Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_011317787.1 AVA_RS04715 glucokinase
Query= curated2:B2J224 (341 letters) >NCBI__GCF_000204075.1:WP_011317787.1 Length = 342 Score = 573 bits (1478), Expect = e-168 Identities = 289/342 (84%), Positives = 309/342 (90%), Gaps = 1/342 (0%) Query: 1 MTLLLAGDIGGTKTILQLVETSDSQGLHTIYQESYHSADFPDLVPIVQQFLIKANTPI-P 59 MTLLLAGDIGGTKTIL+LVE S+S LH IY+ESY S DFPDLVP+VQQFL+KAN P P Sbjct: 1 MTLLLAGDIGGTKTILRLVEVSNSSELHNIYEESYQSGDFPDLVPMVQQFLVKANIPSHP 60 Query: 60 EKACFAIAGPIVKNTAKLTNLAWFLDTERLQQELGIPHIYLINDFAAVGYGISGLQKQDL 119 EKACFAIAGP+V NTAKLTNL WFLDTERL QEL IP I LINDFAAVGYGI GL KQDL Sbjct: 61 EKACFAIAGPVVNNTAKLTNLVWFLDTERLAQELSIPFISLINDFAAVGYGIFGLSKQDL 120 Query: 120 HPLQVGKPQPETPIGIIGAGTGLGQGFLIKQGNNYQVFPSEGGHADFAPRNEIEFQLLKY 179 LQ GK Q E PI IIGAGTGLGQGFLIKQGN YQVFPSEGGHADFAPRNE+EFQLLKY Sbjct: 121 FTLQAGKHQTEAPIAIIGAGTGLGQGFLIKQGNQYQVFPSEGGHADFAPRNELEFQLLKY 180 Query: 180 LLDKHDIQRISVERVVSGMGIVAIYQFLRDRKFAAESPDIAQIVRTWEQEAGQEEKSVDP 239 LLDKHDIQR+SVERVVSG G+VAIYQFLRDRK A ESP+IAQ+VRTWEQ+AGQ EK+VDP Sbjct: 181 LLDKHDIQRVSVERVVSGQGVVAIYQFLRDRKLAIESPEIAQVVRTWEQQAGQAEKTVDP 240 Query: 240 GAAIGTAALEKRDRLSEQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIAPKILPLIQN 299 GAAIG AA++ DRLSEQTLQLFI+AYGAEAGNLALKLLPYGGLYIAGGIAPK+LPLI+N Sbjct: 241 GAAIGKAAVQGSDRLSEQTLQLFIDAYGAEAGNLALKLLPYGGLYIAGGIAPKVLPLIEN 300 Query: 300 SGFLLNFTQKGRMRPLLEEIPVYIILNPQVGLIGAALCAARL 341 S FLLNF+QKGRMRPLLEEIPV+IILNPQVGLIGAALCAARL Sbjct: 301 SNFLLNFSQKGRMRPLLEEIPVHIILNPQVGLIGAALCAARL 342 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: 479 Number of extensions: 12 Number of successful extensions: 2 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: 342 Length adjustment: 29 Effective length of query: 312 Effective length of database: 313 Effective search space: 97656 Effective search space used: 97656 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_011317787.1 AVA_RS04715 (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.3793170.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-113 365.6 0.0 1.3e-113 365.4 0.0 1.0 1 NCBI__GCF_000204075.1:WP_011317787.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000204075.1:WP_011317787.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 365.4 0.0 1.3e-113 1.3e-113 1 315 [] 5 336 .. 5 336 .. 0.95 Alignments for each domain: == domain 1 score: 365.4 bits; conditional E-value: 1.3e-113 TIGR00749 1 lvgdiGGtnarlalveva.pgeieqv..ktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfv 70 l+gdiGGt+++l lvev+ + e++++ + y+s dfp+l+++v+++l +a++ +p k+cfaia+P+++++ NCBI__GCF_000204075.1:WP_011317787.1 5 LAGDIGGTKTILRLVEVSnSSELHNIyeESYQSGDFPDLVPMVQQFLVKANIP-SHPEKACFAIAGPVVNNTA 76 79*************99835688888999******************998875.5699*************** PP TIGR00749 71 rltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatli 143 +ltnl W l e+l+qel++ + lindfaav+y+i +l ++dl l++ k +++a+iai+GaGtGlG+ +li NCBI__GCF_000204075.1:WP_011317787.1 77 KLTNLVWFLDTERLAQELSIPFISLINDFAAVGYGIFGLSKQDLFTLQAGKHQTEAPIAIIGAGTGLGQGFLI 149 ************************************************************************* PP TIGR00749 144 qqsdgrykvlageGghvdfaPrseleillleylrkky..grvsaervlsGsGlvliyealskrkgere...vs 211 +q+ ++y+v+++eGgh+dfaPr+ele++ll+yl k +rvs+erv+sG+G+v iy++l+ rk e ++ NCBI__GCF_000204075.1:WP_011317787.1 150 KQG-NQYQVFPSEGGHADFAPRNELEFQLLKYLLDKHdiQRVSVERVVSGQGVVAIYQFLRDRKLAIEspeIA 221 *76.58**************************96665449*********************999665556799 PP TIGR00749 212 klskeelkekd...........iseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrf 273 ++ +++ ++ i +aa++gsd l++++l+lf+ ++Ga+agnlalkl+++GG+y+aGGi+P++ NCBI__GCF_000204075.1:WP_011317787.1 222 QVVRTWEQQAGqaektvdpgaaIGKAAVQGSDRLSEQTLQLFIDAYGAEAGNLALKLLPYGGLYIAGGIAPKV 294 9999998776678999********************************************************* PP TIGR00749 274 iellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 ++l+++s+f +f++kGr++ ll++iPv+++l+ +vGl+Ga+ NCBI__GCF_000204075.1:WP_011317787.1 295 LPLIENSNFLLNFSQKGRMRPLLEEIPVHIILNPQVGLIGAA 336 ****************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (342 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 28.97 // [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