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 (characterized)
to candidate AO356_24675 AO356_24675 bifunctional glyoxylate/hydroxypyruvate reductase B

Query= SwissProt::Q9C4M5
         (331 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_24675
          Length = 325

 Score =  253 bits (646), Expect = 5e-72
 Identities = 140/272 (51%), Positives = 176/272 (64%), Gaps = 6/272 (2%)

Query: 56  KVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAV 115
           K+D  LL+ AP L+ IA  +VG DN DI+  T+R I +TNTP VLT+ TAD  FAL+LA 
Sbjct: 55  KLDAALLDLAPNLQAIASVSVGVDNYDIDYLTERRILLTNTPDVLTETTADTGFALILAT 114

Query: 116 ARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAK-GFGM 174
           ARR+VE    VRSG W++S    H     G  + GKTLGI+G GRIG+ALA+R   GFGM
Sbjct: 115 ARRVVELANLVRSGGWQQSIGPRH----FGTDVHGKTLGIIGMGRIGEALAQRGHFGFGM 170

Query: 175 KIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNA 234
            ++Y+S + KP  E+  GA Y   ETLL+++DF+ L +PLT ET  +I  +    M+P  
Sbjct: 171 PVLYHSHSPKPAVEQRFGARYCSLETLLQQADFVCLTLPLTAETQGLIDAQAFARMRPET 230

Query: 235 ILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPY-YNEELFKLKNVVLAPHIGSAT 293
           + IN SRG VVD  ALI AL+ G I GAGLDVFE EP   +  L ++ NVV  PH+GSAT
Sbjct: 231 LFINISRGKVVDEAALIDALRNGQIRGAGLDVFEHEPLSADSPLLQMDNVVATPHMGSAT 290

Query: 294 HEAREGMAELVAKNLIAFAKGEIPPNLVNKDV 325
           HE RE MA     NL+A   GE P NLVN  V
Sbjct: 291 HETREAMARCAVDNLLAALAGERPENLVNLGV 322


Lambda     K      H
   0.317    0.137    0.392 

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: 9
Number of successful extensions: 4
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: 331
Length of database: 325
Length adjustment: 28
Effective length of query: 303
Effective length of database: 297
Effective search space:    89991
Effective search space used:    89991
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.

Links

Downloads

Related tools

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