Align Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized)
to candidate WP_041456752.1 AVA_RS11460 ROK family protein
Query= SwissProt::Q9X1I0 (317 letters) >NCBI__GCF_000204075.1:WP_041456752.1 Length = 298 Score = 180 bits (457), Expect = 3e-50 Identities = 103/316 (32%), Positives = 157/316 (49%), Gaps = 20/316 (6%) Query: 1 MPKLKLIGVDLGGTTFSVGLVSEDGKILKKVTRDTLVENGKEDVIRRIAETILEVSDGEE 60 M ++IG+DLGGT +G SEDG + +T +T E V + + I ++ E Sbjct: 1 MGNSQVIGIDLGGTAIKLGRFSEDGTCSQSLTVETPQPATPEAVFLVMVDAIAQIDPDNE 60 Query: 61 APYVGIGSPGSIDRENGIVRFSPNFPDWHNVPLTDELAKRTGKKVFLENDANAFVLGEKW 120 +G+G+PG D + I + + N P W NVPL D L +T K +ENDAN + E W Sbjct: 61 TIAIGVGTPGPADAQGRIAQIAINLPQWENVPLADWLETKTNKPTVIENDANCAGIAEAW 120 Query: 121 FGAGRGHDHIVALTLGTGIGGGVVTHGYLLTGRDGIGAELGHVVVEPNGPMCNCGTRGCL 180 GAGR + + + LTLGTG+GG + G L G G ELG + ++P+GPMC G G L Sbjct: 121 LGAGRHYQNFIMLTLGTGVGGAIFLDGKLFVGHRGAAGELGLITLQPDGPMCKSGNPGSL 180 Query: 181 EAVASATAIRRFLREGYKKYHSSLVYKLAGSPEKADAKHLFDAARQGDRFALMIRDRVVD 240 E S AIRR L G E A+ L A+ GD AL Sbjct: 181 EQYTSIKAIRR----------------LTGK-EPAELGML---AQAGDIEALQFWQEYGQ 220 Query: 241 ALARAVAGYIHIFNPEIVIIGGGISRAGEILFGPLREKVVDYIMPSFVGTYEVVASPLVE 300 L + I++ P+ +++GGG+S + E L+ ++ +M + +++ + L Sbjct: 221 NLGIGLTSLIYVLTPQAIVLGGGVSASHEFFLPTLKAEIEQRVMSTSRAGLQILPAELGN 280 Query: 301 DAGILGAASIIKERIG 316 AG++GAA + ++ G Sbjct: 281 SAGMVGAARLAWKKFG 296 Lambda K H 0.320 0.142 0.418 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: 235 Number of extensions: 10 Number of successful extensions: 2 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: 317 Length of database: 298 Length adjustment: 27 Effective length of query: 290 Effective length of database: 271 Effective search space: 78590 Effective search space used: 78590 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 (21.7 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