Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate N515DRAFT_4210 N515DRAFT_4210 glucokinase
Query= curated2:B4SRZ6 (335 letters) >FitnessBrowser__Dyella79:N515DRAFT_4210 Length = 339 Score = 326 bits (835), Expect = 6e-94 Identities = 170/326 (52%), Positives = 219/326 (67%), Gaps = 6/326 (1%) Query: 2 SASSQPVLVADIGGTNARFALADTSLDAPLQQDSIREYAVAEFPSLGDAARHHLEQIGAT 61 S SS L+AD+GGTN RFALAD +L PL DS+R Y V +FPS+ D R + G + Sbjct: 3 STSSAKTLLADLGGTNVRFALADPALPQPLLLDSVRRYRVKDFPSMADTIRQYFADSGLS 62 Query: 62 ASRGVFAVAGR-VDGDEARITNHPWVISRSRTAAMLGFDELHLINDFAAQAMAISLLQSD 120 A R V A AGR VDG+ ++TN+PW +S AA L FD + LINDFAAQ MA+ LL + Sbjct: 63 AGRAVIAAAGRIVDGETVKVTNNPWQVSAHGLAADLKFDSVRLINDFAAQGMAVPLLACN 122 Query: 121 DVVQVGGAAWVPGKPG--QPRNYAVIGPGTGLGVGGLILRHGRCYPLETEGGHVSFPPGT 178 ++ VG P K G + + V+GPGTGLGV GL+LR GR LETEGGH F T Sbjct: 123 ELQPVGAPQ--PPKIGAHHSQTFVVVGPGTGLGVAGLLLRDGRWTVLETEGGHAGFAAHT 180 Query: 179 PEEIRILEILSEQFGRVSNERLICGPGLVNIHRAVCEMAGIDPGQLQPVDVTARALHG-D 237 E++ IL L+ +FGRVSNER+ICG GLVN++ A+ ++ G+ + P D+T RA G D Sbjct: 181 AEDVEILHRLNARFGRVSNERMICGNGLVNLYLALADIEGLKAEEYTPEDITTRANAGTD 240 Query: 238 PQAMRTVDVFCAVFGAIAGDLVLTQGAWDGVFLTGGLTPKMLDSLQHSGFRQRFEHKGRF 297 P +RTV+ +FG++AGDLVL+ G WDGVFLTGG+ P +L LQH GFR+RFE KGRF Sbjct: 241 PLCVRTVETLAGIFGSVAGDLVLSLGGWDGVFLTGGVLPILLPWLQHGGFRERFESKGRF 300 Query: 298 SSIMARVPSLAVMHPHAGLLGAAAYA 323 M +VP++A+MH GLLGAAA+A Sbjct: 301 KETMEQVPTVAMMHAETGLLGAAAFA 326 Lambda K H 0.321 0.137 0.414 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: 323 Number of extensions: 15 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: 335 Length of database: 339 Length adjustment: 28 Effective length of query: 307 Effective length of database: 311 Effective search space: 95477 Effective search space used: 95477 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 N515DRAFT_4210 N515DRAFT_4210 (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.6963.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-82 260.8 0.0 1e-81 260.6 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_4210 N515DRAFT_4210 glucokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_4210 N515DRAFT_4210 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.6 0.0 1e-81 1e-81 1 315 [] 10 323 .. 10 323 .. 0.94 Alignments for each domain: == domain 1 score: 260.6 bits; conditional E-value: 1e-81 TIGR00749 1 lvgdiGGtnarlalveva...pgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiat 63 l++d+GGtn r+al + a p ++++v+ y+ +dfps+ + +r+y ++ + + + +a a+ lcl|FitnessBrowser__Dyella79:N515DRAFT_4210 10 LLADLGGTNVRFALADPAlpqPLLLDSVRRYRVKDFPSMADTIRQYFADSGLSAGR---AVIAAAG 72 79*************8764346789999*************************999...99***** PP TIGR00749 64 Piig.dfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakv.....e 123 i++ ++v++tn+ W++s + l+ +l + + lindfaa+++a++ l ++l +g+ ++ + lcl|FitnessBrowser__Dyella79:N515DRAFT_4210 73 RIVDgETVKVTNNPWQVSAHGLAADLKFDSVRLINDFAAQGMAVPLLACNELQPVGAPQPpkigaH 138 999548*************************************************99654211215 PP TIGR00749 124 esaaiailGaGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervl 189 +s++ ++G+GtGlGva l+ dgr+ vl +eGgh+ fa + +++ +l+ l +++grvs er++ lcl|FitnessBrowser__Dyella79:N515DRAFT_4210 139 HSQTFVVVGPGTGLGVAGLLL-RDGRWTVLETEGGHAGFAAHTAEDVEILHRLNARFGRVSNERMI 203 678889*************99.8******************************************* PP TIGR00749 190 sGsGlvliyealskrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlal 255 G Glv++y al + l+ ee +++di+ +a +g+d+l+ r++e++ +i+G++ag+l l lcl|FitnessBrowser__Dyella79:N515DRAFT_4210 204 CGNGLVNLYLALADIE------GLKAEEYTPEDITTRANAGTDPLCVRTVETLAGIFGSVAGDLVL 263 ***********98777......68889*************************************** PP TIGR00749 256 klgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 lg Gv+++GG++P ++++l++++fr++fe kGr+ke ++++P ++++++GllGa+ lcl|FitnessBrowser__Dyella79:N515DRAFT_4210 264 SLGGWDGVFLTGGVLPILLPWLQHGGFRERFESKGRFKETMEQVPTVAMMHAETGLLGAA 323 **********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (339 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.70 // [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