGMR+LY+
Sbjct: 117 RVVELANWVRDGRWQANLGPAHF-GSDVHGKTLGIVGMGRIGEALARRAAAGFGMRVLYH 175

Query: 177 DSIRREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNT 236
               + + E         L++LL+++DFV L VPL+  T  +IG  +L  MK  AILVN 
Sbjct: 176 SQRAKPEVEARYAACQCSLDELLQQADFVCLTVPLSASTEGLIGARELALMKPDAILVNI 235

Query: 237 SRGKVVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKLENVVLAPHAASASHETRS 296
           SRG+VVD++AL +AL+   I GAGLDVF  EP+P D PLL+L+NVV  PH  SA+ ETR 
Sbjct: 236 SRGRVVDEQALIEALRARRIRGAGLDVFVHEPLPIDSPLLQLDNVVATPHIGSATEETRQ 295

Query: 297 RMAEMVAENLIAFKRGEIPPNLVN 320
            MA    +NL++   GE P NLVN
Sbjct: 296 AMARCAVDNLLSALAGERPVNLVN 319


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: 258
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: 332
Length of database: 320
Length adjustment: 28
Effective length of query: 304
Effective length of database: 292
Effective search space:    88768
Effective search space used:    88768
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 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