Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_037155368.1 RHSP_RS30180 glucokinase
Query= curated2:B9JYQ5 (340 letters) >NCBI__GCF_000359745.1:WP_037155368.1 Length = 340 Score = 464 bits (1195), Expect = e-135 Identities = 223/336 (66%), Positives = 269/336 (80%), Gaps = 1/336 (0%) Query: 5 HDNDHMPFPVLVGDIGGTNARFWILMDAHAAPKEFANIHTADFPTIDQAIQDCILDKSGF 64 H + PFP+L+GDIGGTNARF IL DA++ F + TA+F TID AI+ L+KS Sbjct: 6 HSDAPQPFPILIGDIGGTNARFSILADANSEQVHFPVVQTANFETIDDAIK-LTLEKSKL 64 Query: 65 QPRSAILAVAGPIKDDEIPLTNCPWVIRPKAMIADLGFDDVLVVNDFEAQALAAASLGRN 124 QPRSAILA+AGP++ DEIPLTNC WVIRPK MIA+LG +DVL++NDFEAQALA A + + Sbjct: 65 QPRSAILAMAGPVQGDEIPLTNCDWVIRPKTMIANLGIEDVLIINDFEAQALAIAEVADD 124 Query: 125 DREPIGPLTETSLNSRVILGPGTGLGVGGLLYTHHTWFPVPGEGGHVDIGPRSDRDWQIF 184 RE IG +E SR +LGPGTGLGV GL++T H W PVPGEGGH+D+GPRS+RD QI+ Sbjct: 125 HRESIGETSENETASRAVLGPGTGLGVAGLIHTQHQWIPVPGEGGHIDLGPRSERDLQIW 184 Query: 185 PHIERIEGRISGEQILCGRGILHLYNAICAADGIEPVWTDPADVTQHALKGNDPVCVETM 244 PH+E IEGRIS EQ++CGRG+ +LY+AIC ADGIEP +PAD+T HAL G D ET+ Sbjct: 185 PHLETIEGRISAEQVICGRGLQNLYHAICKADGIEPSLKEPADITTHALAGTDKQAEETL 244 Query: 245 TLFVTYLGRIAGDMALVFMARGGVFLSGGISQKIIPLLKSPVFRAAFEDKAPHTEMMKTI 304 TLFVTYLGR+AGD+AL+FMARGGV+LSGGISQKI+P L+ P FR AFEDKAPHTEMMKTI Sbjct: 245 TLFVTYLGRVAGDIALIFMARGGVYLSGGISQKILPALQKPEFRDAFEDKAPHTEMMKTI 304 Query: 305 PTFVAIHPQAALSGLAAYARTPSSYGVKHEGRRWQR 340 PT V HP AALSGLA+YAR P+S+G+ EGRRW+R Sbjct: 305 PTHVVTHPLAALSGLASYARKPASFGLATEGRRWRR 340 Lambda K H 0.322 0.140 0.445 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: 433 Number of extensions: 12 Number of successful extensions: 2 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: 340 Length of database: 340 Length adjustment: 28 Effective length of query: 312 Effective length of database: 312 Effective search space: 97344 Effective search space used: 97344 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 (21.9 bits) S2: 49 (23.5 bits)
Align candidate WP_037155368.1 RHSP_RS30180 (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.1712326.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-81 259.7 0.0 2.2e-81 259.5 0.0 1.0 1 NCBI__GCF_000359745.1:WP_037155368.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000359745.1:WP_037155368.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 259.5 0.0 2.2e-81 2.2e-81 1 313 [. 16 318 .. 16 320 .. 0.95 Alignments for each domain: == domain 1 score: 259.5 bits; conditional E-value: 2.2e-81 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrlt 73 l+gdiGGtnar++++ a e + ++ +f+ + +++++ le++k + + + +a+a+P+ gd + lt NCBI__GCF_000359745.1:WP_037155368.1 16 LIGDIGGTNARFSILADANSEQVHFPVVQTANFETIDDAIKLTLEKSKLQPRS---AILAMAGPVQGDEIPLT 85 79***********975555555566899*******************997666...99*************** PP TIGR00749 74 nldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqs 146 n dW + +++ +l+++ + +indf a+a+ai+ + +++ +g +e+a+ a+lG+GtGlGva li+ + NCBI__GCF_000359745.1:WP_037155368.1 86 NCDWVIRPKTMIANLGIEDVLIINDFEAQALAIAEVADDHRESIGETSENETASRAVLGPGTGLGVAGLIH-T 157 ***********************************************************************.9 PP TIGR00749 147 dgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelk 219 + ++ ++geGgh+d+ Prse +++++ l + gr+sae+v+ G Gl ++y+a+ k++g + + ++ NCBI__GCF_000359745.1:WP_037155368.1 158 QHQWIPVPGEGGHIDLGPRSERDLQIWPHLETIEGRISAEQVICGRGLQNLYHAICKADGIEP------SLKE 224 ********************************99*************************7764......3457 PP TIGR00749 220 ekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrl 292 + di+ al+g+d a+++l lf++ lG++ag++al + arGGvy++GGi ++++ l+k fr afedk NCBI__GCF_000359745.1:WP_037155368.1 225 PADITTHALAGTDKQAEETLTLFVTYLGRVAGDIALIFMARGGVYLSGGISQKILPALQKPEFRDAFEDKAPH 297 99*********************************************************************** PP TIGR00749 293 kellasiPvqvvlkkkvGllG 313 e++++iP +vv + + l G NCBI__GCF_000359745.1:WP_037155368.1 298 TEMMKTIPTHVVTHPLAALSG 318 ************998887777 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (340 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: 00:00:00.00 # Mc/sec: 16.35 // [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