Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_029132791.1 A3GO_RS0106965 glucokinase
Query= curated2:B2J224 (341 letters) >NCBI__GCF_000428045.1:WP_029132791.1 Length = 332 Score = 213 bits (542), Expect = 6e-60 Identities = 129/340 (37%), Positives = 183/340 (53%), Gaps = 17/340 (5%) Query: 4 LLAGDIGGTKTILQLVETSDSQGLHTIYQESYHSADFPDLVPIVQQFLIK-ANTPIPEKA 62 +LAGDIGGT +L+ D+ + SY A +P L+P+++ FL A + Sbjct: 3 ILAGDIGGTHA--RLIYVDDNSDCPVRHSGSYACAGYPGLMPVIESFLSHYAIDKSFDAV 60 Query: 63 CFAIAGPIVKNTAKLTNLAWFLDTERLQQELGIPHIYLINDFAAVGYGISGLQKQDLHPL 122 C A+AGP+ A +TNL W + +RL +LG +++LIND AV + + GLQ + L Sbjct: 61 CLAVAGPVFAGEAVITNLPWEISADRLAAQLGTRNMFLINDLVAVAWAVQGLQPDRIVLL 120 Query: 123 QVGKPQPETP--IGIIGAGTGLGQGFLIKQGNNYQVFPSEGGHADFAPRNEIEFQLLKYL 180 Q G QP TP ++G GTGLG L+ +Y F SE GHA FAP + QLL +L Sbjct: 121 QAGLDQPATPRRAAVVGVGTGLGAAELVWSEGHYTAFSSEAGHAGFAPATVEQEQLLAWL 180 Query: 181 LDKHDIQRISVERVVSGMGIVAIYQFLRDRKFAAESPDIAQIVRTWEQEAGQEEKSVDPG 240 +HD R+SVE ++SG GI +Y+F RD ES +A Q ++ DP Sbjct: 181 HQRHD--RVSVEMLLSGNGIHKLYRFFRDVLGVTESSRVAV----------QIAQADDPA 228 Query: 241 AAIGTAALEKRDRLSEQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIAPKILPLIQNS 300 A I AL D L + L F+E GA G++AL P +Y+AGG+ I PL+Q+ Sbjct: 229 ALISRRALAADDELCTRALACFVEILGAAVGDIALHYFPLNAVYLAGGVVAGIAPLLQDH 288 Query: 301 GFLLNFTQKGRMRPLLEEIPVYIILNPQVGLIGAALCAAR 340 FL T+KG MR L+++ V +I++ GL GA A R Sbjct: 289 RFLHALTRKGPMRTHLQKLSVTLIMSGTAGLDGAVAYARR 328 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: 258 Number of extensions: 17 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: 341 Length of database: 332 Length adjustment: 28 Effective length of query: 313 Effective length of database: 304 Effective search space: 95152 Effective search space used: 95152 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_029132791.1 A3GO_RS0106965 (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.13989.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-72 230.1 0.0 2.3e-72 229.9 0.0 1.0 1 lcl|NCBI__GCF_000428045.1:WP_029132791.1 A3GO_RS0106965 glucokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000428045.1:WP_029132791.1 A3GO_RS0106965 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 229.9 0.0 2.3e-72 2.3e-72 1 314 [. 4 322 .. 4 323 .. 0.94 Alignments for each domain: == domain 1 score: 229.9 bits; conditional E-value: 2.3e-72 TIGR00749 1 lvgdiGGtnarlalv.evapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigd 68 l+gdiGGt+arl v + + ++ y + +p l +v+ +l++ ++ c+a+a+P+ lcl|NCBI__GCF_000428045.1:WP_029132791.1 4 LAGDIGGTHARLIYVdDNSDCPVRHSGSYACAGYPGLMPVIESFLSHYAIDKSF-DAVCLAVAGPVFAG 71 79*************7788899************************99876443.478*********** PP TIGR00749 69 fvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaa..iailGaGt 135 +tnl W++s ++l+ +l+ +++ lind++ava+a+++l+ + ++ l++ +++++ a++G Gt lcl|NCBI__GCF_000428045.1:WP_029132791.1 72 EAVITNLPWEISADRLAAQLGTRNMFLINDLVAVAWAVQGLQPDRIVLLQAGLDQPATPrrAAVVGVGT 140 ***********************************************9999866666652279****** PP TIGR00749 136 GlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskr 204 GlG a l+ s+g+y ++++e gh+ faP ++ +ll +l+++ +rvs+e +lsG G+ +y++++ lcl|NCBI__GCF_000428045.1:WP_029132791.1 141 GLGAAELVW-SEGHYTAFSSEAGHAGFAPATVEQEQLLAWLHQRHDRVSVEMLLSGNGIHKLYRFFRDV 208 ********9.*********************************************************** PP TIGR00749 205 kgerevsklskeelkekd....iseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGi 269 g e s++ + + d is++al+ +d l+ ral f+ ilGa g++al+ + vy+aGG+ lcl|NCBI__GCF_000428045.1:WP_029132791.1 209 LGVTESSRVAVQIAQADDpaalISRRALAADDELCTRALACFVEILGAAVGDIALHYFPLNAVYLAGGV 277 *****88888666666667778*********************************************** PP TIGR00749 270 vPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGa 314 v + +ll+ f a+ kG ++++l+++ v +++ ++Gl+Ga lcl|NCBI__GCF_000428045.1:WP_029132791.1 278 VAGIAPLLQDHRFLHALTRKGPMRTHLQKLSVTLIMSGTAGLDGA 322 ********************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (332 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: 6.76 // [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