Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_011384511.1 AMB_RS10655 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >NCBI__GCF_000009985.1:WP_011384511.1 Length = 321 Score = 259 bits (663), Expect = 5e-74 Identities = 146/311 (46%), Positives = 183/311 (58%), Gaps = 4/311 (1%) Query: 1 MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHK--VEVKD 58 M++ LV D+GGT+AR AL GE DY I+ YL EH V K Sbjct: 1 MSQMVLVADIGGTHARFALMG-PDGEAVNPVVLRCADYDGPAPAIKAYLAEHAGGVAPKG 59 Query: 59 GCIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQ 118 G A+A I GD + +TN W FSIAE ++ +G LE++NDFTAV++++ LK EHL+ Sbjct: 60 GAFAVASVIDGDRIELTNSPWRFSIAETRQAVGLQRLEVVNDFTAVALSVRHLKPEHLMS 119 Query: 119 FGGAEPVEGKPIAVYGAGTGLGVAHLV-HVDKRWVSLPGEGGHVDFAPNSEEEAIILEIL 177 GG P G PIAV G GTGLGV+ L+ W +L EGGHV A +E EA IL+ L Sbjct: 120 VGGGMPEAGLPIAVLGPGTGLGVSALIPSASGEWTALATEGGHVTMAAATEREARILDRL 179 Query: 178 RAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLF 237 R + HVSAERVLSG GLVNLY+A+ P IT+R L SC R A+ +F Sbjct: 180 RTQFDHVSAERVLSGQGLVNLYQAVAALSGHQAVFSTPDVITKRGLDGSCPVSREAVEVF 239 Query: 238 CVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVY 297 +MG GNLAL+LG GGVFIAGGI+PR E F+ S FR FE GRF+ Y+ IP + Sbjct: 240 FAMMGTVAGNLALSLGAKGGVFIAGGILPRMAEAFRLSSFRTRFEAHGRFQPYLAAIPTW 299 Query: 298 LIVHDNPGLLG 308 LI H P +G Sbjct: 300 LITHPLPAFVG 310 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: 324 Number of extensions: 20 Number of successful extensions: 3 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: 321 Length adjustment: 28 Effective length of query: 293 Effective length of database: 293 Effective search space: 85849 Effective search space used: 85849 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 WP_011384511.1 AMB_RS10655 (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.23292.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-97 311.1 0.0 5.2e-97 310.8 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011384511.1 AMB_RS10655 glucokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011384511.1 AMB_RS10655 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 310.8 0.0 5.2e-97 5.2e-97 1 313 [. 6 310 .. 6 313 .. 0.95 Alignments for each domain: == domain 1 score: 310.8 bits; conditional E-value: 5.2e-97 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdf 69 lv+diGGt+ar+al+ +++ ++++ d++ ++++ yl e++ + p g+fa+a+ i gd lcl|NCBI__GCF_000009985.1:WP_011384511.1 6 LVADIGGTHARFALMGPDGEAVNP-VVLRCADYDGPAPAIKAYLAEHAGGVA-PKGGAFAVASVIDGDR 72 89************6655555555.59*********************9986.689************* PP TIGR00749 70 vrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlG 138 ++ltn W +si+e++q ++l++le++ndf+ava+++ lk e+l+ +gg +e + +ia+lG+GtGlG lcl|NCBI__GCF_000009985.1:WP_011384511.1 73 IELTNSPWRFSIAETRQAVGLQRLEVVNDFTAVALSVRHLKPEHLMSVGGGMPEAGLPIAVLGPGTGLG 141 ********************************************************************* PP TIGR00749 139 vatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkge 207 v+ li+ + g + +la+eGghv +a e e+ +l+ lr+++++vsaervlsG+Glv++y+a+ g+ lcl|NCBI__GCF_000009985.1:WP_011384511.1 142 VSALIPSASGEWTALATEGGHVTMAAATEREARILDRLRTQFDHVSAERVLSGQGLVNLYQAVAALSGH 210 ***************************************************************999976 PP TIGR00749 208 revsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiel 276 + v ++ i+++ l+gs++++r+a+e+f +++G++agnlal lga+GGv++aGGi+Pr+ e lcl|NCBI__GCF_000009985.1:WP_011384511.1 211 QAV------FSTPDVITKRGLDGSCPVSREAVEVFFAMMGTVAGNLALSLGAKGGVFIAGGILPRMAEA 273 654......45899******************************************************* PP TIGR00749 277 lkkssfraafedkGrlkellasiPvqvvlkkkvGllG 313 ++ ssfr +fe Gr++ +la iP ++ + + ++G lcl|NCBI__GCF_000009985.1:WP_011384511.1 274 FRLSSFRTRFEAHGRFQPYLAAIPTWLITHPLPAFVG 310 ****************************998777666 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (321 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: 6.89 // [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