GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Caulobacter crescentus NA1000

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate CCNA_02549 CCNA_02549 glucokinase

Query= reanno::SB2B:6938110
         (299 letters)



>FitnessBrowser__Caulo:CCNA_02549
          Length = 296

 Score =  312 bits (799), Expect = 7e-90
 Identities = 159/297 (53%), Positives = 197/297 (66%), Gaps = 6/297 (2%)

Query: 1   MMRMGVDLGGTKIELVALGEDGSELFRKRIATPREYQGTLNAVVTLVNEAEATLGTQ-GS 59
           M+R GVD GGTKIE+ AL   G  + R R   P  Y   L  V  LV +AE+  G     
Sbjct: 1   MIRFGVDFGGTKIEVAALNAAGDFVARVRKPNPGNYDEALEVVAALVADAESMAGGSCAR 60

Query: 60  LGIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAA 119
           LG+GIPG ISP TGL++NANST++NG P   +L   L R VR+ANDANC A+SEA DGA 
Sbjct: 61  LGLGIPGSISPRTGLIRNANSTYLNGRPFGENLETRLARPVRIANDANCLALSEAADGAG 120

Query: 120 AGKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLPWMRPDEFNTTECFCGNKD 179
           AG  VVF AI+GTGCG G+  DG++  G NGIGGEWGH PLPW +P+E+   +C+CG K 
Sbjct: 121 AGASVVFAAIVGTGCGGGVVVDGKIINGHNGIGGEWGHAPLPWPKPEEYPGPDCWCGRKG 180

Query: 180 CIETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHVINM 239
           C+ET+++G  F RD     G A NG   M  +  GD  A+   DRY+DRLARSLA V ++
Sbjct: 181 CLETWIAGPAFARD----AGFA-NGQAAMQAIGEGDVKASAALDRYVDRLARSLAVVCDL 235

Query: 240 LDPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNLYGCSSGVRGAAWLW 296
           +DPD IVLGGGMSNV A+Y RLPA +  +V      TPV + ++G SSGVRGA WLW
Sbjct: 236 IDPDIIVLGGGMSNVDALYERLPAAIAPHVFSDIFETPVRKAVHGDSSGVRGAVWLW 292


Lambda     K      H
   0.320    0.139    0.429 

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: 323
Number of extensions: 18
Number of successful extensions: 3
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: 296
Length adjustment: 26
Effective length of query: 273
Effective length of database: 270
Effective search space:    73710
Effective search space used:    73710
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