GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-alpha in Marinobacter adhaerens HP15

Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate GFF1600 HP15_1561 (2Fe-2S)-binding domain protein

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



>FitnessBrowser__Marino:GFF1600
          Length = 153

 Score =  170 bits (431), Expect = 8e-48
 Identities = 84/149 (56%), Positives = 107/149 (71%), Gaps = 2/149 (1%)

Query: 3   LRINQKAYQVDADADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLVDGNVVRSCVTPVA 62
           L IN + Y++D   + PLLWVIRD +GL GTK+GCG++QCGAC+V ++G  +RSCVTPV+
Sbjct: 4   LTINGERYELDVPDNMPLLWVIRDVVGLKGTKFGCGMSQCGACTVHLNGTAIRSCVTPVS 63

Query: 63  GVVGREITTIEAIETDEVGKRVVATWVEHQVAQCGYCQSGQVMAATALLKHTPAPSKAQI 122
              G EITTIEA+  D VG +V   W++  VAQCGYCQ GQ+M ATALLK TP P   +I
Sbjct: 64  AASG-EITTIEAMADDPVGSKVQQAWLDLGVAQCGYCQGGQIMNATALLKRTPNPETGEI 122

Query: 123 -DAAMINLCRCGTYNAIHAAVDDLAKQGG 150
            DA   NLCRCGTYN I AA++  + + G
Sbjct: 123 VDAMAGNLCRCGTYNRILAAIERASGKEG 151


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: 117
Number of extensions: 5
Number of successful extensions: 3
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: 153
Length adjustment: 17
Effective length of query: 134
Effective length of database: 136
Effective search space:    18224
Effective search space used:    18224
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: 43 (21.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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