Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate Synpcc7942_0221 Synpcc7942_0221 glucokinase
Query= curated2:B2J224 (341 letters) >FitnessBrowser__SynE:Synpcc7942_0221 Length = 345 Score = 347 bits (890), Expect = e-100 Identities = 188/344 (54%), Positives = 232/344 (67%), Gaps = 6/344 (1%) Query: 1 MTLLLAGDIGGTKTILQLVETSDSQGLHTIYQESYHSADFPDLVPIVQQFLI---KANTP 57 MTLLLAGDIGGTKT L L SD L ++Q S+ SA +PDLVP+VQ+FL A Sbjct: 1 MTLLLAGDIGGTKTNLMLAIASDCDRLEPLHQASFASAAYPDLVPMVQEFLAAAPSAEVR 60 Query: 58 IPEKACFAIAGPIVKNTAKLTNLAWFLDTERLQQELGIPHIYLINDFAAVGYGISGLQKQ 117 P ACF IAGP+V TAKLTNL W L RL +ELGI + LINDFAA+ YG+ GL + Sbjct: 61 SPVVACFGIAGPVVHGTAKLTNLPWQLSEARLAKELGIAQVALINDFAAIAYGLPGLTAE 120 Query: 118 DLHPLQVGKPQPETPIGIIGAGTGLGQGFLIKQGNNYQVFPSEGGHADFAPRNEIEFQLL 177 D +QVG+ P PI I+GAGTGLG+GF+I QVF SEG HADFAP+ E+E +LL Sbjct: 121 DQVVVQVGEADPAAPIAILGAGTGLGEGFIIPTAQGRQVFGSEGSHADFAPQTELESELL 180 Query: 178 KYLLDKHDIQRISVERVVSGMGIVAIYQFLRDRKFAAESPDIAQIVRTWEQEAGQEEKSV 237 +L + + I+ ISVERVVSG GI AIY FLRDR E+P + I W+ Q + Sbjct: 181 HFLRNFYAIEHISVERVVSGQGIAAIYAFLRDRHPDQENPALGAIASAWQTGGDQ---AP 237 Query: 238 DPGAAIGTAALEKRDRLSEQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIAPKILPLI 297 D AA+ AAL RD L+ Q +Q+F+ AYGAEAGNLALKLL YGG+Y+AGGIA KILPL+ Sbjct: 238 DLAAAVSQAALSDRDPLALQAMQIFVSAYGAEAGNLALKLLSYGGVYVAGGIAGKILPLL 297 Query: 298 QNSGFLLNFTQKGRMRPLLEEIPVYIILNPQVGLIGAALCAARL 341 + FL F KGR++ LL +P+ I+ N +VGLIGA L AA + Sbjct: 298 TDGTFLQAFQAKGRVKGLLTRMPITIVTNHEVGLIGAGLRAAAI 341 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: 349 Number of extensions: 12 Number of successful extensions: 3 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: 345 Length adjustment: 29 Effective length of query: 312 Effective length of database: 316 Effective search space: 98592 Effective search space used: 98592 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 Synpcc7942_0221 Synpcc7942_0221 (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.13085.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-105 336.7 0.3 8.5e-105 336.4 0.3 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_0221 Synpcc7942_0221 glucokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_0221 Synpcc7942_0221 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 336.4 0.3 8.5e-105 8.5e-105 1 315 [] 5 335 .. 5 335 .. 0.95 Alignments for each domain: == domain 1 score: 336.4 bits; conditional E-value: 8.5e-105 TIGR00749 1 lvgdiGGtnarlalv.evapgeieqv..ktyssedfpsleavvrvyleea.kvelkdpikgcfaiatPi 65 l+gdiGGt++ l l + ++e++ + s ++p+l+++v+ +l a e++ p+ +cf ia+P+ lcl|FitnessBrowser__SynE:Synpcc7942_0221 5 LAGDIGGTKTNLMLAiASDCDRLEPLhqASFASAAYPDLVPMVQEFLAAApSAEVRSPVVACFGIAGPV 73 79**********99544445677777667899***************98736799************** PP TIGR00749 66 igdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaG 134 + + +ltnl W+ls ++l++el++a++ lindfaa+ay++++l ed ++++ +++++a+iailGaG lcl|FitnessBrowser__SynE:Synpcc7942_0221 74 VHGTAKLTNLPWQLSEARLAKELGIAQVALINDFAAIAYGLPGLTAEDQVVVQVGEADPAAPIAILGAG 142 ********************************************************************* PP TIGR00749 135 tGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkky..grvsaervlsGsGlvliyeal 201 tGlG ++i+ ++gr +v+ +eG+h+dfaP+ ele ll++lr+ y +++s+erv+sG+G++ iy +l lcl|FitnessBrowser__SynE:Synpcc7942_0221 143 TGLGEGFIIPTAQGR-QVFGSEGSHADFAPQTELESELLHFLRNFYaiEHISVERVVSGQGIAAIYAFL 210 **********99999.79**************************98889******************** PP TIGR00749 202 skrkgere...vsklskeelkekd........iseaalegsdvlarralelflsilGalagnlalklga 259 + r++++e + + ++++ d +s+aal + d+la +a+++f+s++Ga+agnlalkl++ lcl|FitnessBrowser__SynE:Synpcc7942_0221 211 RDRHPDQEnpaLGAIASAWQTGGDqapdlaaaVSQAALSDRDPLALQAMQIFVSAYGAEAGNLALKLLS 279 ******997887888889998888999****************************************** PP TIGR00749 260 rGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 +GGvyvaGGi+ ++++ll ++f +af+ kGr+k ll+ +P+ +v +++vGl+Gag lcl|FitnessBrowser__SynE:Synpcc7942_0221 280 YGGVYVAGGIAGKILPLLTDGTFLQAFQAKGRVKGLLTRMPITIVTNHEVGLIGAG 335 ******************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (345 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: 00:00:00.01 # Mc/sec: 7.86 // [ok]
This GapMind analysis is from Sep 17 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