GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Azospirillum brasilense Sp245

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate AZOBR_RS31390 AZOBR_RS31390 3-ketoacyl-ACP reductase

Query= BRENDA::Q1J2J0
         (255 letters)



>FitnessBrowser__azobra:AZOBR_RS31390
          Length = 252

 Score =  154 bits (390), Expect = 1e-42
 Identities = 101/248 (40%), Positives = 135/248 (54%), Gaps = 12/248 (4%)

Query: 14  FRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFERLNVTD 73
           F L G+ ALVTGG  GIG  IA  LA+AGA + +A   P     A  E  G        D
Sbjct: 5   FDLTGKTALVTGGNGGIGQAIAVALARAGADIAVAGRTPPDETRALVEGLGRRFAAIPAD 64

Query: 74  ADAVADLARRLPD-------VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCR 126
             ++A +   + +       +D+LVNNAG++R     D  + DW AVL VNL  VF+ C+
Sbjct: 65  LSSIAPIPALMEETVGTLGGLDILVNNAGLIRRDDPLDFTEADWDAVLDVNLKSVFFLCQ 124

Query: 127 EFGRTMLARGR-GAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRV 185
            FGR  L  GR G I++ ASM         P  +Y ASK+ +  +TR LA EWA +G+ V
Sbjct: 125 AFGRYALGNGRKGKIINIASMLSFQGGIRVP--SYAASKSGIAGITRLLANEWAGKGINV 182

Query: 186 NAVAPGYTATPLTRRGLETPEWRET-WLKETPLGRLAEPREIAPAVLYLASDAASFVTGH 244
           NA+APGY AT +T   L   E R    L   P GR +EP ++    ++LASDA+ +V G 
Sbjct: 183 NAIAPGYVATSVT-TALRADERRNAEILARIPAGRWSEPADMGGPAVFLASDASDYVHGT 241

Query: 245 TLVVDGGY 252
            L VDGG+
Sbjct: 242 ILPVDGGW 249


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: 198
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: 255
Length of database: 252
Length adjustment: 24
Effective length of query: 231
Effective length of database: 228
Effective search space:    52668
Effective search space used:    52668
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: 47 (22.7 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