GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pseudomonas fluorescens GW456-L13

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate PfGW456L13_2961 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

Query= reanno::BFirm:BPHYT_RS11290
         (321 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2961
          Length = 317

 Score =  134 bits (337), Expect = 3e-36
 Identities = 86/248 (34%), Positives = 130/248 (52%), Gaps = 7/248 (2%)

Query: 56  MLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVV 115
           +L    +LK L T  +     D+      GI ++ T D    +  +  ++LI+A+ R +V
Sbjct: 66  LLRRLPKLKLLVTGGMRNAALDLKTAAALGIQVSGT-DSYKHAAPELTWALIMAATRNLV 124

Query: 116 ELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSA 175
             A  ++AG WQ  +G      D+ GKTL I+GLG IG  VA+   + F M+V+  + + 
Sbjct: 125 VEANALRAGQWQQGLGG-----DLHGKTLAILGLGSIGQRVAQFGQV-FGMRVIAWSENL 178

Query: 176 NPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGA 235
             +     G  RV   EL   AD + + + L+  ++ L+ A  L  MK SA+L+N +RG 
Sbjct: 179 TAERAAQVGVTRVSKQELFEQADVLSVHLVLSERSRGLVDAQALGWMKPSALLVNTARGP 238

Query: 236 TVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMAR 295
            VDE ALI+ALQ   + GA LDVFE EPLP+  P   L NV+A PH+G  + +       
Sbjct: 239 IVDEAALIKALQKQRLAGAALDVFEQEPLPAHHPFRTLDNVLATPHVGYVSQQNYRLFFL 298

Query: 296 NAAENLVA 303
              E++ A
Sbjct: 299 QMIEDIQA 306


Lambda     K      H
   0.317    0.131    0.366 

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: 216
Number of extensions: 6
Number of successful extensions: 2
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: 321
Length of database: 317
Length adjustment: 28
Effective length of query: 293
Effective length of database: 289
Effective search space:    84677
Effective search space used:    84677
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 (21.7 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