GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcE in Pseudomonas fluorescens FW300-N2E3

Align D-lactate oxidase and glycolate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate AO353_21305 AO353_21305 glycolate oxidase

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



>FitnessBrowser__pseudo3_N2E3:AO353_21305
          Length = 352

 Score =  514 bits (1325), Expect = e-150
 Identities = 251/346 (72%), Positives = 286/346 (82%), Gaps = 2/346 (0%)

Query: 7   DASAQLLDQVNQALAANTPLRIQGSGSKSFLGLQADGVLLDTREHRGIVSYDPTELVVTV 66
           DASA+LL+Q+NQA    TPLRIQG+ SK+FLG +  G +LDTR HRGIVSYDPTELV+T 
Sbjct: 8   DASAELLEQINQARENATPLRIQGASSKAFLGREVAGEVLDTRVHRGIVSYDPTELVITA 67

Query: 67  RAGTPLTELETALDEAGQMLPCEPPHFGEGATVGGMIAAGLSGPRRPWSGSVRDFVLGSR 126
           R GTPL EL  ALD AGQMLPCEPP FGE ATVGGMIAAGLSGPRRPW+GS RDFVLG+R
Sbjct: 68  RCGTPLRELLAALDAAGQMLPCEPPSFGEDATVGGMIAAGLSGPRRPWAGSARDFVLGTR 127

Query: 127 VITGQGKHLRFGGEVMKNVAGYDLSRLMAGSFGCLGVLTEVSLKVLPKPRLCTSLRLEID 186
           +ITG GK LRFGGEVMKNVAGYDLSRL+ GSFGCLGV+TEVSLKVLPKPR C S+ LE+D
Sbjct: 128 LITGNGKQLRFGGEVMKNVAGYDLSRLLTGSFGCLGVITEVSLKVLPKPRQCLSISLELD 187

Query: 187 LERALLKLAEWGQQPIPISAASHDGQALHLRLEGGEGSVGAARERIGGEDLDPGYWNDLR 246
              AL KLAEWGQQP+PISAA HDG+ LHLRLEGGEGSV AA +R+GGE LD  +W  L 
Sbjct: 188 SAHALSKLAEWGQQPLPISAACHDGRQLHLRLEGGEGSVSAAHQRLGGEVLDAQFWEALN 247

Query: 247 EQRLAFFADPRPLWRLSLPNNTPALGLPGDQLVDWAGAQRWLKSDADAVTIRGIAIEVGG 306
           EQ+L FF +  PLWRLSLPNN   L LPG+QL+DWAGAQRWLKS+A    I+ +A ++GG
Sbjct: 248 EQQLTFFDEGLPLWRLSLPNNIGPLTLPGEQLIDWAGAQRWLKSEAP--NIQSLAADLGG 305

Query: 307 HATCFTAGATTNPFQPLAAPLLRYHRQLKAALDPQGIFNPGRMYSE 352
           HATC++ G +  PFQPLA  LLRYH+QLKA LDPQG+FNPGRMY+E
Sbjct: 306 HATCYSHGVSDTPFQPLAPALLRYHQQLKAQLDPQGLFNPGRMYAE 351


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: 483
Number of extensions: 17
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: 353
Length of database: 352
Length adjustment: 29
Effective length of query: 324
Effective length of database: 323
Effective search space:   104652
Effective search space used:   104652
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: 49 (23.5 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