GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davA in Burkholderia phytofirmans PsJN

Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate BPHYT_RS00250 BPHYT_RS00250 hydratase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1170
         (264 letters)



>FitnessBrowser__BFirm:BPHYT_RS00250
          Length = 283

 Score =  108 bits (270), Expect = 1e-28
 Identities = 83/244 (34%), Positives = 126/244 (51%), Gaps = 19/244 (7%)

Query: 31  GADLLVLPEMFLTGY--NIGVDAVSVLAEVYNGESAQQVARIAKAAGIAILYGYPERTED 88
           GA+L+VLPE+  TGY  +   +A S+   V +G +    + +A A G+ I+ G  E+  D
Sbjct: 40  GAELVVLPELANTGYVFDSRAEAESLAEPVPDGSTTAAWSEVASALGVYIVAGIAEKA-D 98

Query: 89  GQIYNAVQLIDSDGERVCNYRKTHLFGDLDHSMFSAGSDEFPIVELNGWKLGFLICYDLE 148
           G +YN+  L+  DG  + +YRKTHL+GD +  +F++G    PI +    ++   ICYDL 
Sbjct: 99  GALYNSAVLLGPDGY-LGSYRKTHLWGD-EKKLFASGDRPSPIYDTPLGRIAIAICYDLW 156

Query: 149 FPENARRLALAGAELILVPTANMIPF-------DFVADVTVRARAFENQCYVAYANYCGH 201
           FPE  R  AL GA+++ VPT N +P          +A+    A A  N   VA A+  G 
Sbjct: 157 FPELFRLYALGGAQIVCVPT-NWVPMPNQSADRPAMANTLAMAAAHTNGLVVACADRVGV 215

Query: 202 EGDIHYCGQSSIAAPDG---SRIAQAGLDESLIVG-ELDRQLMVDSRAANRYLLDRRPEL 257
           E    + GQS +    G     +A   L+E +     LD +  V +   N  L DRR ++
Sbjct: 216 ERGQPFEGQSLVVDQSGWPVGDVASRSLEEIVSASITLDARTSVGTH--NDVLADRRADI 273

Query: 258 YGEL 261
           YG +
Sbjct: 274 YGRI 277


Lambda     K      H
   0.321    0.139    0.411 

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: 198
Number of extensions: 13
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: 264
Length of database: 283
Length adjustment: 25
Effective length of query: 239
Effective length of database: 258
Effective search space:    61662
Effective search space used:    61662
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.

Links

Downloads

Related tools

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