Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate Ga0059261_0355 Ga0059261_0355 glucokinase, proteobacterial type
Query= curated2:P21908 (324 letters) >FitnessBrowser__Korea:Ga0059261_0355 Length = 323 Score = 407 bits (1045), Expect = e-118 Identities = 199/323 (61%), Positives = 248/323 (76%), Gaps = 1/323 (0%) Query: 1 MEIVAIDIGGTHARFSIAEVSNGRVLSLGEETTFKTAEHASLQLAWERFGEKLGRPLPRA 60 +E+VA+DIGGTHARF+IAEV GRV+S+GE T KTAEH S QLAW+ LGR +PRA Sbjct: 1 VEVVAVDIGGTHARFAIAEVEGGRVVSIGEPVTQKTAEHGSFQLAWQASARALGREMPRA 60 Query: 61 AAIAWAGPVHGEVLKLTNNPWVLRPATLNEKLDIDTHVLINDFGAVAHAVAHMDSSYLDH 120 AAIA A P++ E++KLTNNPW++RP + E+L++D++ LINDFGAV HAVA + S + H Sbjct: 61 AAIAIASPINDELIKLTNNPWIIRPPLIKERLEVDSYSLINDFGAVGHAVAQLPSEHFLH 120 Query: 121 ICGPDEALPSDGVITILGPGTGLGVAHLLRTEG-RYFVIETEGGHIDFAPLDRLEDKILA 179 ICGPD G IT+ GPGTGLGVA + RT Y VI TEGGH+DFAPLD +ED I+ Sbjct: 121 ICGPDAPFAEKGAITVCGPGTGLGVAQVFRTGPLSYHVISTEGGHMDFAPLDGIEDSIVK 180 Query: 180 RLRERFRRVSIERIISGPGLGNIYEALAAIEGVPFSLLDDIKLWQMALEGKDNLAEAALD 239 RLR + RVS ERI++GPG+ IYE LA IEG L+D ++W +A EGKD+LA AALD Sbjct: 181 RLRSTYTRVSAERIVAGPGIVPIYETLAEIEGKRTHRLNDKEIWTLAFEGKDSLAMAALD 240 Query: 240 RFCLSLGAIAGDLALAQGATSVVIGGGVGLRIASHLPESGFRQRFVSKGRFERVMSKIPV 299 RFCLSLGA+AGDLALA G T VVI GG+GL++ HL SGF QRF++KGRF+ +MS IPV Sbjct: 241 RFCLSLGAVAGDLALAHGPTGVVIAGGLGLKLKDHLVNSGFGQRFIAKGRFQALMSSIPV 300 Query: 300 KLITYPQPGLLGAAAAYANKYSE 322 KLIT+PQPGL GAAAAYA ++++ Sbjct: 301 KLITHPQPGLYGAAAAYAQEHTQ 323 Lambda K H 0.320 0.139 0.411 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: 431 Number of extensions: 17 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: 324 Length of database: 323 Length adjustment: 28 Effective length of query: 296 Effective length of database: 295 Effective search space: 87320 Effective search space used: 87320 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: 48 (23.1 bits)
Align candidate Ga0059261_0355 Ga0059261_0355 (glucokinase, proteobacterial type)
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.27195.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-75 240.2 0.0 2e-75 240.0 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0355 Ga0059261_0355 glucokinase, prot Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0355 Ga0059261_0355 glucokinase, proteobacterial type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 240.0 0.0 2e-75 2e-75 2 315 .] 5 314 .. 4 314 .. 0.91 Alignments for each domain: == domain 1 score: 240.0 bits; conditional E-value: 2e-75 TIGR00749 2 vgdiGGtnarlalvevapgeieqv...ktyssedfpsleavvrvyleeakvelkd..pikgcfaiatPi 65 + diGGt+ar+a+ ev g++ ++ t ++ ++ s++ + + ++ l+ p +++aia+Pi lcl|FitnessBrowser__Korea:Ga0059261_0355 5 AVDIGGTHARFAIAEVEGGRVVSIgepVTQKTAEHGSFQLAWQ----ASARALGRemPRAAAIAIASPI 69 57*******************9997555566666666655444....444444442477********** PP TIGR00749 66 igdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlgg..akveesaaiailG 132 +++++ltn+ W + +k+ l + lindf av+ a++ l +e++ + g a+ e++ai++ G lcl|FitnessBrowser__Korea:Ga0059261_0355 70 NDELIKLTNNPWIIRPPLIKERLEVDSYSLINDFGAVGHAVAQLPSEHFLHICGpdAPFAEKGAITVCG 138 **************************************************99885578899******** PP TIGR00749 133 aGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyeal 201 +GtGlGva++ + + +y+v+++eGgh dfaP + e +++ lr+ y rvsaer+++G+G+v iye l lcl|FitnessBrowser__Korea:Ga0059261_0355 139 PGTGLGVAQVFRTGPLSYHVISTEGGHMDFAPLDGIEDSIVKRLRSTYTRVSAERIVAGPGIVPIYETL 207 ********************************************************************* PP TIGR00749 202 skrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGiv 270 + +g+r + l++k+i a+eg+d+la al+ f+ lGa+ag+lal g+ Gv +aGG+ lcl|FitnessBrowser__Korea:Ga0059261_0355 208 AEIEGKR-THR-----LNDKEIWTLAFEGKDSLAMAALDRFCLSLGAVAGDLALAHGPT-GVVIAGGLG 269 *999655.345.....5599*************************************97.588****** PP TIGR00749 271 PrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 ++ ++l +s+f ++f kGr+++l++siPv+++ + ++Gl Ga+ lcl|FitnessBrowser__Korea:Ga0059261_0355 270 LKLKDHLVNSGFGQRFIAKGRFQALMSSIPVKLITHPQPGLYGAA 314 *******************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (323 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: 8.96 // [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