GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Phaeobacter inhibens BS107

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate GFF1301 PGA1_c13170 sorbitol dehydrogenase PolS

Query= reanno::BFirm:BPHYT_RS04775
         (263 letters)



>FitnessBrowser__Phaeo:GFF1301
          Length = 257

 Score =  142 bits (357), Expect = 9e-39
 Identities = 94/251 (37%), Positives = 130/251 (51%), Gaps = 8/251 (3%)

Query: 12  GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAGVA----DVS 67
           G R LI+GAA GIGAA A+A+ + GA V I D+D A   RA     Q+ A       DV+
Sbjct: 6   GKRALITGAARGIGAAFAEAYANEGARVVIADIDTA---RAEATAAQIGAAAIAVELDVT 62

Query: 68  DCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRK 127
           D A +DR +       GGLD+LINNA +      VE    A ++RT   N++   + ++ 
Sbjct: 63  DQASIDRALSRTVECFGGLDILINNAAVFTAAPLVEVTREA-YQRTFDINVSGTLFMMQA 121

Query: 128 AVPLLKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAI 187
           A   +        II MAS AGR G    + Y A+K A++ + +S  + L  + + VNAI
Sbjct: 122 AAQQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGINVNAI 181

Query: 188 LPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAGQ 247
            PGVV+GE  D V +  A+  G    Q K E  Q +   RM T  D+  MA+FLAS    
Sbjct: 182 APGVVDGEHWDGVDAFFAKYEGKAPGQKKAEVAQSVPYGRMGTAADLTGMAVFLASEDAD 241

Query: 248 NISGQAISVDG 258
            +  Q  +VDG
Sbjct: 242 YVVAQTYNVDG 252


Lambda     K      H
   0.320    0.136    0.391 

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: 160
Number of extensions: 5
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: 263
Length of database: 257
Length adjustment: 24
Effective length of query: 239
Effective length of database: 233
Effective search space:    55687
Effective search space used:    55687
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