GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS03515
          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.

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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