Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate AZOBR_RS05405 AZOBR_RS05405 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__azobra:AZOBR_RS05405 Length = 311 Score = 259 bits (663), Expect = 5e-74 Identities = 138/305 (45%), Positives = 184/305 (60%), Gaps = 4/305 (1%) Query: 6 LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLE--EHKVEVKDGCIAI 63 LV D+G TNAR L D I ++ D+PSLEA YL H G AI Sbjct: 1 LVADIGATNARFGLIDGTG--IHGSRVLRCADFPSLEAAALAYLGGVAHDARPSRGAFAI 58 Query: 64 ACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAE 123 A P+TGD V MTN W+FS AE++ LG L +INDFTAV++++P L + Q G Sbjct: 59 AGPVTGDAVLMTNRGWSFSTAEVRGKLGLERLAVINDFTAVALSVPRLTAADVRQVGEGA 118 Query: 124 PVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGH 183 PV G+ + V G G+GLGV+ LV + W +L EGGHV AP S+ E+ +L LR H Sbjct: 119 PVPGRVVGVVGPGSGLGVSGLVPGAEGWTALAAEGGHVTMAPVSDRESAVLAQLRKSFEH 178 Query: 184 VSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGR 243 VSAERVLSGPGLVNLY+A+ D++ PE P +++ A A++ C A+ +FC ++G Sbjct: 179 VSAERVLSGPGLVNLYQALCVLDHQEPEPFTPAQVSDAATANTNPHCVEAVEMFCAMLGT 238 Query: 244 FGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDN 303 GNLAL LG GG++IAGGIVP+ F S FR F +KGR ++++ IP Y+I H+ Sbjct: 239 VAGNLALTLGARGGIYIAGGIVPKLGTLFTHSRFRKRFMEKGRMRDFLAPIPTYVITHEL 298 Query: 304 PGLLG 308 P LG Sbjct: 299 PAFLG 303 Lambda K H 0.322 0.141 0.426 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: 317 Number of extensions: 17 Number of successful extensions: 3 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: 321 Length of database: 311 Length adjustment: 27 Effective length of query: 294 Effective length of database: 284 Effective search space: 83496 Effective search space used: 83496 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 (21.9 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