Alignments for a candidate for nagB in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments 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_00569 CCNA_00569 glucosamine-6-phosphate deaminase

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



>FitnessBrowser__Caulo:CCNA_00569
          Length = 358

 Score =  560 bits (1443), Expect = e-164
 Identities = 297/363 (81%), Positives = 314/363 (86%), Gaps = 5/363 (1%)

Query: 1   MEATVLTRHETPAPTGASPPSLAPASTHMFREAGEAARVAAVQLTANAPKIQALAQRLRA 60
           MEATVLTR     P GA+P  L+P  T MF EAGE A V    L ANA ++ ALA+RLRA
Sbjct: 1   MEATVLTR-----PEGAAPARLSPEDTRMFLEAGEGAAVVRTLLAANAERVAALAERLRA 55

Query: 61  NPPRVVVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQ 120
           +PPRVVVTCARGSSDHAATFARYLIETKAGVLTSSAG SVSSVYDASPNLEGAL LA+SQ
Sbjct: 56  HPPRVVVTCARGSSDHAATFARYLIETKAGVLTSSAGLSVSSVYDASPNLEGALCLAVSQ 115

Query: 121 SGKSPDLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAAL 180
           SGKSPDLLA+VKAAKAAGAHAVA VNV DSPLAALAD VIPLHAGPELSVAATKSYIAAL
Sbjct: 116 SGKSPDLLASVKAAKAAGAHAVAFVNVEDSPLAALADVVIPLHAGPELSVAATKSYIAAL 175

Query: 181 VAVTQLIAAWTEDAELTAALQDLPTALAAAWTLDWSLAVERLKTASNLYVLGRGVGFGVA 240
            A+TQLIAAWT+D  LTAAL+ LP  L AAW LDWS AVE L+ A NLYVLGRGVGFGVA
Sbjct: 176 AAITQLIAAWTQDEALTAALEGLPLQLEAAWNLDWSSAVEGLRHAINLYVLGRGVGFGVA 235

Query: 241 LEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEMAAGLRAR 300
           LEAALKFKETCGLHAEAFSAAEVLHGPMALVK+GFPALVFAQNDESR SV EMA GLR R
Sbjct: 236 LEAALKFKETCGLHAEAFSAAEVLHGPMALVKEGFPALVFAQNDESRESVVEMAQGLRQR 295

Query: 301 GASVLIAGGGGDAPDALPTLASHPVLEPILMIQSFYRMANALSVARGYDPDSPPHLNKVT 360
           GASVL+A  G DAP  LPT  SHPVLEPILM+QSFYRMANALSVARGY+PDSPPHLNKVT
Sbjct: 296 GASVLMAAPGDDAPGGLPTPLSHPVLEPILMVQSFYRMANALSVARGYNPDSPPHLNKVT 355

Query: 361 ETI 363
           ET+
Sbjct: 356 ETL 358


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: 502
Number of extensions: 10
Number of successful extensions: 2
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: 358
Length adjustment: 29
Effective length of query: 334
Effective length of database: 329
Effective search space:   109886
Effective search space used:   109886
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 (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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources