Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_012970537.1 ALVIN_RS06545 glucokinase
Query= curated2:B2J224 (341 letters) >NCBI__GCF_000025485.1:WP_012970537.1 Length = 326 Score = 233 bits (595), Expect = 4e-66 Identities = 144/332 (43%), Positives = 185/332 (55%), Gaps = 14/332 (4%) Query: 4 LLAGDIGGTKTILQLVETSDSQGLHTIYQESYHSADFPDLVPIVQQFLIKANTPIPEKAC 63 LL GDIGGTKT L L ET D + Y SA F L IVQ++L++ A Sbjct: 3 LLVGDIGGTKTALGLAET-DGGSVRLGETRRYPSASFGSLDQIVQRYLLETGATC-RFAV 60 Query: 64 FAIAGPIVKNTAKLTNLAWFLDTERLQQELGIPHIYLINDFAAVGYGISGLQKQDLHPLQ 123 FA+AGPI + TNL W LD E L+Q LG+ + L+ND AV +G+ L DL L Sbjct: 61 FAVAGPIHDRRCETTNLPWVLDAEALEQSLGLTCVELLNDLEAVAWGVPILSSDDLAELH 120 Query: 124 VGKPQPETPIGIIGAGTGLGQGFLIKQGNNYQVFPSEGGHADFAPRNEIEFQLLKYLLDK 183 G P + ++ AGTGLGQ L G + F +EGGH+DFAP +++EF LL YL K Sbjct: 121 PGDPCSQGNACVVAAGTGLGQAGLFWDGLRHHAFATEGGHSDFAPADDLEFALLTYL--K 178 Query: 184 HDIQRISVERVVSGMGIVAIYQFLRDRKFAAESPDIAQIVRTWEQEAGQEEKSVDPGAAI 243 R+S ERVVSG GIV ++ FLR + ++PD Q V + D A I Sbjct: 179 SRFGRVSWERVVSGPGIVNLFDFLRFH-HSVQAPDWLQAV---------IDTGGDTAATI 228 Query: 244 GTAALEKRDRLSEQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIAPKILPLIQNSGFL 303 AA + R L +TL LF+ YG EAGN ALK + GG+Y+ GGIA K L ++ GFL Sbjct: 229 AQAAADDRCPLCRETLNLFMRLYGREAGNAALKHMALGGVYLGGGIALKNLACLRRGGFL 288 Query: 304 LNFTQKGRMRPLLEEIPVYIILNPQVGLIGAA 335 F KGRM L+ +PV +IL P L+GAA Sbjct: 289 EGFFDKGRMGSLMRRMPVRVILQPNTPLLGAA 320 Lambda K H 0.320 0.140 0.408 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: 282 Number of extensions: 17 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: 341 Length of database: 326 Length adjustment: 28 Effective length of query: 313 Effective length of database: 298 Effective search space: 93274 Effective search space used: 93274 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 WP_012970537.1 ALVIN_RS06545 (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.18470.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-87 278.9 0.0 3.2e-87 278.7 0.0 1.0 1 lcl|NCBI__GCF_000025485.1:WP_012970537.1 ALVIN_RS06545 glucokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025485.1:WP_012970537.1 ALVIN_RS06545 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 278.7 0.0 3.2e-87 3.2e-87 1 315 [] 4 320 .. 4 320 .. 0.93 Alignments for each domain: == domain 1 score: 278.7 bits; conditional E-value: 3.2e-87 TIGR00749 1 lvgdiGGtnarlalvevapgeieqv..ktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiig 67 lvgdiGGt++ l+l e g ++ + y s f sl ++v+ yl e+ + + + fa+a+Pi + lcl|NCBI__GCF_000025485.1:WP_012970537.1 4 LVGDIGGTKTALGLAETDGGSVRLGetRRYPSASFGSLDQIVQRYLLETGATCRF---AVFAVAGPIHD 69 89*************99999999773366999*****************999998...*********** PP TIGR00749 68 dfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtG 136 ++ tnl W l e l+q+l+l+ +el+nd+ ava++++ l ++dl+ l ++ ++ ++ aGtG lcl|NCBI__GCF_000025485.1:WP_012970537.1 70 RRCETTNLPWVLDAEALEQSLGLTCVELLNDLEAVAWGVPILSSDDLAELHPGDPCSQGNACVVAAGTG 138 ***************************************************99999999999******* PP TIGR00749 137 lGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrk 205 lG+a l r++++a+eGgh dfaP ++le+ ll yl++++grvs erv+sG+G+v+++++l+ ++ lcl|NCBI__GCF_000025485.1:WP_012970537.1 139 LGQAGLFW-DGLRHHAFATEGGHSDFAPADDLEFALLTYLKSRFGRVSWERVVSGPGIVNLFDFLRFHH 206 *******9.456999***************************************************999 PP TIGR00749 206 gerevsklskeelkekd....iseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGiv 270 + + l+ + d i++aa ++ ++l+r++l+lf+ ++G++agn alk a GGvy+ GGi+ lcl|NCBI__GCF_000025485.1:WP_012970537.1 207 SVQAPDWLQAVIDTGGDtaatIAQAAADDRCPLCRETLNLFMRLYGREAGNAALKHMALGGVYLGGGIA 275 888855554444333334445************************************************ PP TIGR00749 271 PrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 + + l++++f ++f dkGr+++l+ +Pv+v+l+ ++ llGa+ lcl|NCBI__GCF_000025485.1:WP_012970537.1 276 LKNLACLRRGGFLEGFFDKGRMGSLMRRMPVRVILQPNTPLLGAA 320 *******************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (326 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.37 // [ok]
This GapMind analysis is from Sep 24 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