Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate RR42_RS37395 RR42_RS37395 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__Cup4G11:RR42_RS37395 Length = 345 Score = 220 bits (560), Expect = 4e-62 Identities = 130/320 (40%), Positives = 180/320 (56%), Gaps = 8/320 (2%) Query: 6 LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYL---EEHKVEVKDGCIA 62 L+GDVGGTN R AL + A I D+PSLEA ++ YL + I Sbjct: 7 LLGDVGGTNVRFAL-ETAPQRIGPVTALKVADFPSLEAAVQHYLGGLPPGSARPRHAAIG 65 Query: 63 IACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGA 122 +A P+TGD V +TNH WAFSI++M+++LG L INDFTA+++ +P L L Sbjct: 66 LANPVTGDRVKLTNHAWAFSISQMQRSLGLDLLLAINDFTALALGLPHLGAHDLTLLRQG 125 Query: 123 EPVEGKPIAVYGAGTGLGVAHLVHVDKR-WVSLPGEGGHVDFAPNSEEEAIILEILRAEI 181 V G P+A+ G GTGLGV+ LV V+L GEGGH++ P +E+E + Sbjct: 126 VAVTGAPLALVGPGTGLGVSGLVPARSGPAVALAGEGGHIELMPQTEDEWTAWRAAQQAF 185 Query: 182 GHVSAERVLSGPGLVNLYRAIVKADNRLP--ENLKPKDITERALADSCTDCRRALSLFCV 239 G VSAER+LSG GL +L A + A+ P L+P ++TE A+ C RAL++FC Sbjct: 186 GRVSAERLLSGMGL-SLTHAALHAETGTPLARQLEPAEVTEGAIHRHDPLCERALAVFCG 244 Query: 240 IMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLI 299 ++G ++AL LG GGV++ GGIVPRF+ + S F A F KGR Y+ +PVY+I Sbjct: 245 LLGSVAADIALVLGARGGVYLGGGIVPRFVPALRNSAFNARFTAKGRLSAYLESLPVYVI 304 Query: 300 VHDNPGLLGSGAHLRQTLGH 319 P L G L + + H Sbjct: 305 NAQYPALPGLAQALEEAITH 324 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: 361 Number of extensions: 20 Number of successful extensions: 5 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: 345 Length adjustment: 28 Effective length of query: 293 Effective length of database: 317 Effective search space: 92881 Effective search space used: 92881 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 RR42_RS37395 RR42_RS37395 (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.14865.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-95 305.3 0.0 3.1e-95 305.0 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS37395 RR42_RS37395 glucokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS37395 RR42_RS37395 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 305.0 0.0 3.1e-95 3.1e-95 1 313 [. 7 313 .. 7 315 .. 0.97 Alignments for each domain: == domain 1 score: 305.0 bits; conditional E-value: 3.1e-95 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdf 69 l+gd+GGtn r+al e ap++i +v +++ dfpslea+v+ yl p ++++ +a P++gd lcl|FitnessBrowser__Cup4G11:RR42_RS37395 7 LLGDVGGTNVRFAL-ETAPQRIGPVTALKVADFPSLEAAVQHYLGGLPPGSARPRHAAIGLANPVTGDR 74 79************.****************************************************** PP TIGR00749 70 vrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlG 138 v+ltn+ Wa+si +++++l+l l indf+a a++++ l+ +dl+ l ++++a+ a++G+GtGlG lcl|FitnessBrowser__Cup4G11:RR42_RS37395 75 VKLTNHAWAFSISQMQRSLGLDLLLAINDFTALALGLPHLGAHDLTLLRQGVAVTGAPLALVGPGTGLG 143 ************************************************999999*************** PP TIGR00749 139 vatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkge 207 v+ l++ g ++lageGgh+++ P+ e e+ ++ +++ +grvsaer+lsG+Gl l + al+ + g lcl|FitnessBrowser__Cup4G11:RR42_RS37395 144 VSGLVPARSGPAVALAGEGGHIELMPQTEDEWTAWRAAQQAFGRVSAERLLSGMGLSLTHAALHAETGT 212 ************************************************************999888854 PP TIGR00749 208 revsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiel 276 l +l++ +++e a++ +d+l++ral +f+++lG++a+++al lgarGGvy+ GGivPrf++ lcl|FitnessBrowser__Cup4G11:RR42_RS37395 213 ----PLA-RQLEPAEVTEGAIHRHDPLCERALAVFCGLLGSVAADIALVLGARGGVYLGGGIVPRFVPA 276 ....455.5678********************************************************* PP TIGR00749 277 lkkssfraafedkGrlkellasiPvqvvlkkkvGllG 313 l++s+f a+f kGrl ++l+s+Pv+v+ + + l G lcl|FitnessBrowser__Cup4G11:RR42_RS37395 277 LRNSAFNARFTAKGRLSAYLESLPVYVINAQYPALPG 313 ****************************999988877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (345 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: 9.33 // [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