GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Novosphingobium barchaimii LL02

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_059151148.1 V474_RS08875 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD

Query= BRENDA::Q1J2J0
         (255 letters)



>NCBI__GCF_001046635.1:WP_059151148.1
          Length = 251

 Score =  145 bits (365), Expect = 1e-39
 Identities = 101/251 (40%), Positives = 141/251 (56%), Gaps = 19/251 (7%)

Query: 14  FRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIA---------DLNPDVGEGAAR-ELD 63
           F L+G+ ALVTG   GIG  IA  LAQAGA V +A         DL    G  A   + D
Sbjct: 5   FSLEGKSALVTGANTGIGQAIAVALAQAGADVAVAGRSEPAETLDLIAQTGRKAVNIKAD 64

Query: 64  -GTFERLNVTDADAVADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVF 122
             + E +    A+AVA L +    +DVLVNNAGI+R        ++DW AV+  NL  +F
Sbjct: 65  LSSIEPVQRVIAEAVAGLGK----LDVLVNNAGIIRRDDLLQFSEEDWDAVIDTNLKTLF 120

Query: 123 WCCREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRG 182
           +  +   + M+ +G G IV+ AS+         P  +Y A+K+ V  +T+++A E A RG
Sbjct: 121 FLSQAAAKGMVEQGSGKIVNIASLLTFQGGIRVP--SYAAAKSGVSGVTKAMANELAPRG 178

Query: 183 VRVNAVAPGYTATPLTRRGLETPEWRETW-LKETPLGRLAEPREIAPAVLYLASDAASFV 241
           V+VNA+APGY +T  T   L+  E R    L+  P GR   P +IA A ++LAS A+++V
Sbjct: 179 VQVNAIAPGYISTNNT-AALQGDETRNRQILERIPTGRWGNPDDIAGAAVFLASPASNYV 237

Query: 242 TGHTLVVDGGY 252
           TGH L VDGG+
Sbjct: 238 TGHVLAVDGGW 248


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: 170
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: 251
Length adjustment: 24
Effective length of query: 231
Effective length of database: 227
Effective search space:    52437
Effective search space used:    52437
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