Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_011803057.1 PNAP_RS18470 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >NCBI__GCF_000015505.1:WP_011803057.1 Length = 335 Score = 226 bits (577), Expect = 5e-64 Identities = 128/316 (40%), Positives = 183/316 (57%), Gaps = 7/316 (2%) Query: 7 VGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKD-GCIAIAC 65 +GD+GGTNAR S IS + ++ SL + YL E + IA Sbjct: 19 LGDIGGTNARFGWQASESAAISHVQVLPCAEHESLLEAAQSYLREQGLSTPPCAAFGIAN 78 Query: 66 PITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEPV 125 P+TGD VAMTNH W FS++ ++++LG + ++NDFTA+++++P L + H GG + Sbjct: 79 PVTGDQVAMTNHHWKFSVSALRESLGLARFLLLNDFTALALSLPQLPEAHRRAVGGGQAA 138 Query: 126 EGKPIAVYGAGTGLGVAHLVHV--DKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGH 183 I + GAGTGLGV+ L+ + +W+ + GEGGHV + + E ++ L+ GH Sbjct: 139 PDAAIGLIGAGTGLGVSGLLPLGHQNKWIPIAGEGGHVTLSAATALEFAAIQHLQKRYGH 198 Query: 184 VSAERVLSGPGLVNLYRAIVKA-DNRLPENLKPKDITERALADSCTDCRRALSLFCVIMG 242 VSAERV+SG GLV+LY A+ D + E P D+ RA + +AL +FC +G Sbjct: 199 VSAERVISGAGLVDLYHALCDLKDGQGREITTPADVMARAQDVPLSTANQALDMFCGFLG 258 Query: 243 RFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHD 302 G+LAL LG GG++I GGIVPR E F+AS FRA FEDKGRFK Y+ IP + ++H Sbjct: 259 SVAGDLALTLGARGGIYIGGGIVPRMGERFEASPFRARFEDKGRFKPYLQAIPTW-VIHS 317 Query: 303 --NPGLLGSGAHLRQT 316 +P L G+ L T Sbjct: 318 PVSPALQGASQALSLT 333 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: 360 Number of extensions: 24 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: 335 Length adjustment: 28 Effective length of query: 293 Effective length of database: 307 Effective search space: 89951 Effective search space used: 89951 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_011803057.1 PNAP_RS18470 (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.24485.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-90 288.9 0.0 2.9e-90 288.7 0.0 1.0 1 lcl|NCBI__GCF_000015505.1:WP_011803057.1 PNAP_RS18470 glucokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015505.1:WP_011803057.1 PNAP_RS18470 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 288.7 0.0 2.9e-90 2.9e-90 2 314 .. 19 326 .. 18 327 .. 0.95 Alignments for each domain: == domain 1 score: 288.7 bits; conditional E-value: 2.9e-90 TIGR00749 2 vgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfv 70 +gdiGGtnar++ + + i+ v+++ + +++sl ++ + yl+e+ l p ++f ia P++gd v lcl|NCBI__GCF_000015505.1:WP_011803057.1 19 LGDIGGTNARFGWQASESAAISHVQVLPCAEHESLLEAAQSYLREQG--LSTPPCAAFGIANPVTGDQV 85 79***********9999**************************9976..667889************** PP TIGR00749 71 rltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGv 139 ++tn++W++s+ l+++l+la+ l+ndf+a a++++ l e + +gg ++ ++aai ++GaGtGlGv lcl|NCBI__GCF_000015505.1:WP_011803057.1 86 AMTNHHWKFSVSALRESLGLARFLLLNDFTALALSLPQLPEAHRRAVGGGQAAPDAAIGLIGAGTGLGV 154 ********************************************************************* PP TIGR00749 140 atliqqs.dgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkge 207 + l++ + ++++ +ageGghv ++ le+ ++ l+k+yg+vsaerv+sG+Glv +y+al k lcl|NCBI__GCF_000015505.1:WP_011803057.1 155 SGLLPLGhQNKWIPIAGEGGHVTLSAATALEFAAIQHLQKRYGHVSAERVISGAGLVDLYHALCDLK-- 221 ****9753789****************************************************9988.. PP TIGR00749 208 revsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiel 276 +e ++ d+ +a + + a++al++f++ lG++ag+lal+lgarGG+y+ GGivPr+ e lcl|NCBI__GCF_000015505.1:WP_011803057.1 222 ---DGQGREITTPADVMARAQDVPLSTANQALDMFCGFLGSVAGDLALTLGARGGIYIGGGIVPRMGER 287 ...344567889********************************************************* PP TIGR00749 277 lkkssfraafedkGrlkellasiPvqvvlk.kkvGllGa 314 +++s+fra+fedkGr+k +l+ iP v+ + l Ga lcl|NCBI__GCF_000015505.1:WP_011803057.1 288 FEASPFRARFEDKGRFKPYLQAIPTWVIHSpVSPALQGA 326 *************************99965235666666 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (335 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: 9.47 // [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