GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Magnetospirillum magneticum AMB-1

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_011385057.1 AMB_RS13470 3-hydroxybutyrate dehydrogenase

Query= uniprot:B2T9V3
         (247 letters)



>NCBI__GCF_000009985.1:WP_011385057.1
          Length = 260

 Score =  142 bits (357), Expect = 9e-39
 Identities = 93/263 (35%), Positives = 138/263 (52%), Gaps = 27/263 (10%)

Query: 5   LAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLA-GKPVEARKLDVRDDAAIK 63
           L GK AL+T +  GIGL  A   A +GA V+     ++G   G  +EA +  +  +  + 
Sbjct: 2   LNGKRALVTGSTSGIGLGIARALAAQGASVM-----LNGFGDGAEIEALRAGLAKEFGVT 56

Query: 64  AL-------------------AAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVK 104
            L                    A +G VD+L N AG  H   + E   E WD    +N+ 
Sbjct: 57  VLYNGADLSKPDGAGVLVRDAEARLGGVDILVNNAGIQHVSPVEEFPLERWDAVIAINLT 116

Query: 105 AMYRMIRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFIT 164
           ++++ IRA LP M  +G G IIN++SA   V  V N+ AY ASK  V+GLTK V  +   
Sbjct: 117 SVFQAIRAALPGMKARGWGRIINVASAHGLVASV-NKSAYVASKHGVLGLTKVVGLETAE 175

Query: 165 RGVRCNAICPGTVASPSLEQRIVAQAQAQGATLD-AVQAAFVARQPMGRIGKPEEIAALA 223
             V CNAICPG V +P ++++I A+A+AQG  ++ A +     +QP  +   PE+I  LA
Sbjct: 176 TDVTCNAICPGWVLTPLVQKQIDARAEAQGVPVEQAGRDLLSEKQPSKKFTTPEQIGDLA 235

Query: 224 LYLGSDESSFTTGHAHVIDGGWS 246
           ++L S   +  TG +  +DGGW+
Sbjct: 236 VFLCSGAGANMTGTSLTMDGGWT 258


Lambda     K      H
   0.320    0.133    0.381 

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: 160
Number of extensions: 9
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: 247
Length of database: 260
Length adjustment: 24
Effective length of query: 223
Effective length of database: 236
Effective search space:    52628
Effective search space used:    52628
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 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