GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Pedobacter sp. GW460-11-11-14-LB5

Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate CA265_RS08355 CA265_RS08355 short-chain dehydrogenase

Query= reanno::WCS417:GFF2259
         (257 letters)



>FitnessBrowser__Pedo557:CA265_RS08355
          Length = 254

 Score =  128 bits (322), Expect = 1e-34
 Identities = 88/256 (34%), Positives = 128/256 (50%), Gaps = 11/256 (4%)

Query: 1   MKRLEGKSALITGSARGIGRAFAQAYIAEGATVAIADIDLQRAQATAAEL---GPQAYAV 57
           M  L+ K A++TG   GIG+A A     +GA V I ++  + AQ T  E+   G  A++ 
Sbjct: 1   MFSLKNKKAVVTGGGSGIGKAIATILAKQGAEVHIIELGTEHAQDTLDEIKTNGGVAFSY 60

Query: 58  AMDVTDQASIDGAITAVVAQAGKLDILINNAALFDLAPIVDITRDSYDRLFSINVAGTLF 117
             DV+D      A+ AV  + G ++ILINNA +  +          +DR+  +NV G   
Sbjct: 61  GCDVSDHQ----AVAAVFNEIGNINILINNAGIAHIGKADTTDEADFDRVMRVNVKGVYN 116

Query: 118 TLQAAARQMIRQGHGGKIINMASQAGRRGEPLVAIYCATKAAVISLTQSAGLNLIKQGIN 177
            L AA  Q IR   GG IINMAS A   G P   +Y A K AV ++T S   + I + I 
Sbjct: 117 CLHAAIPQ-IRLSGGGVIINMASIAALIGLPDRFVYSAAKGAVKAITMSVAKDYIGENIR 175

Query: 178 VNAIAPGVVDGEHWDGVDALFAKHEGLAPGEKKQRVGAEVPFGRMGTAEDLTGMAIFLAS 237
            N+I+P  V   H   VD    K+      E  +++    P GRM   E++  +A++L S
Sbjct: 176 CNSISPARV---HTPFVDGFLQKNYPDNIPEMFEKLSKTQPIGRMAKPEEVGALALYLCS 232

Query: 238 KEADYVVAQTYNVDGG 253
            EA ++    Y +DGG
Sbjct: 233 DEASFITGCDYPIDGG 248


Lambda     K      H
   0.318    0.133    0.374 

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: 148
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: 257
Length of database: 254
Length adjustment: 24
Effective length of query: 233
Effective length of database: 230
Effective search space:    53590
Effective search space used:    53590
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 (21.7 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