Align hexokinase (EC 2.7.1.1) (characterized)
to candidate WP_008410212.1 DESHY_RS02610 hexokinase
Query= BRENDA::Q6X271 (513 letters) >NCBI__GCF_000315365.1:WP_008410212.1 Length = 436 Score = 224 bits (572), Expect = 4e-63 Identities = 163/471 (34%), Positives = 244/471 (51%), Gaps = 50/471 (10%) Query: 44 TSKTVQQAEKMSQEFRQSSSTPLPLLHQVADALVQEMYAGLASEGGSDQLKMLPTYVENL 103 T +Q+ E++ F SS + ++A L EM GL +G L+MLPT+++ L Sbjct: 2 TKLLIQKLEQIENAFYLSSVQ----VRELAKKLQTEM-TGLPGQGS---LQMLPTFMQ-L 52 Query: 104 PSGSEKGLFYAVDLGGTNFRVLRVELGGKTGQILSQEFKEVVIPPE------LMVGTGKD 157 P+GSE G F AVD GGTN R+ VEL G+ + ++ + P TG+ Sbjct: 53 PAGSETGTFLAVDFGGTNVRLQLVELLGRGQYAIKKQHSFRLKDPSGRYDFTARETTGEA 112 Query: 158 LFDFIAGTLASFVDTEDESIKAHFVQSGKTRESGFAFSFPVRQTSVKSGIVIHWTKGFKV 217 LFDF+AG +ASF++ F S G FSFP RQ + +++HWTK F+ Sbjct: 113 LFDFLAGQIASFME-------GTFATS-----LGLTFSFPCRQLAANKAVLLHWTKEFQT 160 Query: 218 DDAVGKDIVKQFQDAIS-RSNHQIMISALVNDTVGTLAGGRFNFDEETMIGCIIGTGTNA 276 VG++I+ A++ R + +AL+NDT GTL ++ + IG I GTG N Sbjct: 161 SAVVGREIMGLLAGALADRGLAHLQPAALINDTTGTLLTAAYS-NPHADIGSICGTGHNT 219 Query: 277 CYVERADAVHKWDEPLPKSGEMVINMEWGNFRSPYLPRTFADETVDKDSVNPGDQWFEKM 336 CY + K M+INME GNF+ L T D +D +S PG Q EK Sbjct: 220 CYFKT------------KEPAMIINMEAGNFKQFAL--TAYDRLLDSNSRRPGTQLLEKA 265 Query: 337 ISGMYLGEIVRLVLARMAKEAELFGGNVPVKLLERLTLGTPHVSKIHLDNSPDLDVVAKV 396 ++G YLGEI RL+L M ++ LF G++P + ++ T+ T ++ + DNSP L + + Sbjct: 266 VAGRYLGEICRLILLDMVEQGLLFRGSIPALVRQQQTIDTSELALLAADNSPSLLHIDRW 325 Query: 397 LKDVFEIETTTLEERKIVHEVCDIMGERGGRLAAAGLYGILKKIGRTGKSRNGSKKKTVI 456 L I TTL +R+++ ++ + R RL A GIL++I G +++ VI Sbjct: 326 LAARQNIHPTTLTDRQVLKKIALTVISRSARLVGATYIGILQQID------PGLQRRHVI 379 Query: 457 AMDGGLFEHHVRYRSYMEEALQELMGSDAAYEVALRLQNDGSGIGAALLAA 507 +DG LFE Y S + L+E+ +D A + L +GSGIGAA+ AA Sbjct: 380 GLDGSLFEKMPGYLSKVRAVLREVF-NDKAQSILPVLTGNGSGIGAAIAAA 429 Lambda K H 0.318 0.135 0.388 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: 440 Number of extensions: 26 Number of successful extensions: 9 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: 513 Length of database: 436 Length adjustment: 33 Effective length of query: 480 Effective length of database: 403 Effective search space: 193440 Effective search space used: 193440 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 (21.7 bits) S2: 51 (24.3 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