GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Shewanella amazonensis SB2B

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate 6937023 Sama_1197 putative ROK-family protein (RefSeq)

Query= reanno::SB2B:6937235
         (310 letters)



>FitnessBrowser__SB2B:6937023
          Length = 335

 Score =  171 bits (432), Expect = 3e-47
 Identities = 113/306 (36%), Positives = 161/306 (52%), Gaps = 17/306 (5%)

Query: 5   GIDLGGTKIELVTLNEKGEEVFRKRVPTP-KDYRATLEAVAGLVHDSEKETGQVS----- 58
           G+D+GGTKI L   ++    V R ++PTP  DY   L+ V   +  +++   Q S     
Sbjct: 4   GLDIGGTKIALALFDDSMACVERWQIPTPVADYGQFLDEVCAQIERADELAQQHSGVTVQ 63

Query: 59  -------SVGIGIPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAV 111
                  SVGI +PGV+ +  G V +SN   LNG+ + ++L   LGR V + ND  CFA+
Sbjct: 64  PAEVSKGSVGIALPGVILS-DGTVLSSNVPCLNGRTVAQELTVRLGRPVALGNDCRCFAL 122

Query: 112 SESVDGGGAGKTLVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLP--WMTADEFN 169
           SE + G G G   V G ILGTG G G+ I+ K+  G + + GE+GH  LP   +   +  
Sbjct: 123 SEVLLGAGVGFERVLGVILGTGLGGGVCISQKLILGAHCLAGEFGHIGLPASVIIKHQLP 182

Query: 170 STRCFCGNADCIETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRL 229
              C CG   C ET+VSGTG  R ++  GG A + + + A    G+  A + F  ++D L
Sbjct: 183 LFECGCGLTGCAETYVSGTGLGRLYQHFGGTADTYVWL-ADYRSGKAEAISTFDAYMDAL 241

Query: 230 ARALAHVINLLDPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGV 289
              LA  I  LDPD +V GGG+S + EI   LP    +++       +      GA+SGV
Sbjct: 242 GSVLAGQILSLDPDCLVFGGGISEVKEIIAALPDATARHLFASAKLPEFRVAEFGAASGV 301

Query: 290 RGAAWL 295
           RGAA L
Sbjct: 302 RGAALL 307


Lambda     K      H
   0.318    0.138    0.424 

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: 348
Number of extensions: 20
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 310
Length of database: 335
Length adjustment: 28
Effective length of query: 282
Effective length of database: 307
Effective search space:    86574
Effective search space used:    86574
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: 41 (21.6 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