GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Lactobacillus pobuzihii E100301

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_017867501.1 LACPOB_RS0103790 SDR family oxidoreductase

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



>NCBI__GCF_000349725.1:WP_017867501.1
          Length = 253

 Score =  102 bits (253), Expect = 1e-26
 Identities = 71/254 (27%), Positives = 119/254 (46%), Gaps = 20/254 (7%)

Query: 12  GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAGV---ADVSD 68
           G   +++GA+ GIGAA A+ F   GANV I D++P+    A+         +    DV+D
Sbjct: 8   GKTAIVTGASGGIGAATAKLFAQNGANVVIGDINPSGQKVAQEIKDAGGKAIFVKTDVAD 67

Query: 69  CAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKA 128
              V  +ID A    G +D+  NNAG+A       D+   E+++ +  +    F  ++  
Sbjct: 68  STSVKNLIDQAIQAYGKIDVAFNNAGMANLPDKASDMPEEEYDKAMNVDAKCVFLCMKYE 127

Query: 129 VPLLKETSANPGIIAMASVAGRLGYAFRT-PYAASKWAIVGMVKSLAIELGPNNVRVNAI 187
           +  +++ +    I+  +S++G         PY A+K A++GM +S A +     +RVN I
Sbjct: 128 LDNMRKHNGG-AIVNTSSISGLSAKPDNMLPYIAAKHAVIGMTRSAAFDHAKEGIRVNTI 186

Query: 188 LPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVH---DVAAMALFLASP 244
            PG++E E  +            G+     ++ +   L  M       D+A M LFL S 
Sbjct: 187 APGLIETEMTE------------GYKDTPEKWAEMTGLNPMNAAGKPIDIANMVLFLCSD 234

Query: 245 AGQNISGQAISVDG 258
           A +  +   ISVDG
Sbjct: 235 ASRFTTASVISVDG 248


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: 143
Number of extensions: 8
Number of successful extensions: 4
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: 253
Length adjustment: 24
Effective length of query: 239
Effective length of database: 229
Effective search space:    54731
Effective search space used:    54731
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 24 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