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.
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:
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