GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Pontimonas salivibrio CL-TW6

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_104913435.1 C3B54_RS04510 ROK family protein

Query= SwissProt::A5U654
         (265 letters)



>NCBI__GCF_002950575.1:WP_104913435.1
          Length = 254

 Score =  209 bits (533), Expect = 4e-59
 Identities = 106/242 (43%), Positives = 156/242 (64%), Gaps = 4/242 (1%)

Query: 18  RHGFGIDVGGSGIKGGIVDLDTGQLIGDRIKLLTPQPATPLAVAKTIAEVVNGFGWRG-- 75
           +H  GIDVGG+GIKG +VD   G+L+ +RIK  TP+  TP  + + IA++V+  G     
Sbjct: 4   QHAVGIDVGGTGIKGALVDTQAGELLSERIKYPTPEGGTPGDIFEVIAQIVDDCGPDAAG 63

Query: 76  -PLGVTYPGVVTHGVVRTAANVDKSWIGTNARDTIGAELGGQQVTILNDADAAGLAETRY 134
            PLGV  P VV +G   TAAN+   W+G +A + +   LG + +  LNDAD+AG+AE  Y
Sbjct: 64  LPLGVCVPSVVKNGRTLTAANISTEWVGLDAEEALEDRLG-RDIVFLNDADSAGVAEAHY 122

Query: 135 GAGKNNPGLVVLLTFGTGIGSAVIHNGTLIPNTEFGHLEVGGKEAEERAASSVKEKNDWT 194
           G      GL +L T GTGIGSA+I +G LIPNTE GHLE+ G+ AE R+++  +++   +
Sbjct: 123 GEAVGQEGLTILTTLGTGIGSALIQDGVLIPNTELGHLELDGEVAEHRSSAVARQRLGQS 182

Query: 195 YPKWAKQVIRVLIAIENAIWPDLFIAGGGISRKADKWVPLLENRTPVVPAALQNTAGIVG 254
           + +WA  + R  + +     PDLF+ GGG+S++AD+++ L+    P+  AAL+N AGI+G
Sbjct: 183 FEQWAAGLERYYLHLNRLFSPDLFLLGGGVSKEADQFLHLISLPVPIRTAALRNNAGILG 242

Query: 255 AA 256
           AA
Sbjct: 243 AA 244


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: 212
Number of extensions: 5
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: 254
Length adjustment: 24
Effective length of query: 241
Effective length of database: 230
Effective search space:    55430
Effective search space used:    55430
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