Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate CCNA_02133 CCNA_02133 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__Caulo:CCNA_02133 Length = 331 Score = 209 bits (533), Expect = 6e-59 Identities = 125/313 (39%), Positives = 176/313 (56%), Gaps = 6/313 (1%) Query: 6 LVGDVGGTNARLALCDIASGE--ISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKD-GCIA 62 LVGD+GGTNAR AL + + + + Y G DY + E I YL + V+ D +A Sbjct: 11 LVGDIGGTNARFALVEFDGQDPRLIEPTAYRGEDYGTAEDAIEEYLRKVGVKHPDQAVVA 70 Query: 63 IACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGA 122 +A PI V MTN W S +++ GF + ++INDFTA ++A P + + L Q G Sbjct: 71 VAGPIDHGQVHMTNLDWRISEDGLRRAGGFRNAKLINDFTAQALAAPRVGPKDLRQIGEL 130 Query: 123 EPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEIL--RAE 180 +A+ G GTG GVA LV + + L EGGHV FAP + E +L L R + Sbjct: 131 PTSGEGDLAILGPGTGFGVAGLVRRHGQEIPLATEGGHVAFAPVDDVEIEVLRALTRRLD 190 Query: 181 IGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI 240 G VS ER+LSGPG+ +L+ + A+ R E L K ITERA+ + C D ++ FC I Sbjct: 191 GGRVSVERILSGPGMEDLHVDLAAAEGRGVEALTAKQITERAV-EGCADSLATVNRFCAI 249 Query: 241 MGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIV 300 +G G++AL LG GGVFIAGGI PR ++ + S FR F+ KGR + IP ++I+ Sbjct: 250 LGSTAGDIALTLGARGGVFIAGGIAPRIIDILEKSPFRERFDSKGRLSGFTRSIPTHVIL 309 Query: 301 HDNPGLLGSGAHL 313 H + L+G+ L Sbjct: 310 HPHTALIGAAVAL 322 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: 319 Number of extensions: 14 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: 331 Length adjustment: 28 Effective length of query: 293 Effective length of database: 303 Effective search space: 88779 Effective search space used: 88779 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: 48 (23.1 bits)
Align candidate CCNA_02133 CCNA_02133 (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.28773.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-90 288.6 0.0 3.6e-90 288.4 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_02133 CCNA_02133 glucokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_02133 CCNA_02133 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 288.4 0.0 3.6e-90 3.6e-90 1 315 [] 11 319 .. 11 319 .. 0.95 Alignments for each domain: == domain 1 score: 288.4 bits; conditional E-value: 3.6e-90 TIGR00749 1 lvgdiGGtnarlalvevapgeieqv..ktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvr 71 lvgdiGGtnar+alve ++ + + +y++ed+ e+++ yl++ v +k+p ++ +a+a+Pi v+ lcl|FitnessBrowser__Caulo:CCNA_02133 11 LVGDIGGTNARFALVEFDGQDPRLIepTAYRGEDYGTAEDAIEEYLRK--VGVKHPDQAVVAVAGPIDHGQVH 81 89*************87766666665469*****************85..6789999**************** PP TIGR00749 72 ltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliq 144 +tnldW +s + l++ ++++ +lindf+a+a+a + ++ +dl q+g ++ ++ ailG+GtG+Gva l++ lcl|FitnessBrowser__Caulo:CCNA_02133 82 MTNLDWRISEDGLRRAGGFRNAKLINDFTAQALAAPRVGPKDLRQIGELPTSGEGDLAILGPGTGFGVAGLVR 154 ************************************************************************9 PP TIGR00749 145 qsdgrykvlageGghvdfaPrseleillleylrkky..grvsaervlsGsGlvliyealskrkgerevsklsk 215 +g+ la+eGghv faP ++ ei +l+ l +++ grvs+er+lsG+G+ ++ l ++g r v lcl|FitnessBrowser__Caulo:CCNA_02133 155 -RHGQEIPLATEGGHVAFAPVDDVEIEVLRALTRRLdgGRVSVERILSGPGMEDLHVDLAAAEG-RGV----- 220 .7899999************************999999*********************99993.334..... PP TIGR00749 216 eelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafed 288 e l+ k+i+e+a+eg ++++ +++ f++ilG+ ag++al+lgarGGv++aGGi+Pr+i++l+ks+fr++f+ lcl|FitnessBrowser__Caulo:CCNA_02133 221 EALTAKQITERAVEG-CADSLATVNRFCAILGSTAGDIALTLGARGGVFIAGGIAPRIIDILEKSPFRERFDS 292 566799*******98.778899*************************************************** PP TIGR00749 289 kGrlkellasiPvqvvlkkkvGllGag 315 kGrl + siP +v+l+ ++ l+Ga+ lcl|FitnessBrowser__Caulo:CCNA_02133 293 KGRLSGFTRSIPTHVILHPHTALIGAA 319 *************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (331 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.98 // [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