GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Paucidesulfovibrio gracilis DSM 16080

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_078715956.1 B5D49_RS01965 3-oxoacyl-[acyl-carrier-protein] reductase

Query= BRENDA::Q1J2J0
         (255 letters)



>NCBI__GCF_900167125.1:WP_078715956.1
          Length = 247

 Score =  134 bits (338), Expect = 1e-36
 Identities = 94/242 (38%), Positives = 136/242 (56%), Gaps = 16/242 (6%)

Query: 21  ALVTGGAQGIGFEIARGLAQAGARVTIADLN-PDVGEGAAREL---DGTFE--RLNVTDA 74
           ALVTGG++GIG   A  LA  G  V +  ++ P+  E   + +    GT    +L+ +D 
Sbjct: 8   ALVTGGSRGIGRACAERLAADGFEVWLTYVSKPEAAETVVQTIADAGGTARAVQLDSSDR 67

Query: 75  DAVA----DLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFGR 130
           +AVA    D  +    +  LVNNAGI R+        +DW +VL +NL G F C +E  +
Sbjct: 68  EAVASFFKDEIKGKVHLAALVNNAGITRDGLLIRMKPEDWDSVLDINLTGAFSCLQEAAK 127

Query: 131 TMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAVAP 190
            M  +  G+I++ +S+ G + N    QA Y A+KA +I LT++ A E A RGVRVNAVAP
Sbjct: 128 IMARQRGGSIINISSVVGQMGN--AGQANYVAAKAGLIGLTKAAARELAGRGVRVNAVAP 185

Query: 191 GYTATPLTRRGLETPEWR-ETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLVVD 249
           G+  T +T+   + PE   E+     PL RL  P +IA AV +LA + A ++TG  L V+
Sbjct: 186 GFIETDMTK---DLPEKTVESMKTMIPLSRLGSPGDIAAAVSFLAGNGAGYITGQVLAVN 242

Query: 250 GG 251
           GG
Sbjct: 243 GG 244


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: 183
Number of extensions: 8
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: 247
Length adjustment: 24
Effective length of query: 231
Effective length of database: 223
Effective search space:    51513
Effective search space used:    51513
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