GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Burkholderia phytofirmans PsJN

Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate BPHYT_RS20310 BPHYT_RS20310 alpha/beta hydrolase

Query= reanno::pseudo3_N2E3:AO353_17230
         (266 letters)



>FitnessBrowser__BFirm:BPHYT_RS20310
          Length = 272

 Score = 75.9 bits (185), Expect = 9e-19
 Identities = 77/263 (29%), Positives = 112/263 (42%), Gaps = 29/263 (11%)

Query: 2   GFVQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFR-VLRFDTRGHGR 60
           G+V+     + Y   G   APV++L   LG + + W  Q+PA     R V+  D+RGHGR
Sbjct: 30  GYVEHEGARIWYASYGAG-APVILLHGGLGHSGN-WGYQVPALLDAGRRVVVVDSRGHGR 87

Query: 61  SLVTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVV--C 118
           S     PY  E +  DVLA++D L +ERA   G S G  +   LG  A ER+  +    C
Sbjct: 88  STRDARPYRYELMASDVLAVMDTLQLERAALVGWSDGACVAMVLGATAAERVAGVFFFGC 147

Query: 119 NTAAKIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAA 178
           N      DPS   P + T   +   +  A   A ++   TPD  +A           +  
Sbjct: 148 NM-----DPSGTRPFVPTPAIERCFSRHAKDYAQLSA--TPDDFEAFVGA----VSTMMK 196

Query: 179 TSPQGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEF 238
           T P  Y+A             LA I VP  ++    D    P    ++   + GAE    
Sbjct: 197 TEP-NYSAG-----------DLAQIRVPVAIVQSEHDEFIKPEHADYLARSIPGAELILL 244

Query: 239 -YAAHLSNVQAGSAFSDRVLSFL 260
              +H + +Q  + F+  VL FL
Sbjct: 245 PGVSHFAPLQRPAQFNRVVLDFL 267


Lambda     K      H
   0.321    0.136    0.410 

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: 193
Number of extensions: 12
Number of successful extensions: 2
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: 266
Length of database: 272
Length adjustment: 25
Effective length of query: 241
Effective length of database: 247
Effective search space:    59527
Effective search space used:    59527
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 (21.9 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