GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Burkholderia phytofirmans PsJN

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate BPHYT_RS02320 BPHYT_RS02320 3-oxoadipate enol-lactonase

Query= BRENDA::Q13KT2
         (263 letters)



>FitnessBrowser__BFirm:BPHYT_RS02320
          Length = 262

 Score =  173 bits (438), Expect = 4e-48
 Identities = 92/258 (35%), Positives = 135/258 (52%), Gaps = 8/258 (3%)

Query: 6   VNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGHGHSEA 65
           +NG E  Y +  E  G  PW+   + LG DLS+W          + VLRYD RGHG + A
Sbjct: 5   INGIETRYVLSNE--GGGPWLTFIHQLGGDLSVWDQLAGYFRDDYTVLRYDVRGHGKTAA 62

Query: 66  PKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALCNTAAR 125
              P+ I  L+ D+  L+D L     +  G+SMGG+        H  R++ + + +++  
Sbjct: 63  SSAPFGIADLSHDLATLLDALGAPTTHLVGMSMGGMIAQQFTLDHPTRVDSLTIADSSG- 121

Query: 126 IGSPE----VWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDKE 181
            G+P+     W  RA  AR +GM +L  A L RW T D+    P  +  IRDV  +T  E
Sbjct: 122 -GTPQEARATWDQRAATARRDGMVSLVPATLSRWLTPDFQAAHPEAVEQIRDVLTNTLSE 180

Query: 182 GYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARYVELDASH 241
           GYA  CEA+   D+R +   I+ P L ++G HD    PA  + +A AI GAR+  LDA+H
Sbjct: 181 GYAMACEALRDFDVRSKLGAIRCPTLTVAGRHDTGTPPASTQAIADAIEGARFELLDAAH 240

Query: 242 ISNIERADAFTKTVVDFL 259
           ++ IE++  F   +  FL
Sbjct: 241 LAPIEQSHRFAALLETFL 258


Lambda     K      H
   0.320    0.134    0.402 

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: 196
Number of extensions: 6
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 263
Length of database: 262
Length adjustment: 25
Effective length of query: 238
Effective length of database: 237
Effective search space:    56406
Effective search space used:    56406
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: 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