GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Pseudomonas fluorescens FW300-N1B4

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate Pf1N1B4_1004 Glyoxylate reductase (EC 1.1.1.79) / Glyoxylate reductase (EC 1.1.1.26) / Hydroxypyruvate reductase (EC 1.1.1.81); 2-ketoaldonate reductase, broad specificity (EC 1.1.1.215) (EC 1.1.1.-)

Query= SwissProt::Q9C4M5
         (331 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1004
          Length = 324

 Score =  263 bits (673), Expect = 3e-75
 Identities = 142/271 (52%), Positives = 190/271 (70%), Gaps = 5/271 (1%)

Query: 56  KVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAV 115
           K+ +  LENA KL++++  +VGYDN D+    +RGI +TNTP VLT++TADLAFALL++ 
Sbjct: 55  KLGRAQLENASKLEVVSSVSVGYDNYDLAYFNERGIMLTNTPDVLTESTADLAFALLMSS 114

Query: 116 ARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAK-GFGM 174
           ARR+ E DA+ ++G+W+ + VG  PL   G  + GKTLGIVG G IG A+A+R + GF M
Sbjct: 115 ARRVAELDAWTKAGQWQAT-VG-APLF--GSDVHGKTLGIVGMGNIGAAIARRGRLGFNM 170

Query: 175 KIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNA 234
            IIY   +RK E E+E+GA++   + LL E+DF+ L VPL+++T H+I  +EL LMKP+A
Sbjct: 171 PIIYSGNSRKTELEQELGAQFRSLDQLLAEADFVCLVVPLSEKTRHLISHRELALMKPSA 230

Query: 235 ILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATH 294
           IL+N +RG VVD  ALI+AL+   I GAGLDV+E+EP     LF+LKN V  PHIGSATH
Sbjct: 231 ILVNIARGPVVDEPALIEALQNNRIRGAGLDVYEKEPLAESPLFQLKNAVTLPHIGSATH 290

Query: 295 EAREGMAELVAKNLIAFAKGEIPPNLVNKDV 325
           E RE MA     NL +   GE P +LVN  V
Sbjct: 291 ETREAMANRALANLRSALLGERPQDLVNPQV 321


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: 258
Number of extensions: 12
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: 331
Length of database: 324
Length adjustment: 28
Effective length of query: 303
Effective length of database: 296
Effective search space:    89688
Effective search space used:    89688
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 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