GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcE in Pseudomonas fluorescens FW300-N2E2

Align D-lactate oxidase and glycolate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate Pf6N2E2_136 Glycolate dehydrogenase (EC 1.1.99.14), FAD-binding subunit GlcE

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_136
          Length = 352

 Score =  505 bits (1301), Expect = e-148
 Identities = 251/347 (72%), Positives = 285/347 (82%), Gaps = 2/347 (0%)

Query: 7   DASAQLLDQVNQALAANTPLRIQGSGSKSFLGLQADGVLLDTREHRGIVSYDPTELVVTV 66
           DAS  LL+QVN+A A  TPLRIQGS SK+FLG +  G +LDTR HRGIV YDPTELV+T 
Sbjct: 8   DASDLLLEQVNRARANATPLRIQGSNSKAFLGREVAGEVLDTRVHRGIVHYDPTELVITA 67

Query: 67  RAGTPLTELETALDEAGQMLPCEPPHFGEGATVGGMIAAGLSGPRRPWSGSVRDFVLGSR 126
           RAGTPL EL  ALD AGQ LPCEPP FG+ ATVGGM+AAGLSGPRRPW+GSVRDFVLG+R
Sbjct: 68  RAGTPLLELLAALDAAGQRLPCEPPAFGDDATVGGMVAAGLSGPRRPWAGSVRDFVLGTR 127

Query: 127 VITGQGKHLRFGGEVMKNVAGYDLSRLMAGSFGCLGVLTEVSLKVLPKPRLCTSLRLEID 186
           +I+G G  LRFGGEVMKNVAGYDLSRL+AGSFGCLGV+TEVSLKVLPKPR   S+RLE+D
Sbjct: 128 LISGHGTLLRFGGEVMKNVAGYDLSRLLAGSFGCLGVITEVSLKVLPKPRHSLSIRLELD 187

Query: 187 LERALLKLAEWGQQPIPISAASHDGQALHLRLEGGEGSVGAARERIGGEDLDPGYWNDLR 246
              AL KLAEWG+QP+PISAASHDG  LHLRLEGGEGSV AA +R GGE +D  YW  L 
Sbjct: 188 STEALGKLAEWGRQPLPISAASHDGDCLHLRLEGGEGSVSAAHQRFGGEVIDDQYWTALN 247

Query: 247 EQRLAFFADPRPLWRLSLPNNTPALGLPGDQLVDWAGAQRWLKSDADAVTIRGIAIEVGG 306
           E +LAFF +  PLWRLSLPN+T  L LPG QL+DWAGAQRW+K++AD  T++ +A EVGG
Sbjct: 248 EHQLAFFDEGLPLWRLSLPNHTGPLTLPGAQLIDWAGAQRWVKTEAD--TVQALAHEVGG 305

Query: 307 HATCFTAGATTNPFQPLAAPLLRYHRQLKAALDPQGIFNPGRMYSEV 353
           HATC+  GA+  PFQPLA  LLRYHRQLKA LDP G+FNPGRMY E+
Sbjct: 306 HATCYRQGASDTPFQPLAPALLRYHRQLKAQLDPLGLFNPGRMYPEL 352


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: 505
Number of extensions: 15
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