Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate SMc02835 SMc02835 glucokinase
Query= curated2:B9JYQ5 (340 letters) >FitnessBrowser__Smeli:SMc02835 Length = 339 Score = 457 bits (1177), Expect = e-133 Identities = 225/338 (66%), Positives = 268/338 (79%), Gaps = 1/338 (0%) Query: 4 PHDNDH-MPFPVLVGDIGGTNARFWILMDAHAAPKEFANIHTADFPTIDQAIQDCILDKS 62 P+ ++H PFP+L+GDIGGTNARF +L DA+ PK+ A I T DF TI++A+Q ILDK+ Sbjct: 2 PNASEHSFPFPILIGDIGGTNARFALLTDAYGEPKQLAPIRTGDFATIEEAMQKGILDKT 61 Query: 63 GFQPRSAILAVAGPIKDDEIPLTNCPWVIRPKAMIADLGFDDVLVVNDFEAQALAAASLG 122 QPRSAILAVAGPIK DEIPLTN WVIRPK M+A LG +DVLV+NDFEAQALA A+ Sbjct: 62 SVQPRSAILAVAGPIKGDEIPLTNAGWVIRPKDMLAGLGLEDVLVINDFEAQALAIAAPA 121 Query: 123 RNDREPIGPLTETSLNSRVILGPGTGLGVGGLLYTHHTWFPVPGEGGHVDIGPRSDRDWQ 182 D IG +SRV+LGPGTGLGV GL+Y HTW PVPGEGGHVDIGPR++RD++ Sbjct: 122 DQDVVQIGGGAVRPFHSRVVLGPGTGLGVAGLVYAQHTWIPVPGEGGHVDIGPRTERDFR 181 Query: 183 IFPHIERIEGRISGEQILCGRGILHLYNAICAADGIEPVWTDPADVTQHALKGNDPVCVE 242 I+P +E IEGR++GEQILCGRGI++LY A+CAA+G E V D A VT AL G D VE Sbjct: 182 IWPFLEPIEGRMAGEQILCGRGIMNLYRAVCAANGEEAVLADQAAVTTSALSGADAAAVE 241 Query: 243 TMTLFVTYLGRIAGDMALVFMARGGVFLSGGISQKIIPLLKSPVFRAAFEDKAPHTEMMK 302 T++LF TYLGR+AGDMAL+FMARGGVFL+GGISQKI+P L P FRAAFEDKAPH+ +M+ Sbjct: 242 TVSLFATYLGRVAGDMALIFMARGGVFLAGGISQKILPALTKPEFRAAFEDKAPHSALMR 301 Query: 303 TIPTFVAIHPQAALSGLAAYARTPSSYGVKHEGRRWQR 340 TIPTF IHP AALSGLAA+ARTP +GV EGRRW+R Sbjct: 302 TIPTFAVIHPMAALSGLAAFARTPRDFGVAMEGRRWRR 339 Lambda K H 0.322 0.140 0.445 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: 440 Number of extensions: 11 Number of successful extensions: 1 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: 340 Length of database: 339 Length adjustment: 28 Effective length of query: 312 Effective length of database: 311 Effective search space: 97032 Effective search space used: 97032 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 SMc02835 SMc02835 (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.30585.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-73 232.6 0.1 4.1e-73 232.3 0.1 1.0 1 lcl|FitnessBrowser__Smeli:SMc02835 SMc02835 glucokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc02835 SMc02835 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 232.3 0.1 4.1e-73 4.1e-73 1 313 [. 14 317 .. 14 319 .. 0.95 Alignments for each domain: == domain 1 score: 232.3 bits; conditional E-value: 4.1e-73 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrv.yleeakvelkdpikgcfaiatPiigdfvrltn 74 l+gdiGGtnar+al+ a ge +q+ ++ df +e++++ l+++ v+ p + +a+a+Pi gd + ltn lcl|FitnessBrowser__Smeli:SMc02835 14 LIGDIGGTNARFALLTDAYGEPKQLAPIRTGDFATIEEAMQKgILDKTSVQ---PRSAILAVAGPIKGDEIPLTN 85 79**********************************999987255655554...5679***************** PP TIGR00749 75 ldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqsdgr 149 W + +++ l+l+ + +indf a+a+ai+a ++d++q+gg v + + +lG+GtGlGva l+ ++ lcl|FitnessBrowser__Smeli:SMc02835 86 AGWVIRPKDMLAGLGLEDVLVINDFEAQALAIAAPADQDVVQIGGGAVRPFHSRVVLGPGTGLGVAGLVY-AQHT 159 *********************************************************************9.9*** PP TIGR00749 150 ykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelkekdis 224 + ++geGghvd Pr e ++ ++ +l gr++ e++l G G++++y+a+ ++ge+ v l + ++ lcl|FitnessBrowser__Smeli:SMc02835 160 WIPVPGEGGHVDIGPRTERDFRIWPFLEPIEGRMAGEQILCGRGIMNLYRAVCAANGEEAV--LA----DQAAVT 228 *****************************99*************************98865..44....45679* PP TIGR00749 225 eaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasi 299 +al g d+ a ++++lf + lG++ag++al + arGGv++aGGi ++++ l k fraafedk +l+ +i lcl|FitnessBrowser__Smeli:SMc02835 229 TSALSGADAAAVETVSLFATYLGRVAGDMALIFMARGGVFLAGGISQKILPALTKPEFRAAFEDKAPHSALMRTI 303 *************************************************************************** PP TIGR00749 300 PvqvvlkkkvGllG 313 P v++ + l G lcl|FitnessBrowser__Smeli:SMc02835 304 PTFAVIHPMAALSG 317 *******9998887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (339 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: 00:00:00.00 # Mc/sec: 12.04 // [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