GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Dechlorosoma suillum PS

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate Dsui_0801 Dsui_0801 transcriptional regulator/sugar kinase

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



>FitnessBrowser__PS:Dsui_0801
          Length = 296

 Score =  313 bits (803), Expect = 2e-90
 Identities = 157/296 (53%), Positives = 198/296 (66%), Gaps = 1/296 (0%)

Query: 2   MRMGVDLGGTKIELVALGEDGSELFRKRIATPR-EYQGTLNAVVTLVNEAEATLGTQGSL 60
           MR+G+DLGG+KIE++ALG+DG EL R+R+ TPR +Y  TL AV  LV EAEA L   GS+
Sbjct: 1   MRLGIDLGGSKIEIIALGDDGRELLRRRVPTPRGDYGATLQAVAGLVREAEAALQMTGSV 60

Query: 61  GIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAAA 120
           G+G+PG  S  +G ++NANST + G PL RDL ALL R VR+ANDANCFA+SEA+DGA  
Sbjct: 61  GVGMPGSESILSGHIRNANSTCLIGQPLGRDLEALLQRPVRLANDANCFALSEAMDGAGR 120

Query: 121 GKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLPWMRPDEFNTTECFCGNKDC 180
           G R VFG ILGTG G GL  DG+V  G NGI GEWGH PLP    D+     C+CG   C
Sbjct: 121 GARCVFGVILGTGVGGGLVIDGQVLRGANGIAGEWGHIPLPGAGADDLPLPPCYCGRHGC 180

Query: 181 IETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHVINML 240
           +ET++SG     D +  GG A   A I +    GD        RY  RLAR+LA V+N++
Sbjct: 181 VETYLSGPALAADHQRHGGEAMEAAAIATAAATGDARCEAALQRYEARLARALATVMNIV 240

Query: 241 DPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNLYGCSSGVRGAAWLW 296
           DPD IVLGGG+SN+Q +YA +P +   +V      T ++  ++G SSGVRGAAWLW
Sbjct: 241 DPDVIVLGGGLSNLQRLYANVPRLWAPHVFSDHIATRLLPPVHGDSSGVRGAAWLW 296


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: 291
Number of extensions: 11
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: 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