GapMind for catabolism of small carbon sources

 

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

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate AO353_23650 AO353_23650 3-carboxymuconate cyclase

Query= uniprot:Q9HWH7
         (388 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_23650
          Length = 391

 Score =  395 bits (1015), Expect = e-114
 Identities = 214/389 (55%), Positives = 277/389 (71%), Gaps = 9/389 (2%)

Query: 1   MRRLPTLCLLALAPLTGVAPQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSVKG-PL 59
           MR+L  L +       G++  + +A  + LLVGTYT+G S+GI   +FD   G +   PL
Sbjct: 3   MRKLWPLLMAGSVGAMGLS--SASAESFQLLVGTYTQGQSQGIYRLKFDSQSGQLDATPL 60

Query: 60  RVAHTSNPSYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLA 119
           +V  ++NPS+LT + DQR LFVVNENG G + D VGR +S+  +P +  L  I+QVQ+L 
Sbjct: 61  QVVKSANPSWLTLSSDQRRLFVVNENGPG-QADPVGRVSSFAVEPNTHALSLINQVQSLG 119

Query: 120 DHPTYSSLSHDGRYLFVANYSV--QPEGSVAVLPVRADGSLAPVVQVESHQASKVHP-RQ 176
           + PT+SSLS DG+YLFV+NYSV   P G++A LPV  DG LAP VQ+ SHQ S+V+P RQ
Sbjct: 120 NEPTHSSLSADGKYLFVSNYSVAEDPGGNLAALPVSTDGKLAPPVQLSSHQPSRVNPERQ 179

Query: 177 VSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYAPE-QAERPLQAADPAFVPTPPGSGPRH 235
           +S HVHS VSSPDGQY+FA DLGADKVFVYRY P+   ERPL AA PA V  PPGSGPRH
Sbjct: 180 MSAHVHSTVSSPDGQYVFANDLGADKVFVYRYDPKANPERPLTAATPASVQLPPGSGPRH 239

Query: 236 LIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGR 295
           L+FSADG+ AYLTLE+S QV VF ++  G+L Q Q  DLA      +  A ALH S+DG+
Sbjct: 240 LLFSADGKHAYLTLEMSAQVAVFDYQA-GKLTQRQMVDLAAGKPAAQKAAAALHASSDGK 298

Query: 296 FLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQL 355
           FL V NRG  N+L+ FA+DPASG+L+ ++RR VEG  PREF+  P G+FVLVANQ S+Q+
Sbjct: 299 FLYVSNRGTTNELLVFAIDPASGELKELQRRPVEGDHPREFSLDPSGKFVLVANQKSNQI 358

Query: 356 RVFARDPQSGQVGKTLQSVEVGSPSDLRF 384
            + ARD ++G +GKT+Q +   SPSD++F
Sbjct: 359 VIIARDVKTGLLGKTVQKLPFDSPSDIKF 387


Lambda     K      H
   0.318    0.135    0.395 

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: 569
Number of extensions: 38
Number of successful extensions: 15
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: 388
Length of database: 391
Length adjustment: 30
Effective length of query: 358
Effective length of database: 361
Effective search space:   129238
Effective search space used:   129238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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