Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate H281DRAFT_00163 H281DRAFT_00163 glucokinase /transcriptional regulator, RpiR family
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__Burk376:H281DRAFT_00163 Length = 638 Score = 262 bits (670), Expect = 1e-74 Identities = 138/316 (43%), Positives = 191/316 (60%), Gaps = 4/316 (1%) Query: 6 LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKV-EVKDGCIAIA 64 L+ D+GGTNAR AL + GEI Y DYP + VI+ YL++ K+ V IAIA Sbjct: 22 LLADIGGTNARFAL-ETGPGEIGSVHVYPCADYPGVAEVIKKYLKDTKIGRVNHAAIAIA 80 Query: 65 CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124 P+ GD V+MTNH W+FSI ++ LGF L ++NDFTA++MA+P L +Q GG Sbjct: 81 NPVDGDQVSMTNHDWSFSIEATRRALGFDTLLVVNDFTALAMALPGLTDAQRVQVGGGTR 140 Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHV 184 I + G GTG+GV+ L+ D RW++L EGGH FAP E E I+L+ R + HV Sbjct: 141 RPNSVIGLLGPGTGMGVSGLIPADDRWIALGSEGGHATFAPADEREDIVLQYARKKWSHV 200 Query: 185 SAERVLSGPGLVNLYRAIVKAD-NRLPENLKPKDITERALADSCTDCRRALSLFCVIMGR 243 S ERV +GPG+ +YRA+ D R+ N+ +I +RAL ++ +FC I+G Sbjct: 201 SFERVAAGPGIEVIYRALAGRDKKRVAANVDTVEIVKRALEGEPL-AAESVDVFCGILGT 259 Query: 244 FGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDN 303 F GN+A+ LG GG++I GG+VPR EFF S FR FE KGRF+ Y+ ++P Y+I + Sbjct: 260 FAGNIAVTLGALGGIYIGGGVVPRLGEFFARSSFRKRFEAKGRFEAYLQNVPTYVITAEY 319 Query: 304 PGLLGSGAHLRQTLGH 319 P LG A L + L + Sbjct: 320 PAFLGVSAILAEQLSN 335 Lambda K H 0.322 0.141 0.426 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: 578 Number of extensions: 25 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: 321 Length of database: 638 Length adjustment: 33 Effective length of query: 288 Effective length of database: 605 Effective search space: 174240 Effective search space used: 174240 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: 51 (24.3 bits)
Align candidate H281DRAFT_00163 H281DRAFT_00163 (glucokinase /transcriptional regulator, RpiR family)
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.3713.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-101 324.5 0.0 5.6e-101 323.9 0.0 1.3 1 lcl|FitnessBrowser__Burk376:H281DRAFT_00163 H281DRAFT_00163 glucokinase /tra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_00163 H281DRAFT_00163 glucokinase /transcriptional regulator, RpiR family # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 323.9 0.0 5.6e-101 5.6e-101 1 313 [. 22 324 .. 22 326 .. 0.96 Alignments for each domain: == domain 1 score: 323.9 bits; conditional E-value: 5.6e-101 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPii 66 l++diGGtnar+al e pgei +v++y + d+p + +v++ yl+++k+ + ++++aia P+ lcl|FitnessBrowser__Burk376:H281DRAFT_00163 22 LLADIGGTNARFAL-ETGPGEIGSVHVYPCADYPGVAEVIKKYLKDTKIGRVN--HAAIAIANPVD 84 79************.*******************************9987777..8********** PP TIGR00749 67 gdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailG 132 gd v +tn+dW++sie +++ l++ l ++ndf+a a+a+++l + + +q+gg +++ i +lG lcl|FitnessBrowser__Burk376:H281DRAFT_00163 85 GDQVSMTNHDWSFSIEATRRALGFDTLLVVNDFTALAMALPGLTDAQRVQVGGGTRRPNSVIGLLG 150 ****************************************************************** PP TIGR00749 133 aGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliy 198 +GtG+Gv+ li+ +d+r+ +l +eGgh+ faP +e e ++l+y+rkk+++vs erv +G+G+ +iy lcl|FitnessBrowser__Burk376:H281DRAFT_00163 151 PGTGMGVSGLIP-ADDRWIALGSEGGHATFAPADEREDIVLQYARKKWSHVSFERVAAGPGIEVIY 215 ************.9**************************************************** PP TIGR00749 199 ealskrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvy 264 +al r+ +k ++ +i ++aleg+ +la +++++f++ilG++agn+a++lga GG+y lcl|FitnessBrowser__Burk376:H281DRAFT_00163 216 RALAGRD-----KKRVAANVDTVEIVKRALEGE-PLAAESVDVFCGILGTFAGNIAVTLGALGGIY 275 *****99.....33334677788999*****97.788899************************** PP TIGR00749 265 vaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllG 313 + GG+vPr+ e++ +ssfr++fe kGr++++l+++P +v+ + + +lG lcl|FitnessBrowser__Burk376:H281DRAFT_00163 276 IGGGVVPRLGEFFARSSFRKRFEAKGRFEAYLQNVPTYVITAEYPAFLG 324 *****************************************99998887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (638 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 19.38 // [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