GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Phaeobacter inhibens BS107

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate GFF2436 PGA1_c24680 glyoxylate reductase GyaR

Query= SwissProt::Q9C4M5
         (331 letters)



>FitnessBrowser__Phaeo:GFF2436
          Length = 318

 Score =  220 bits (561), Expect = 3e-62
 Identities = 129/318 (40%), Positives = 181/318 (56%), Gaps = 9/318 (2%)

Query: 1   MKPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKE 60
           M  K++ITR +           +  E+ ++      G     +RE D ++  + D+ D  
Sbjct: 1   MSGKLWITRPMTAAVEARARSEFGAEIRQETTPLTAGERQRALREFDVVMPTLGDQFDAA 60

Query: 61  LLE--NAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARR 118
                +AP+ +++A + VGY++ID++ A   GI V+NTPG +TDATAD A  L+L  ARR
Sbjct: 61  SFAGVSAPRCRLLANFGVGYNHIDVDAAKTAGIAVSNTPGAVTDATADTALTLMLMTARR 120

Query: 119 IVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAK-GFGMKII 177
             E +  VRSG+W+    GWHP   LG  L GK +GIVGFGRIG+A+A+R   GFGM + 
Sbjct: 121 AGEGERLVRSGQWQ----GWHPTQMLGLHLTGKHVGIVGFGRIGEAIARRCHFGFGMSVS 176

Query: 178 YYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILI 237
           Y +R+ K      + A+      L    D + L VP   ET H+I  + L  M+P A+LI
Sbjct: 177 YLARSEKSPGFPAVRAD--SLTALAASVDVLVLAVPGGAETRHLINAEVLAAMRPEALLI 234

Query: 238 NTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAR 297
           N +RG VVD  ALI AL+ G IAGAGLDV+E EP     L +++ V L PH+G+AT E R
Sbjct: 235 NIARGEVVDEAALISALQTGQIAGAGLDVYEFEPEVPLALQQMEQVTLLPHLGTATEEVR 294

Query: 298 EGMAELVAKNLIAFAKGE 315
             M  L   N+ AF  G+
Sbjct: 295 SDMGHLALDNVAAFLAGK 312


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: 213
Number of extensions: 9
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: 318
Length adjustment: 28
Effective length of query: 303
Effective length of database: 290
Effective search space:    87870
Effective search space used:    87870
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