GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcE in Burkholderia phytofirmans PsJN

Align D-lactate oxidase and glycolate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate BPHYT_RS03515 BPHYT_RS03515 D-lactate dehydrogenase

Query= reanno::psRCH2:GFF3771
         (353 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS03515 BPHYT_RS03515 D-lactate
           dehydrogenase
          Length = 471

 Score = 94.4 bits (233), Expect = 6e-24
 Identities = 56/156 (35%), Positives = 86/156 (55%), Gaps = 7/156 (4%)

Query: 23  NTPLRIQGSGSK---SFLGLQADGVLLDTREHRGIVSYDPTELVVTVRAGTPLTELETAL 79
           N P+   G+GS      L +Q  GV +D  E   ++S +  +L VTV  G    +L  AL
Sbjct: 75  NVPIIPYGNGSSLEGHLLAVQG-GVSIDLSEMNRVLSINAEDLTVTVEPGISRKQLNEAL 133

Query: 80  DEAGQMLPCEPPHFGEGATVGGMIAAGLSGPRRPWSGSVRDFVLGSRVITGQGKHLRFGG 139
            + G   P +P   G  A++GGM A   SG      G++R+ VLG  V+   G+ ++ G 
Sbjct: 134 RDTGLFFPIDP---GADASIGGMSATRASGTNAVRYGTMRENVLGLTVVLADGRVIKTGT 190

Query: 140 EVMKNVAGYDLSRLMAGSFGCLGVLTEVSLKVLPKP 175
              K+ AGYDL+R+  GS G LGV+TE+++++ P+P
Sbjct: 191 RARKSSAGYDLTRMFVGSEGTLGVITEITVRLYPQP 226



 Score = 27.3 bits (59), Expect = 8e-04
 Identities = 9/20 (45%), Positives = 15/20 (75%)

Query: 332 RQLKAALDPQGIFNPGRMYS 351
           R +K ALDP  + NPG++++
Sbjct: 449 RSIKHALDPHNLMNPGKIFT 468


Lambda     K      H
   0.319    0.137    0.417 

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: 394
Number of extensions: 24
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: 2
Length of query: 353
Length of database: 471
Length adjustment: 31
Effective length of query: 322
Effective length of database: 440
Effective search space:   141680
Effective search space used:   141680
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 (21.7 bits)
S2: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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