GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdhA in Pseudomonas fluorescens GW456-L13

Align L-serine dehydratase, alpha chain; Short=SDH; EC 4.3.1.17 (characterized, see rationale)
to candidate PfGW456L13_1089 L-serine dehydratase (EC 4.3.1.17)

Query= uniprot:P33073
         (292 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089
          Length = 458

 Score =  138 bits (348), Expect = 2e-37
 Identities = 95/290 (32%), Positives = 151/290 (52%), Gaps = 24/290 (8%)

Query: 3   NTAREIIDVCNERGIKIYDLVLEEEIKNSHTTEEEIRKKLDAVIDVMHASATKNLTQSDV 62
           ++A E++++C +  +++ +L++  E      +E+EIR  L  +   M     + L    +
Sbjct: 174 SSAAELLELCKKHNLRVAELMMANE--RVWRSEDEIRSGLMKLWRAMQDCVEQGLKHEGI 231

Query: 63  T----EYKMIDGFAKRTYEYANSGKSIVGDFLAK---AMAMAFSTSEVNASMGKIVAAPT 115
                  +       R+ +  N   +++G  L+        A + +E NA+ G++V APT
Sbjct: 232 LPGGLNVRRRAAKLHRSLQELNK-PNVIGSTLSAMEWVNLFALAVNEENAAGGRMVTAPT 290

Query: 116 AGSSGIMPAML-------VAATEKYNFDRTTIQNGFLTSIGIGQVITKYATFAGAEGGCQ 168
            G++GI+PA+L        A T+        + + FL +  +G +  K A+ +GAE GCQ
Sbjct: 291 NGAAGIIPAVLHYFMKFSEAVTD------ANVVDYFLGAAAVGILCKKNASISGAEVGCQ 344

Query: 169 AECGSASAMAAAALVEMLGGTVEQALHAASITIINVLGLVCDPIAGLVQYPCTFRNASGV 228
            E GSA AMAAA L E+LG T EQ  +AA I + + LGL CDP+ GLVQ PC  RNA   
Sbjct: 345 GEVGSACAMAAAGLAEILGATPEQLCNAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAA 404

Query: 229 INAFISADLALAG-VESLVPFDEVVIAMGEVGNSMIEALRETGLGGLAGS 277
           + A  +A +AL G  +  +  D V+  M + G  M +  +ET  GGLA S
Sbjct: 405 VKAINAAQMALRGDGQHFISLDRVIRTMRDTGADMHDKYKETSRGGLAVS 454


Lambda     K      H
   0.317    0.132    0.361 

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: 246
Number of extensions: 11
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: 292
Length of database: 458
Length adjustment: 30
Effective length of query: 262
Effective length of database: 428
Effective search space:   112136
Effective search space used:   112136
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: 49 (23.5 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