GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-alpha in Rhizobium leguminosarum bv. trifolii WSM1325

Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate WP_012759947.1 RLEG_RS32870 (2Fe-2S)-binding protein

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



>NCBI__GCF_000023185.1:WP_012759947.1
          Length = 174

 Score =  132 bits (332), Expect = 3e-36
 Identities = 63/143 (44%), Positives = 90/143 (62%), Gaps = 1/143 (0%)

Query: 1   MELRINQKAYQVDADADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLVDGNVVRSCVTP 60
           + L +N   ++V A  +TPLL+++R+DL L G KYGCGL +CGAC+VLVDG  VRSC  P
Sbjct: 7   VSLNVNDALWRVSAKPETPLLYILRNDLCLNGPKYGCGLGECGACAVLVDGRPVRSCTVP 66

Query: 61  VAGVVGREITTIEAIETDEVGKRVVATWVEHQVAQCGYCQSGQVMAATALLKHTPAPSKA 120
           +  +  R + T+E +  D +   V   ++E   AQCGYC +G ++A   LL+    P ++
Sbjct: 67  LGAIGKRRVITLEGLAVDGLLHPVQQAFIEEAAAQCGYCLNGMIIATVGLLQRNTDPDES 126

Query: 121 QI-DAAMINLCRCGTYNAIHAAV 142
            I DA   +LCRCGT+  I AAV
Sbjct: 127 DIRDALRHHLCRCGTHVEILAAV 149


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: 104
Number of extensions: 4
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: 174
Length adjustment: 18
Effective length of query: 133
Effective length of database: 156
Effective search space:    20748
Effective search space used:    20748
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 Apr 09 2024. 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