GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Neiella marina J221

Align Polyphosphate glucokinase; Poly(P) glucokinase; ATP-dependent glucokinase; Polyphosphate--glucose phosphotransferase; EC 2.7.1.63; EC 2.7.1.2 (characterized)
to candidate WP_087506863.1 CBE68_RS14725 ROK family protein

Query= SwissProt::A5U654
         (265 letters)



>NCBI__GCF_002165625.1:WP_087506863.1
          Length = 256

 Score =  227 bits (578), Expect = 2e-64
 Identities = 110/237 (46%), Positives = 158/237 (66%), Gaps = 2/237 (0%)

Query: 22  GIDVGGSGIKGGIVDLDTGQLIGDRIKLLTPQPATPLAVAKTIAEVVNGFGWRGPLGVTY 81
           GID+GGSGIKG +VD+ TG+LI +R+++ TPQPATP AVA T+AE+ +   W G +G  +
Sbjct: 5   GIDIGGSGIKGAVVDVTTGELISERLRIPTPQPATPEAVAATVAEICDQLHWHGLVGCGF 64

Query: 82  PGVVTHGVVRTAANVDKSWIGTNARDTIGAELGGQQVTILNDADAAGLAETRYGAGKNNP 141
           P  + HG+ RTAANVD SW+G N +  I  +       + NDAD AGLAE ++GAGK   
Sbjct: 65  PAAIQHGIARTAANVDDSWLGANVQ-KIFCDATHLPCYVGNDADVAGLAEMQFGAGKELD 123

Query: 142 GLVVLLTFGTGIGSAVIHNGTLIPNTEFGHL-EVGGKEAEERAASSVKEKNDWTYPKWAK 200
           GLV ++T GTG+G+A+ +NG L+ NTE GHL +  G+E E RA+ + +++++  +  W K
Sbjct: 124 GLVFMVTIGTGLGTALFNNGELVANTELGHLFDSKGREWEHRASDAARKRDELDWKYWGK 183

Query: 201 QVIRVLIAIENAIWPDLFIAGGGISRKADKWVPLLENRTPVVPAALQNTAGIVGAAM 257
           +  + L+ +E   WPD FI GGG S+K DK+   ++    V PA   N AGI+GAA+
Sbjct: 184 RFNKYLVTLEQLFWPDAFILGGGASKKFDKFADAIDVAATVTPAESLNQAGIIGAAI 240


Lambda     K      H
   0.314    0.134    0.402 

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: 217
Number of extensions: 11
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: 265
Length of database: 256
Length adjustment: 24
Effective length of query: 241
Effective length of database: 232
Effective search space:    55912
Effective search space used:    55912
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: 42 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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