GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-alpha in Pedobacter sp. GW460-11-11-14-LB5

Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate CA265_RS09870 CA265_RS09870 2Fe-2S ferredoxin

Query= metacyc::MONOMER-20832
         (151 letters)



>FitnessBrowser__Pedo557:CA265_RS09870
          Length = 207

 Score =  117 bits (292), Expect = 1e-31
 Identities = 62/152 (40%), Positives = 91/152 (59%), Gaps = 4/152 (2%)

Query: 1   MELRINQKAYQVDADADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLVDGNVVRSCVTP 60
           ++L +N KAYQ   +    LL  +R++L LTGTK GC   QCGAC+V VDG  V SC++ 
Sbjct: 55  LKLTVNNKAYQTTVEPRVTLLDYLREELHLTGTKKGCDHGQCGACTVHVDGQRVNSCLSL 114

Query: 61  VAGVVGREITTIEAIETDEVGKRVVATWVEHQVAQCGYCQSGQVMAATALLKHTPAPSKA 120
                G++ITTIE +   +    + A +++H   QCGYC  GQ+M+A A ++     S+A
Sbjct: 115 AVMNEGKKITTIEGLANGDTLHPMQAAFIKHDGFQCGYCTPGQIMSAVACVREGHTGSRA 174

Query: 121 QIDAAMI-NLCRCGTY-NAIHAAVDDLAKQGG 150
           +I   M  N+CRCG Y N + A ++   K+GG
Sbjct: 175 EISEYMSGNICRCGAYPNIVDAIIE--VKEGG 204


Lambda     K      H
   0.320    0.134    0.410 

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: 99
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: 151
Length of database: 207
Length adjustment: 19
Effective length of query: 132
Effective length of database: 188
Effective search space:    24816
Effective search space used:    24816
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: 44 (21.6 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