GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Pseudomonas fluorescens FW300-N2C3

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate AO356_26030 AO356_26030 hydroxyacid dehydrogenase

Query= curated2:Q9YAW4
         (335 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26030
          Length = 320

 Score =  176 bits (447), Expect = 5e-49
 Identities = 108/285 (37%), Positives = 156/285 (54%), Gaps = 11/285 (3%)

Query: 34  PPPYETLLSKAREADALYTLLTDRI-DCDLLSQAPRLRIVAQMAVGFDNIDVECATRLGI 92
           P   +TL  + +  + +  +    + D  LL + P L+++    +    +D++ A  LGI
Sbjct: 37  PADRDTLAERLQHFEVICVMRERTVFDEGLLRRLPNLKLLLTGGMRNAALDLKAAAELGI 96

Query: 93  YVTNTPGVLTEATAEFTWALILAAARRVVEADHFVRWGEWWRLRTGWHPMMMLGVELRGK 152
            V  T      A  E TW LI+A AR +V+  + +R G W            LG +L GK
Sbjct: 97  QVCGTDSY-KHAAPELTWTLIMALARNLVQEANALRAGLW---------QQGLGGDLHGK 146

Query: 153 TLGILGMGRIGSRVAEIGKAFGMRIIYHSRSRKREIEKELGAEYRSLEDLLRESDILSIH 212
           TL ILG+G IG+RVA+ G+ FGMR+I  S++   E   E+G  Y S + L  ++DILSIH
Sbjct: 147 TLAILGLGSIGTRVAQFGQVFGMRVIAWSQNLSAERAAEVGVTYVSKQALFEQADILSIH 206

Query: 213 LPLTDETRHLIGESELKLMKKTAILVNTGRGAIVDTGALVKALREGWIAAAALDVFEEEP 272
           L L + TR L+    L  MK  A+LVNT RG IVD  AL+ ALR   +A AALDVF +EP
Sbjct: 207 LVLGERTRGLVDAQALGWMKPEALLVNTSRGPIVDEAALIDALRHRRLAGAALDVFAQEP 266

Query: 273 LNPNHPLTAFKNVVLAPHAASATRETRLRMAMMAAENLVAFAQGK 317
           L   HP    +NV+  PH    +R+   +   +  E+L+A+A G+
Sbjct: 267 LPLAHPFRTLENVLATPHVGYVSRQNYQQFYSLMIEDLLAWAAGQ 311


Lambda     K      H
   0.322    0.136    0.406 

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: 254
Number of extensions: 10
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: 335
Length of database: 320
Length adjustment: 28
Effective length of query: 307
Effective length of database: 292
Effective search space:    89644
Effective search space used:    89644
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 (21.9 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