Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_026223745.1 A3OW_RS0119510 glucokinase
Query= curated2:B2J224 (341 letters) >NCBI__GCF_000372865.1:WP_026223745.1 Length = 333 Score = 212 bits (540), Expect = 9e-60 Identities = 130/333 (39%), Positives = 181/333 (54%), Gaps = 14/333 (4%) Query: 3 LLLAGDIGGTKTILQLVETSDSQGLHTIYQE-SYHSADFPDLVPIVQQFLIKANTPIPEK 61 ++LAGDIGGTKT+L L+ T ++ G ++E S+ S DF + I+ FL A P+ + Sbjct: 1 MILAGDIGGTKTVLALL-TRETDGTWISHREQSFVSRDFLNFYDILAAFL-PAGLPV-DF 57 Query: 62 ACFAIAGPIVKNTAKLTNLAWFLDTERLQQELGIPHIYLINDFAAVGYGISGLQKQDLHP 121 ACF +AGP+V TNL W LD L+Q L IP + L+ND A+ G+ L ++DL Sbjct: 58 ACFGVAGPVVNQRCHTTNLPWVLDAAELRQTLAIPRVKLLNDLEAMAAGMLYLPEKDLLE 117 Query: 122 LQVGKPQPETPIGIIGAGTGLGQGFLIKQGNNYQVFPSEGGHADFAPRNEIEFQLLKYLL 181 L +I AGTGLG+ L G + +EGGH DFAP + QLL YL Sbjct: 118 LNPNAQSQPGNKAVIAAGTGLGEAILYWDGGRHHPIATEGGHCDFAPLTPQQDQLLAYLR 177 Query: 182 DKHDIQRISVERVVSGMGIVAIYQFLRDRKFAAESPDIAQIVRTWEQEAGQEEKSVDPGA 241 +S ER++SG G +Y FL R+ A P + +G +D A Sbjct: 178 TIFP-DHVSCERIISGDGFGHLYDFLCARQGTAPCPAV---------PSGAGSGEIDRNA 227 Query: 242 AIGTAALEKRDRLSEQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIAPKILPLIQNSG 301 I + D + + ++LF E YGAE GNLALK L GG++I GGIA KILP ++ Sbjct: 228 VISRLGVHGEDPVCAEAVRLFTELYGAETGNLALKSLALGGVFIGGGIAEKILPAMRQGA 287 Query: 302 FLLNFTQKGRMRPLLEEIPVYIILNPQVGLIGA 334 F+ F KGR P+L+++ V I LNP+ L+GA Sbjct: 288 FIEAFKAKGRFFPMLDKMSVKISLNPRTPLLGA 320 Lambda K H 0.320 0.140 0.408 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: 280 Number of extensions: 17 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: 341 Length of database: 333 Length adjustment: 28 Effective length of query: 313 Effective length of database: 305 Effective search space: 95465 Effective search space used: 95465 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_026223745.1 A3OW_RS0119510 (glucokinase)
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR00749.hmm # target sequence database: /tmp/gapView.7563.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00749 [M=315] Accession: TIGR00749 Description: glk: glucokinase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-71 226.5 0.0 2.8e-71 226.3 0.0 1.0 1 lcl|NCBI__GCF_000372865.1:WP_026223745.1 A3OW_RS0119510 glucokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000372865.1:WP_026223745.1 A3OW_RS0119510 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 226.3 0.0 2.8e-71 2.8e-71 1 314 [. 3 320 .. 3 321 .. 0.93 Alignments for each domain: == domain 1 score: 226.3 bits; conditional E-value: 2.8e-71 TIGR00749 1 lvgdiGGtnarlalv..evapgeieqv.ktyssedfpsleavvrvyleeakvelkdpi.kgcfaiatPi 65 l+gdiGGt+++lal+ e i+ + + s df ++ +++ +l + p+ +cf +a+P+ lcl|NCBI__GCF_000372865.1:WP_026223745.1 3 LAGDIGGTKTVLALLtrETDGTWISHReQSFVSRDFLNFYDILAAFLPA-----GLPVdFACFGVAGPV 66 79************9877777777766699**************99964.....567767********* PP TIGR00749 66 igdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaG 134 +++ ++ tnl W l +el+q+la+ +++l+nd+ a+a ++l l e+dl l+ + + +a++ aG lcl|NCBI__GCF_000372865.1:WP_026223745.1 67 VNQRCHTTNLPWVLDAAELRQTLAIPRVKLLNDLEAMAAGMLYLPEKDLLELNPNAQSQPGNKAVIAAG 135 ******************************************************99999********** PP TIGR00749 135 tGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkky.grvsaervlsGsGlvliyeals 202 tGlG a l gr++ +a+eGgh dfaP +++ +ll ylr+ + ++vs er++sG G+ +y++l lcl|NCBI__GCF_000372865.1:WP_026223745.1 136 TGLGEAILYW-DGGRHHPIATEGGHCDFAPLTPQQDQLLAYLRTIFpDHVSCERIISGDGFGHLYDFLC 203 ******9998.6799****************************************************** PP TIGR00749 203 krkgere.....vsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyva 266 r+g s e ++ is+ ++g+d+++ +a+ lf ++Ga++gnlalk +a GGv++ lcl|NCBI__GCF_000372865.1:WP_026223745.1 204 ARQGTAPcpavpSGAGSGEIDRNAVISRLGVHGEDPVCAEAVRLFTELYGAETGNLALKSLALGGVFIG 272 ***9999433322233445566667******************************************** PP TIGR00749 267 GGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGa 314 GGi+ ++++ +++++f +af+ kGr+ +l ++ v++ l+ ++ llGa lcl|NCBI__GCF_000372865.1:WP_026223745.1 273 GGIAEKILPAMRQGAFIEAFKAKGRFFPMLDKMSVKISLNPRTPLLGA 320 ******************************************999998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (333 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.72 // [ok]
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