GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Pseudomonas fluorescens FW300-N2E2

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Pf6N2E2_1212 Oxidoreductase, short chain dehydrogenase/reductase family

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1212
          Length = 285

 Score =  136 bits (343), Expect = 4e-37
 Identities = 96/268 (35%), Positives = 134/268 (50%), Gaps = 16/268 (5%)

Query: 11  PEPPKGE-------RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAA 63
           P P  GE       RL NK+ L+TGA  GIG A+  AFA + A + I+ +   +     A
Sbjct: 25  PYPDCGEQSYTGSGRLANKIALITGADSGIGRAVAIAFAREGADVAIAYLDEHEDAKETA 84

Query: 64  HWRER-GADVHALKADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLE-MTEED 121
            W E+ G     L  D++N+     +    V R G IDVLVN A   +  + LE +++E+
Sbjct: 85  RWVEQAGRQCLLLPGDLANKDQCRKIVDETVARFGHIDVLVNNAAFQMTHESLEQISDEE 144

Query: 122 WRRCFAIDLDGAWYGCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLT 181
           W R F I++   +  C+A +P M  +  GSIIN +S +S    P    Y   K  +   T
Sbjct: 145 WVRTFDINITAMFRICQAAVPHM--KPGGSIINTSSVNSDMPKPTLLAYATTKGAIANFT 202

Query: 182 RALGIEYAPKGVRVNAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVA 241
             L     PKG+RVN++APG I T L V        P  E Q      P  R GQP+EVA
Sbjct: 203 GGLAQMLGPKGIRVNSVAPGPIWTPLIV-----ATMPEEEVQNFGSQTPLGRPGQPVEVA 257

Query: 242 MTAVFLASDEAPFINASCITIDGGRSVM 269
              V LASDEA +I+ +   I GG+ ++
Sbjct: 258 PIYVLLASDEASYISGTRYGITGGKPIL 285


Lambda     K      H
   0.321    0.137    0.419 

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: 174
Number of extensions: 9
Number of successful extensions: 5
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: 272
Length of database: 285
Length adjustment: 25
Effective length of query: 247
Effective length of database: 260
Effective search space:    64220
Effective search space used:    64220
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 (21.8 bits)
S2: 47 (22.7 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