GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Burkholderia phytofirmans PsJN

Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate BPHYT_RS24170 BPHYT_RS24170 gluconolactonase

Query= BRENDA::Q64374
         (299 letters)



>FitnessBrowser__BFirm:BPHYT_RS24170
          Length = 309

 Score =  133 bits (334), Expect = 6e-36
 Identities = 97/308 (31%), Positives = 150/308 (48%), Gaps = 24/308 (7%)

Query: 5   KVECVLRENYRCGESPVWEEASQSLLFVDIPSKIICRWDTVSNQVQRVAVDAPVSSVALR 64
           +VE   +     GESPVW  A Q+L +VDIP++ I R    S +     +   V+ +A  
Sbjct: 11  RVEAAGQAPAAVGESPVWRAAEQALYWVDIPAQKIVRLRIDSGERSEWLLPEKVACIAFD 70

Query: 65  QLGGYVATIGTKFCALNW-----ENQSVFV----LAMVDEDKKNNRFNDGKVDPAGRYFA 115
             G  +A   T   AL         ++V V    LA  D    + RFNDG+ D  GR++A
Sbjct: 71  HRGTVLAGCETGLFALTLTESAANGEAVQVTGRKLAAPDFACDDMRFNDGRCDRQGRFWA 130

Query: 116 GTMAEETAPAVLERHQGSLYSLFPDHSVKK--YFDQVDISNGLDWSLDHKIFYYIDS--L 171
           GTM ++ A A   +  G+LY  F +  +      +++   NGL WS D    Y  DS  L
Sbjct: 131 GTMVQDMAAA---KPAGALYR-FDERGMLSAPVVEELITQNGLAWSPDGATMYLSDSHPL 186

Query: 172 SYTVDAFDYDLQTGQISNRRIVYKMEKDEQIPDGMCIDAEGKLWVACYNGGRVIRLDPET 231
              + AFDYD+++G+  NRR+   + +    PDG  +DA+G  W+   + G ++R  PE 
Sbjct: 187 RRQIWAFDYDIESGEPRNRRVFADLNQHAGRPDGAAVDADGCYWICANDAGLLLRFTPE- 245

Query: 232 GKRLQTVKLPVDKTTSCCFGGKDYSEMYVTCARDGLNAEGLLRQPDAGNIFKITGLGVKG 291
           GK  + + +P  K   C FGG++   ++VT  R   NA         G++F +   G+ G
Sbjct: 246 GKLDRQIAVPAIKPAMCAFGGRELDTLFVTSIRPAANA-----SEHDGHLFAVRP-GITG 299

Query: 292 IAPYSYAG 299
           +    +AG
Sbjct: 300 LPEPEFAG 307


Lambda     K      H
   0.319    0.137    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: 270
Number of extensions: 17
Number of successful extensions: 5
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: 309
Length adjustment: 27
Effective length of query: 272
Effective length of database: 282
Effective search space:    76704
Effective search space used:    76704
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 (21.8 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