GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagB in Caulobacter crescentus NA1000

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate CCNA_00453 CCNA_00453 glucosamine-6-phosphate deaminase

Query= reanno::Caulo:CCNA_00453
         (363 letters)



>lcl|FitnessBrowser__Caulo:CCNA_00453 CCNA_00453
           glucosamine-6-phosphate deaminase
          Length = 363

 Score =  697 bits (1800), Expect = 0.0
 Identities = 363/363 (100%), Positives = 363/363 (100%)

Query: 1   MEATVLTRHETPAPTGASPPSLAPASTHMFREAGEAARVAAVQLTANAPKIQALAQRLRA 60
           MEATVLTRHETPAPTGASPPSLAPASTHMFREAGEAARVAAVQLTANAPKIQALAQRLRA
Sbjct: 1   MEATVLTRHETPAPTGASPPSLAPASTHMFREAGEAARVAAVQLTANAPKIQALAQRLRA 60

Query: 61  NPPRVVVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQ 120
           NPPRVVVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQ
Sbjct: 61  NPPRVVVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQ 120

Query: 121 SGKSPDLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAAL 180
           SGKSPDLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAAL
Sbjct: 121 SGKSPDLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAAL 180

Query: 181 VAVTQLIAAWTEDAELTAALQDLPTALAAAWTLDWSLAVERLKTASNLYVLGRGVGFGVA 240
           VAVTQLIAAWTEDAELTAALQDLPTALAAAWTLDWSLAVERLKTASNLYVLGRGVGFGVA
Sbjct: 181 VAVTQLIAAWTEDAELTAALQDLPTALAAAWTLDWSLAVERLKTASNLYVLGRGVGFGVA 240

Query: 241 LEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEMAAGLRAR 300
           LEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEMAAGLRAR
Sbjct: 241 LEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEMAAGLRAR 300

Query: 301 GASVLIAGGGGDAPDALPTLASHPVLEPILMIQSFYRMANALSVARGYDPDSPPHLNKVT 360
           GASVLIAGGGGDAPDALPTLASHPVLEPILMIQSFYRMANALSVARGYDPDSPPHLNKVT
Sbjct: 301 GASVLIAGGGGDAPDALPTLASHPVLEPILMIQSFYRMANALSVARGYDPDSPPHLNKVT 360

Query: 361 ETI 363
           ETI
Sbjct: 361 ETI 363


Lambda     K      H
   0.315    0.128    0.360 

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: 591
Number of extensions: 6
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: 363
Length of database: 363
Length adjustment: 29
Effective length of query: 334
Effective length of database: 334
Effective search space:   111556
Effective search space used:   111556
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 (21.6 bits)
S2: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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