Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_012385834.1 BIND_RS14705 glucokinase
Query= curated2:B9JYQ5 (340 letters) >NCBI__GCF_000019845.1:WP_012385834.1 Length = 334 Score = 195 bits (495), Expect = 2e-54 Identities = 122/333 (36%), Positives = 171/333 (51%), Gaps = 4/333 (1%) Query: 9 HMPFPVLVGDIGGTNARFWILMDAHAAPKEFANIHTADFPTIDQAIQDCILDKSGFQPRS 68 H PFP L+ DIGGTN RF I+ + T F + A+ L+ QPRS Sbjct: 2 HFPFPHLLADIGGTNVRFAIVDRPGGELRTGFAGKTGAFFNFEAALA-VALEDFAVQPRS 60 Query: 69 AILAVAGPIKDDEIPLTNCPWVIRPKAMIADLGFDDVLVVNDFEAQALAAASLGRNDREP 128 I AGP+++ + +TN W I A+ G + L++NDFEAQA + A L + P Sbjct: 61 LIACAAGPVQNRCVQMTNAHWRIDGAAVAPLFGLEQGLLLNDFEAQAYSLAVLRPDLIHP 120 Query: 129 IGPLTETSLNSRVILGPGTGLGVGGLLYTHHTWFPVPGEGGHVDIGPRSDRDWQIFPHIE 188 IG E ++VILGPGTGLGV L+ ++ + E GHVD GP SD + ++P+I+ Sbjct: 121 IGAQGEKLAGAQVILGPGTGLGVAALVMVKDAYYALVSEAGHVDFGPASDEEAALWPYID 180 Query: 189 RIE-GRISGEQILCGRGILHLYNA--ICAADGIEPVWTDPADVTQHALKGNDPVCVETMT 245 R GRIS E +L G G+L L+ A E D + + A K T+ Sbjct: 181 REPLGRISAESLLSGPGLLRLHRARLTMVKHPPEKAIQDVGVLIEQAHKNEVGEEAATVR 240 Query: 246 LFVTYLGRIAGDMALVFMARGGVFLSGGISQKIIPLLKSPVFRAAFEDKAPHTEMMKTIP 305 LF++ L R + DMA+ F++RGGV +GGI ++I L FR FE+K PH + IP Sbjct: 241 LFLSLLARFSSDMAVTFVSRGGVTFAGGILPRLIDFLDVATFRTHFENKPPHKAWVSQIP 300 Query: 306 TFVAIHPQAALSGLAAYARTPSSYGVKHEGRRW 338 T + + A GLAA P Y + + R W Sbjct: 301 TRLIMDEAALFQGLAAIGAKPELYLINYAKRAW 333 Lambda K H 0.322 0.140 0.445 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: 316 Number of extensions: 19 Number of successful extensions: 4 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: 340 Length of database: 334 Length adjustment: 28 Effective length of query: 312 Effective length of database: 306 Effective search space: 95472 Effective search space used: 95472 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: 49 (23.5 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