GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Maridesulfovibrio zosterae DSM 11974

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_027723082.1 H589_RS0116710 3-oxoacyl-ACP reductase FabG

Query= BRENDA::Q1J2J0
         (255 letters)



>NCBI__GCF_000425265.1:WP_027723082.1
          Length = 240

 Score =  117 bits (292), Expect = 3e-31
 Identities = 87/242 (35%), Positives = 123/242 (50%), Gaps = 20/242 (8%)

Query: 21  ALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAAREL------DGTFERLNVTDA 74
           AL+TG ++GIG  IA  LA+ G  + +   + D G     E         T  + +VTD 
Sbjct: 5   ALITGASKGIGAAIAVQLAEDGYDIWLNYRSDDAGAHKTAEQIKQHGQQCTLLKFDVTDE 64

Query: 75  DAVAD-----LARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFG 129
            AV +     L +++P +  +VNNAG  R++        DW  VL V+L G F   +   
Sbjct: 65  KAVEENLSSLLEKKVPYI--VVNNAGFTRDSIMMMMDSSDWNKVLQVHLTGFFNVTKPVV 122

Query: 130 RTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAVA 189
             ML +  G I++ AS SG        Q  Y A+KA +I  T+SLA E A R + VNAV 
Sbjct: 123 SRMLRKRTGRIINIASTSG--ETGVAGQTNYCAAKAGLIGATKSLAMEVAKRNILVNAVT 180

Query: 190 PGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLVVD 249
           PG+  T +    L   E + T     PL RL  P+E+A  V +L SD AS++TG T+ V+
Sbjct: 181 PGFIDTDMLSE-LPVDEIKNT----IPLKRLGTPKEVAGVVSFLCSDKASYITGQTIAVN 235

Query: 250 GG 251
           GG
Sbjct: 236 GG 237


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: 137
Number of extensions: 11
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: 240
Length adjustment: 24
Effective length of query: 231
Effective length of database: 216
Effective search space:    49896
Effective search space used:    49896
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 Apr 09 2024. 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