GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Synechococcus elongatus PCC 7942

Align Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized)
to candidate Synpcc7942_2111 Synpcc7942_2111 xylose repressor

Query= SwissProt::Q9X1I0
         (317 letters)



>FitnessBrowser__SynE:Synpcc7942_2111
          Length = 302

 Score =  181 bits (460), Expect = 1e-50
 Identities = 107/310 (34%), Positives = 159/310 (51%), Gaps = 20/310 (6%)

Query: 6   LIGVDLGGTTFSVGLVSEDGKILKKVTRDTLVENGKEDVIRRIAETILEVSDGEEAPYVG 65
           +IGVDLGGT   +G  + +G+  +++T  T   +   +V   + E I ++    EA  +G
Sbjct: 7   VIGVDLGGTAMKLGRYTIEGQCQQELTVPTPTPSTPSNVRAALVEAIRQLDPQAEALAIG 66

Query: 66  IGSPGSIDRENGIVRFSPNFPDWHNVPLTDELAKRTGKKVFLENDANAFVLGEKWFGAGR 125
           IG+PG  D    + R + N   W  VPL D L     + V L NDAN   LGE W G GR
Sbjct: 67  IGTPGPADAAGRVARVAINLDGWTEVPLADWLEADLQRPVILANDANCAGLGEVWLGGGR 126

Query: 126 GHDHIVALTLGTGIGGGVVTHGYLLTGRDGIGAELGHVVVEPNGPMCNCGTRGCLEAVAS 185
           G+   + LTLGTG+GG +V +G L  GR G  AELG + ++P GP CN G +G LE  AS
Sbjct: 127 GYRDAILLTLGTGVGGAIVLNGELFVGRTGTAAELGLITLDPAGPHCNSGNQGSLEQYAS 186

Query: 186 ATAIRRFLREGYKKYHSSLVYKLAGSPEKADAKHLFDAARQGDRFALMIRDRVVDALARA 245
             A++R  R G                   D K L D A QGD  A+         LA  
Sbjct: 187 IGAVQR--RFG------------------CDPKDLGDRASQGDPEAIAAWQDYGRTLAAG 226

Query: 246 VAGYIHIFNPEIVIIGGGISRAGEILFGPLREKVVDYIMPSFVGTYEVVASPLVEDAGIL 305
           +A  +++  PE++I+GGGIS +       L E++   ++P+     ++  + L  +AG +
Sbjct: 227 LASLVYVLTPEVIILGGGISGSAAFFLPALTEELHRRVLPTSREDLQIAIAALGNEAGRV 286

Query: 306 GAASIIKERI 315
           GAA +  +++
Sbjct: 287 GAAKLAWDKL 296


Lambda     K      H
   0.320    0.142    0.418 

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: 213
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: 317
Length of database: 302
Length adjustment: 27
Effective length of query: 290
Effective length of database: 275
Effective search space:    79750
Effective search space used:    79750
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 (21.7 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