GapMind for catabolism of small carbon sources

 

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

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate GFF829 PGA1_c08430 short chain dehydrogenase / reductase

Query= metacyc::MONOMER-20835
         (262 letters)



>FitnessBrowser__Phaeo:GFF829
          Length = 257

 Score =  201 bits (511), Expect = 1e-56
 Identities = 110/247 (44%), Positives = 153/247 (61%), Gaps = 3/247 (1%)

Query: 14  RVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATRADVSDAAQIE 73
           RVLI+ G +GIG  +A  +  AG QV V DVS  ALA   D   G   T  D +D A ++
Sbjct: 8   RVLITAGGSGIGRAMAEGFAAAGHQVWVTDVSAEALA---DVPEGWRTTVVDATDEAGVK 64

Query: 74  AVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAVPMLK 133
            +F       GGLDVL  NAGIAGPT  I+ I+  +W+  +++NL   +  A +A PM+K
Sbjct: 65  GLFAEITVEWGGLDVLCANAGIAGPTALIEDIALEDWRTCVSVNLEGCFLAAKYAAPMMK 124

Query: 134 ESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGIVEG 193
            +  G ++  +S AG+ GY  R PYA+ KWA++GLMK+LA ELG   IR N + PG VEG
Sbjct: 125 AAKAGAIIVTSSTAGQYGYPNRAPYASAKWAVIGLMKTLAMELGPFGIRANVICPGAVEG 184

Query: 194 PRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVTGQAI 253
           PRM+GV+   A   G+   ++ + Y +  S++  V A+D+A MA+FL S AAR V+GQ I
Sbjct: 185 PRMEGVLEREAAAKGMTRDQVYEGYASGTSMRSFVEAQDIANMAVFLGSDAARLVSGQVI 244

Query: 254 SVDGNVE 260
           +VDG+ E
Sbjct: 245 AVDGHTE 251


Lambda     K      H
   0.318    0.133    0.383 

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: 194
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: 262
Length of database: 257
Length adjustment: 24
Effective length of query: 238
Effective length of database: 233
Effective search space:    55454
Effective search space used:    55454
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 (21.7 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