GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Brucella inopinata BO1

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_025200128.1 BIBO1_RS11530 7-alpha-hydroxysteroid dehydrogenase

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



>NCBI__GCF_000182725.1:WP_025200128.1
          Length = 304

 Score =  133 bits (335), Expect = 4e-36
 Identities = 84/246 (34%), Positives = 132/246 (53%), Gaps = 16/246 (6%)

Query: 16  LISGGAAGIGEVLAAAYLEAGAQVHVCDV----SESALAVFRDKYPGTVATRADVSDAAQ 71
           +++G AAGIG  +A  + +AGA V V D+    +E+  A  R      +    +V+D   
Sbjct: 64  IVTGAAAGIGRAIAGTFAKAGASVVVTDLKSEGAEAVAATIRQAGGKAIGLECNVTDEQH 123

Query: 72  IEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAVPM 131
            EAV K   +  G + VLVNNAG  GP      +SD EW     +NL + +R +  A P 
Sbjct: 124 REAVIKAALDQFGKITVLVNNAGGGGPKPFDMPLSDFEW--AFKLNLFSVFRLSQLAAPH 181

Query: 132 LKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGIV 191
           ++++ HG +L+I+S+AG         Y ++K A+  L +++A ++G   IRVNA+ PG +
Sbjct: 182 MQKAGHGAILNISSMAGENTNVRMASYGSSKAAVNHLTRNIAFDVGPMGIRVNAIAPGAI 241

Query: 192 EGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVTGQ 251
           +   +  V+         PE E  +  L    L R+  A+D+A  ALFLCSPAA  ++GQ
Sbjct: 242 KTDALATVL--------TPEIE--RAMLKHTPLGRLGEAQDIANAALFLCSPAAAWISGQ 291

Query: 252 AISVDG 257
            ++V G
Sbjct: 292 VLTVSG 297


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: 200
Number of extensions: 6
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: 262
Length of database: 304
Length adjustment: 26
Effective length of query: 236
Effective length of database: 278
Effective search space:    65608
Effective search space used:    65608
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 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