GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Paraburkholderia bryophila 376MFSha3.1

Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate H281DRAFT_05322 H281DRAFT_05322 gluconolactonase (EC 3.1.1.17)

Query= BRENDA::Q64374
         (299 letters)



>FitnessBrowser__Burk376:H281DRAFT_05322
          Length = 317

 Score =  128 bits (322), Expect = 1e-34
 Identities = 91/303 (30%), Positives = 140/303 (46%), Gaps = 30/303 (9%)

Query: 17  GESPVWEEASQSLLFVDIPSKIICRWDTVSNQVQRVAVDAPVSSVALRQLGGYVATIGTK 76
           GESPVW  A Q+L +VDIP++ I R    + +     +   V+ +A  + G  +A   T 
Sbjct: 23  GESPVWRVAEQALYWVDIPAQKIVRLVVETGKRSEWLLPEKVACIAFDRRGTVLAGCETA 82

Query: 77  FCALNWENQSVFVLAMVDEDKK-----------------NNRFNDGKVDPAGRYFAGTMA 119
             A+     S    A      +                 + RFNDG+ D  GR++AGTM 
Sbjct: 83  LFAVTLSGSSTDATAQAVRASEPVEVTGRKLAAPVFPFDDMRFNDGRCDRQGRFWAGTMV 142

Query: 120 EETAPAVLERHQGSLYSLFPDHSVKK-YFDQVDISNGLDWSLDHKIFYYIDS--LSYTVD 176
           ++ +   L    G+LY       +     D +   NGL WS D K  Y  DS  L   + 
Sbjct: 143 QDMS---LANPAGALYRFDAQGVLSAPVVDGLITQNGLGWSPDGKTMYLSDSHPLRRQIW 199

Query: 177 AFDYDLQTGQISNRRIVYKMEKDEQIPDGMCIDAEGKLWVACYNGGRVIRLDPETGKRLQ 236
           AFDY+++TG+ +NRR+   +      PDG  +DA+G  W+   + G ++R  P+ GK  +
Sbjct: 200 AFDYEVETGEPNNRRVFADLNHYVGRPDGAAVDADGCYWICANDAGALLRFTPQ-GKLDR 258

Query: 237 TVKLPVDKTTSCCFGGKDYSEMYVTCARDGLNAEGLLRQPDAGNIFKITGLGVKGIAPYS 296
            + +P  K   C FGG+D   ++VT  R G  A         G++F +   GV G+    
Sbjct: 259 QIAVPAIKPAMCAFGGRDLDTLFVTSIRPGAGA-----SEHDGHLFAVRP-GVSGLPEPE 312

Query: 297 YAG 299
           +AG
Sbjct: 313 FAG 315


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: 284
Number of extensions: 20
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: 317
Length adjustment: 27
Effective length of query: 272
Effective length of database: 290
Effective search space:    78880
Effective search space used:    78880
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