GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SB2B:6937023 Sama_1197 putative ROK-family
           protein (RefSeq)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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