Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_024850593.1 N745_RS0102655 glucokinase
Query= curated2:B2J224 (341 letters) >NCBI__GCF_000526715.1:WP_024850593.1 Length = 330 Score = 224 bits (570), Expect = 3e-63 Identities = 125/343 (36%), Positives = 196/343 (57%), Gaps = 18/343 (5%) Query: 1 MTLLLAGDIGGTKTILQLVETSDSQGLHTIYQESYHSADFPDLVPIVQQFLIKANTPIPE 60 M+L+LAGDIGGTKT+L + ++ ++ L + ++SY S + + +++ F I ++ + + Sbjct: 1 MSLILAGDIGGTKTLLAIFKSQNNGKLEELCKKSYPSNSYTNFNSLLKNF-ISEHSSLAD 59 Query: 61 K---ACFAIAGPIVKNTAKLTNLAWFLDTERLQQELGIPHIYLINDFAAVGYGISGLQKQ 117 K A F +AGP++ T L W ++ + E IP+++L+ND A YGI L Sbjct: 60 KVITATFGVAGPVLDQRCMTTKLPWIINAIEISNEFQIPNVHLLNDLEATAYGI--LTLN 117 Query: 118 DLHPLQVGKPQPETPIGIIGAGTGLGQGFLIKQGNNYQVFPSEGGHADFAPRNEIEFQLL 177 H L + +I AGTGLG+ + G Y PSEGGH DFAP+ +E QL+ Sbjct: 118 HFHSLNPNAQEKSGHFSVIAAGTGLGEVTVFFDGREYHTMPSEGGHCDFAPQTPLEDQLI 177 Query: 178 KYLLDKHDIQRISVERVVSGMGIVAIYQFLRDRKFAAESPDIAQIVRTWEQEAGQEEKSV 237 +L ++ +S++R++SG G +Y FL+ FA +P + E+ QE+++ Sbjct: 178 AFLRNRFK-GHVSMDRILSGDGFGNLYDFLKSINFAPVNPPL-------EERMKQEDRN- 228 Query: 238 DPGAAIGTAALEKRDRLSEQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIAPKILPLI 297 A I A L D L + ++LF YGAEAGNLALK LP+GG+YIAGGIA KI P + Sbjct: 229 ---AVISHAGLHNEDPLCTEVMKLFCRIYGAEAGNLALKALPFGGIYIAGGIAKKIRPAL 285 Query: 298 QNSGFLLNFTQKGRMRPLLEEIPVYIILNPQVGLIGAALCAAR 340 ++ F+ F KGR+ +E IP+ ++ N + L+GAA A++ Sbjct: 286 ESGIFMEGFLDKGRLSHSIEHIPIRLVDNEEAPLLGAANFASK 328 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: 309 Number of extensions: 19 Number of successful extensions: 5 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: 330 Length adjustment: 28 Effective length of query: 313 Effective length of database: 302 Effective search space: 94526 Effective search space used: 94526 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_024850593.1 N745_RS0102655 (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.20859.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-79 251.9 0.0 5.2e-79 251.7 0.0 1.0 1 lcl|NCBI__GCF_000526715.1:WP_024850593.1 N745_RS0102655 glucokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000526715.1:WP_024850593.1 N745_RS0102655 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 251.7 0.0 5.2e-79 5.2e-79 1 315 [] 5 323 .. 5 323 .. 0.93 Alignments for each domain: == domain 1 score: 251.7 bits; conditional E-value: 5.2e-79 TIGR00749 1 lvgdiGGtnarlalv.evapgeieqv..ktyssedfpsleavvrvyleeakvelkdpikgcfaiatPii 66 l+gdiGGt++ la+ g++e + k y s+ + +++++++ + +e+ + i ++f +a+P++ lcl|NCBI__GCF_000526715.1:WP_024850593.1 5 LAGDIGGTKTLLAIFkSQNNGKLEELckKSYPSNSYTNFNSLLKNFISEHSSLADKVITATFGVAGPVL 73 79************954567888876779*********************9999999************ PP TIGR00749 67 gdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGt 135 ++ + t l W + e+ +e+ + +++l+nd+ a ay+il+l +++ l+ e+s+ +++ aGt lcl|NCBI__GCF_000526715.1:WP_024850593.1 74 DQRCMTTKLPWIINAIEISNEFQIPNVHLLNDLEATAYGILTL--NHFHSLNPNAQEKSGHFSVIAAGT 140 ****************************************998..67889999999************* PP TIGR00749 136 GlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkky.grvsaervlsGsGlvliyealsk 203 GlG t+ + + y+++++eGgh dfaP+ +le +l+ +lr+++ g+vs++r+lsG G+ ++y++l+ lcl|NCBI__GCF_000526715.1:WP_024850593.1 141 GLGEVTVFFD-GREYHTMPSEGGHCDFAPQTPLEDQLIAFLRNRFkGHVSMDRILSGDGFGNLYDFLKS 208 *******994.457*****************************************************98 PP TIGR00749 204 rkgere...vsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGi 269 + ++ +k+e ++ is+a l+++d+l+ + ++lf+ i+Ga+agnlalk +++GG+y+aGGi lcl|NCBI__GCF_000526715.1:WP_024850593.1 209 INFAPVnppLEERMKQEDRNAVISHAGLHNEDPLCTEVMKLFCRIYGAEAGNLALKALPFGGIYIAGGI 277 7633322366666678888888*********************************************** PP TIGR00749 270 vPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 + ++ + l+++ f+++f dkGrl + +++iP+++v ++++ llGa+ lcl|NCBI__GCF_000526715.1:WP_024850593.1 278 AKKIRPALESGIFMEGFLDKGRLSHSIEHIPIRLVDNEEAPLLGAA 323 ********************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (330 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: 11.63 // [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