Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate N515DRAFT_0593 N515DRAFT_0593 glucokinase
Query= curated2:Q2W5F9 (321 letters) >FitnessBrowser__Dyella79:N515DRAFT_0593 Length = 353 Score = 208 bits (530), Expect = 1e-58 Identities = 123/323 (38%), Positives = 175/323 (54%), Gaps = 8/323 (2%) Query: 6 LVADIGGTHARFALMGPDGEAVNPVVL------RCADYDGPAPAIKAYLAEHAGGVAPKG 59 L AD+GGTHAR L+ + PV + CA++ +K ++++ G V Sbjct: 21 LAADVGGTHARIGLVSQRPDGARPVTVLQYHRYACAEWPSLTAVLKDFVSQLGGAVQVDQ 80 Query: 60 GAFAVASVIDGDRIELTNSPWRFSIAETRQAVGLQRLEVVNDFTAVALSVRHLKPEHLMS 119 A A A + GD I N PW SI + R ++G++RL VVNDF AVA + + L Sbjct: 81 CAVASAGYVLGDAIVNDNLPWPVSIRDIRDSLGIERLAVVNDFEAVAYATQFLVHADTTP 140 Query: 120 VGGGMPEAGL-PIAVLGPGTGLGVSALIPSASGEWTALATEGGHVTMAAATEREARILDR 178 V G+ P+ V+GPGTGLG + L+P T LATE G + ++ ERE IL Sbjct: 141 VIEAQTPGGVGPVLVMGPGTGLGSAVLLPGKPHA-TVLATEAGQIALSPGNEREIEILRV 199 Query: 179 LRTQFDHVSAERVLSGQGLVNLYQAVAALSGHQAVFSTPDVITKRGLDGSCPVSREAVEV 238 L + +VS E LSG GL+NLY+A+ L G V + P IT+ LD S + EA+EV Sbjct: 200 LAGERPYVSFEHALSGPGLLNLYRALCVLRGQSPVLAKPSEITRAALDASDAAAVEALEV 259 Query: 239 FFAMMGTVAGNLALSLGAKGGVFIAGGILPRMAEAFRLSSFRTRFEAHGRFQPYLAAIPT 298 F ++G+ G+L L GA+GGVF+AGGILP++ + SSFR RF G + +L +P Sbjct: 260 FCGLLGSFVGDLTLLYGARGGVFLAGGILPQIRDVLLTSSFRERFFNKGVMRAFLQQVPV 319 Query: 299 WLITHPLPAFVGLAGLVTDPKNA 321 L+ H +G AG+ + A Sbjct: 320 RLMEHGQLGVIGAAGMYLEGHTA 342 Lambda K H 0.320 0.136 0.403 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: 379 Number of extensions: 22 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: 353 Length adjustment: 28 Effective length of query: 293 Effective length of database: 325 Effective search space: 95225 Effective search space used: 95225 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: 49 (23.5 bits)
Align candidate N515DRAFT_0593 N515DRAFT_0593 (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.3798.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-72 227.9 0.0 1.1e-71 227.7 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0593 N515DRAFT_0593 glucokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0593 N515DRAFT_0593 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 227.7 0.0 1.1e-71 1.1e-71 1 315 [] 21 333 .. 21 333 .. 0.95 Alignments for each domain: == domain 1 score: 227.7 bits; conditional E-value: 1.1e-71 TIGR00749 1 lvgdiGGtnarlalvevapgeieqv.....ktyssedfpsleavvrvyleeakvelkdpikgcfai 61 l++d+GGt+ar++lv p +++v + y + ++psl+av++ + ++ ++ + ++a lcl|FitnessBrowser__Dyella79:N515DRAFT_0593 21 LAADVGGTHARIGLVSQRPDGARPVtvlqyHRYACAEWPSLTAVLKDFVSQLGGAVQV-DQCAVAS 85 79*************999999999988877889*****************98777765.46889** PP TIGR00749 62 atPiigdfvrltnldWalsieelkqelalaklelindfaavayailalkeedli.qlggakveesa 126 a+ ++gd + nl W +si +++ +l++++l ++ndf avaya + l + d + ++++ + + lcl|FitnessBrowser__Dyella79:N515DRAFT_0593 86 AGYVLGDAIVNDNLPWPVSIRDIRDSLGIERLAVVNDFEAVAYATQFLVHADTTpVIEAQTPGGVG 151 ***********************************************999888747888899999* PP TIGR00749 127 aiailGaGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGs 192 ++ ++G+GtGlG a l++ ++ + vla+e g + ++P +e ei +l++l + vs e lsG+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0593 152 PVLVMGPGTGLGSAVLLP-GKPHATVLATEAGQIALSPGNEREIEILRVLAGERPYVSFEHALSGP 216 ******************.9999******************************************* PP TIGR00749 193 GlvliyealskrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklg 258 Gl ++y+al +g+ v k+ +i++aal+ sd+ a +ale+f+++lG++ g+l+l g lcl|FitnessBrowser__Dyella79:N515DRAFT_0593 217 GLLNLYRALCVLRGQSPV------LAKPSEITRAALDASDAAAVEALEVFCGLLGSFVGDLTLLYG 276 *********998865443......35999************************************* PP TIGR00749 259 arGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 arGGv++aGGi+P++ + l +ssfr++f +kG ++++l+++Pv+++ + + G++Ga+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0593 277 ARGGVFLAGGILPQIRDVLLTSSFRERFFNKGVMRAFLQQVPVRLMEHGQLGVIGAA 333 *******************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (353 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: 9.90 // [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