GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Pantoea rwandensis LMG 26275

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_084935308.1 HA51_RS14510 3-oxoacyl-ACP reductase FabG

Query= BRENDA::Q1J2J0
         (255 letters)



>NCBI__GCF_002095475.1:WP_084935308.1
          Length = 244

 Score =  154 bits (388), Expect = 2e-42
 Identities = 100/241 (41%), Positives = 139/241 (57%), Gaps = 10/241 (4%)

Query: 17  DGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAAREL--DGTFERLNVTDA 74
           +G+ ALVTG ++GIG  IA  L   GA+V     +    E  +  L  +G    LNVTDA
Sbjct: 4   EGKVALVTGASRGIGRAIAETLVARGAKVVGTATSESGAEAISAYLGDNGKGLLLNVTDA 63

Query: 75  DAVADLARRLP----DVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFGR 130
            ++  +  ++     +VD+LVNNAGI R+       DD+W  +L  NL  VF   +   R
Sbjct: 64  ASIESVLEKVRAEFGEVDILVNNAGITRDNLLMRMKDDEWADILDTNLTSVFRLSKAVLR 123

Query: 131 TMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAVAP 190
            M+ +  G I++  S+ G + N    QA Y A+KA +I  ++SLA E ASRG+ VN VAP
Sbjct: 124 AMMKKRVGRIITIGSVVGTMGN--AGQANYAAAKAGLIGFSKSLAREIASRGITVNVVAP 181

Query: 191 GYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLVVDG 250
           G+  T +TR   E  + R   L E P GRL +P+EIA AV +LASD AS++TG TL V+G
Sbjct: 182 GFIETDMTRALNE--DQRSGILAEVPAGRLGDPQEIANAVAFLASDEASYITGETLHVNG 239

Query: 251 G 251
           G
Sbjct: 240 G 240


Lambda     K      H
   0.319    0.134    0.408 

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: 179
Number of extensions: 10
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: 255
Length of database: 244
Length adjustment: 24
Effective length of query: 231
Effective length of database: 220
Effective search space:    50820
Effective search space used:    50820
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 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