GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Pseudomonas simiae WCS417

Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate GFF3393 PS417_17365 gluconolactonase

Query= BRENDA::Q15493
         (299 letters)



>FitnessBrowser__WCS417:GFF3393
          Length = 291

 Score =  139 bits (349), Expect = 1e-37
 Identities = 94/291 (32%), Positives = 139/291 (47%), Gaps = 15/291 (5%)

Query: 7   ECVLPENCRCGESPVWEEVSNSLLFVDIPAKKVCRWDSFTKQVQRVTMDAPVSSVALRQS 66
           E ++      GE PVW    N+L +VDIP   + RW + T  V   T    ++ +A   +
Sbjct: 4   ELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDA 63

Query: 67  GGYVATIGTKFCAL---NWKEQSAVVLATVDNDKKNNRFNDGKVDPAGRYFAGTMAEETA 123
           G +VA + T F  L   N       +LA V++ +++ R NDG+ D  GR++AG+M     
Sbjct: 64  GNWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNMG 123

Query: 124 PAVLERHQGALYSLFPDHHVKKYFDQVDISNGLDWSLDHKIFYYIDS--LSYSVDAFDYD 181
              L   +G LY            D     NGL +S D +  Y  DS  L   + AFDYD
Sbjct: 124 ---LNAAEGTLYRYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYD 180

Query: 182 LQTGQISNRRSVYKLEKEEQIPDGMCIDAEGKLWVACYNGGRVIRLDPVTGKRLQTVKLP 241
           + TG  SNRR    + K    PDG  +DA+G  W+   + G + R  P  G+  +++ +P
Sbjct: 181 IDTGTPSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSP-DGRLDRSLTVP 239

Query: 242 VDKTTSCCFGGKNYSEMYVTCARDGMDPEGLLRQPEAGGIFKITGLGVKGI 292
           V K T C FGG     ++VT  RD    + L     +GG+F +   GV G+
Sbjct: 240 VKKPTMCAFGGSRLDTLFVTSIRDDQSEQSL-----SGGVFALNP-GVVGL 284


Lambda     K      H
   0.319    0.136    0.421 

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: 260
Number of extensions: 17
Number of successful extensions: 4
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: 299
Length of database: 291
Length adjustment: 26
Effective length of query: 273
Effective length of database: 265
Effective search space:    72345
Effective search space used:    72345
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: 48 (23.1 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