GapMind for catabolism of small carbon sources

 

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

Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate Pf6N2E2_3581 L-pipecolate oxidase (1.5.3.7)

Query= metacyc::G1G01-5614-MONOMER
         (432 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3581
          Length = 427

 Score =  588 bits (1517), Expect = e-173
 Identities = 281/425 (66%), Positives = 335/425 (78%)

Query: 8   LRQQCLWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIG 67
           LR++CLWE ++        L GE  ADVCVIG G TGLSAA+HLLEQGK V+VLEA + G
Sbjct: 3   LREECLWEKLTPQRPENSGLTGEVTADVCVIGAGFTGLSAAVHLLEQGKRVVVLEAHRAG 62

Query: 68  HGGSGRNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQH 127
           HGGSGRNVGLVNAG WI PDD+EA  G+  GS+LN++LG APA VF++I++  IDCQ + 
Sbjct: 63  HGGSGRNVGLVNAGLWIPPDDIEAGFGEAVGSQLNRMLGAAPALVFSLIDKYNIDCQLRR 122

Query: 128 KGTLHMAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTIN 187
           +GTLHMAHNA G ADL +R EQW+RRGA VELLTG  C +  GT KI+AALLDRRAGT+N
Sbjct: 123 EGTLHMAHNARGEADLRSREEQWKRRGAPVELLTGQACVDATGTSKIAAALLDRRAGTLN 182

Query: 188 PMGYTQGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGD 247
           PM YT GLA A T LGG++F  S V  LER+G  W V+TA+GAV AE+VVI++ AYTEGD
Sbjct: 183 PMAYTSGLAKAATDLGGQLFDHSPVTHLERQGQRWSVQTAQGAVLAEQVVIASNAYTEGD 242

Query: 248 WSNLQKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLG 307
           W+ L++ FF GYYYQVAS PL   AA ++LP GQGSWDTR VLSSIRRD  GRLLLGSLG
Sbjct: 243 WTELRRNFFPGYYYQVASVPLTDEAARRILPGGQGSWDTRQVLSSIRRDKDGRLLLGSLG 302

Query: 308 RVDNKPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTG 367
             + KP WF+++WADR+Q HY+P L  VEWE  WTGCI FTPDHLMRLFEPAPGLVAVTG
Sbjct: 303 NGNRKPTWFLKAWADRVQQHYFPYLKSVEWECTWTGCIAFTPDHLMRLFEPAPGLVAVTG 362

Query: 368 YNGRGNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLYHAGQC 427
           YNGRG TTGTV+G+AFA++L  G A +LPIPF+PM  ++   LR+  YE+GFSLYHAGQC
Sbjct: 363 YNGRGVTTGTVVGKAFADYLCHGNAQALPIPFAPMQPLAGVGLRSCLYEAGFSLYHAGQC 422

Query: 428 LRVVL 432
           LR+V+
Sbjct: 423 LRIVI 427


Lambda     K      H
   0.319    0.135    0.419 

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: 661
Number of extensions: 22
Number of successful extensions: 1
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: 432
Length of database: 427
Length adjustment: 32
Effective length of query: 400
Effective length of database: 395
Effective search space:   158000
Effective search space used:   158000
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: 51 (24.3 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