Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_017548855.1 C792_RS0107525 ROK family glucokinase
Query= BRENDA::H6UH58 (328 letters) >NCBI__GCF_000330705.1:WP_017548855.1 Length = 319 Score = 321 bits (822), Expect = 2e-92 Identities = 163/319 (51%), Positives = 209/319 (65%), Gaps = 2/319 (0%) Query: 4 IILAADVGGTTCKLGIFTPELEQLHKWSIHTDTSDSTGYTLLKGIYDSFVEKVNENNYNF 63 +ILAAD+GGT+CKLG+F EL + KW I TD S+ G +L + DSF K + Sbjct: 3 VILAADIGGTSCKLGVFDEELNLIEKWEIPTDISEE-GSHILADVLDSFRSKEEILGFKV 61 Query: 64 SNVLGVGIGVPGPVDFEKGTVNGAVNLYWPEKVNVREIFEQFVDCPVYVDNDANIAALGE 123 LG G+G+PGPVDFEKG +NG +NL K ++ IF + VDNDAN+AALGE Sbjct: 62 EECLGTGLGMPGPVDFEKGILNGCINLNIKGKRSIATIFSELSGSAAIVDNDANVAALGE 121 Query: 124 KHKGAGEGADDVVAITLGTGLGGGIISNGEIVHGHNGSGAEIGHFRADFDQRFKCNCGRS 183 + KGAG G +VV ITLGTG+GGG+IS G ++HG GSG EIGH DFD RF+CNCG+ Sbjct: 122 QSKGAGHGHSEVVMITLGTGVGGGVISEGRLIHGTGGSGGEIGHITVDFDGRFQCNCGKK 181 Query: 184 GCIETVASATGVVNLVNFYYPKLTFRSSILELIKENKVTAKAVFDAAKAGDQFCIFITEK 243 GC+ETVASATG+VNL Y+ S ++ IKE +T+KA+ DAA GD F+ E+ Sbjct: 182 GCLETVASATGMVNLAG-YHSDDHENSVLIAAIKEGTLTSKAIVDAAMTGDPLAEFVVEE 240 Query: 244 VANYIGYLCSIISVTSNPKYIVLGGGMSTAGPILIENIKTEYHNLTFAPAQFETEIVQAK 303 A Y+ S ISV +NP Y V GGG+S AG L + IK Y +L F PA + EIV A+ Sbjct: 241 AARYLAVAMSSISVITNPGYFVFGGGVSRAGRYLTDKIKKYYDSLIFPPAADDVEIVMAE 300 Query: 304 LGNDAGITGAAGLIKTYVL 322 LGNDAG+ GAA L+K Y++ Sbjct: 301 LGNDAGMYGAARLVKQYLI 319 Lambda K H 0.318 0.138 0.409 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: 309 Number of extensions: 10 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: 328 Length of database: 319 Length adjustment: 28 Effective length of query: 300 Effective length of database: 291 Effective search space: 87300 Effective search space used: 87300 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 24 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