GapMind for catabolism of small carbon sources

 

Alignments for a candidate for KDF-hydrolase in Sinorhizobium meliloti 1021

Align 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (Catechol pathway) protein; EC 4.2.1.80 (characterized, see rationale)
to candidate SMc04240 SMc04240 hypothetical protein

Query= uniprot:D8INW0
         (281 letters)



>FitnessBrowser__Smeli:SMc04240
          Length = 228

 Score =  112 bits (281), Expect = 6e-30
 Identities = 74/217 (34%), Positives = 105/217 (48%), Gaps = 14/217 (6%)

Query: 61  PRIGACVG-NIGKFICIGLNYADHAAE-SNLPIPAEPVVFNKWTSAVVGPNDNVKIPRGS 118
           P  G+ VG  + +  C+G NYA HA E  + P    P  F K    ++ P +N   P  S
Sbjct: 14  PISGSSVGFPVRRVYCVGRNYAAHAREMGHDPDREAPFFFQKNADNLLPPGENFPYPTRS 73

Query: 119 KKTDWEVELGVIIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIER---GGTWDKGKGC 175
                EVEL V +  GG+ I   +A  H+ GY V  D + R+ Q E    G  W   K  
Sbjct: 74  SDVHHEVELVVAMRTGGADIPVSEAADHIFGYGVGIDFTRRDLQAEAKKAGKPWTAAKAF 133

Query: 176 DTFGPIGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFNVAHIVSYLSRFMSLQP 235
           +   P+   +V    +  P    +WL+V+G+  Q G+   MI+ V  I++ LSR  +L P
Sbjct: 134 EHSAPVSA-IVPVTAIGHPASGNIWLKVNGELRQQGDLDQMIWKVPEIIAELSRLFTLAP 192

Query: 236 GDVISTGTPPGVGMGVKPEAVYLRAGQTIRLGIDGLG 272
           GD+I TGTP GVG         +  G  +  GIDG+G
Sbjct: 193 GDIIMTGTPSGVGP--------VTQGDVVACGIDGIG 221


Lambda     K      H
   0.316    0.139    0.421 

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: 181
Number of extensions: 10
Number of successful extensions: 3
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: 281
Length of database: 228
Length adjustment: 24
Effective length of query: 257
Effective length of database: 204
Effective search space:    52428
Effective search space used:    52428
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 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