GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Brucella inopinata BO1

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate WP_025200128.1 BIBO1_RS11530 7-alpha-hydroxysteroid dehydrogenase

Query= SwissProt::O93868
         (262 letters)



>NCBI__GCF_000182725.1:WP_025200128.1
          Length = 304

 Score =  102 bits (254), Expect = 9e-27
 Identities = 74/245 (30%), Positives = 122/245 (49%), Gaps = 11/245 (4%)

Query: 15  IVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQCDVSNTD 74
           IVTG   GIG A     A AGA+V V    ++ A  V   + ++ G K    +C+V++  
Sbjct: 64  IVTGAAAGIGRAIAGTFAKAGASVVVTDLKSEGAEAVAATI-RQAGGKAIGLECNVTDEQ 122

Query: 75  IVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNTCRAVAKL 134
                I+      G I+ L+ NAG    KP  ++   DF++ + +N+F VF   +  A  
Sbjct: 123 HREAVIKAALDQFGKITVLVNNAGGGGPKPF-DMPLSDFEWAFKLNLFSVFRLSQLAAP- 180

Query: 135 WLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAEWASAGIRV 194
            +QK   G+I+  SSM+ +       N ++    Y SSKAA ++L + +A +    GIRV
Sbjct: 181 HMQKAGHGAILNISSMAGE-------NTNVRMASYGSSKAAVNHLTRNIAFDVGPMGIRV 233

Query: 195 NALSPGYVNTDQTAH-MDKKIRDHQASNIPLNRFAQPEEMTGQAILLLSDHATYMTGGEY 253
           NA++PG + TD  A  +  +I      + PL R  + +++   A+ L S  A +++G   
Sbjct: 234 NAIAPGAIKTDALATVLTPEIERAMLKHTPLGRLGEAQDIANAALFLCSPAAAWISGQVL 293

Query: 254 FIDGG 258
            + GG
Sbjct: 294 TVSGG 298


Lambda     K      H
   0.317    0.130    0.372 

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: 175
Number of extensions: 15
Number of successful extensions: 5
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 ( 7.3 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