Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_057508150.1 ABB28_RS08110 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >NCBI__GCF_001431535.1:WP_057508150.1 Length = 335 Score = 242 bits (617), Expect = 1e-68 Identities = 140/315 (44%), Positives = 178/315 (56%), Gaps = 9/315 (2%) Query: 6 LVGDVGGTNARLALCDIASGEI---SQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIA 62 LV D+GGTNAR AL D A + + +D+PSL R YL+E E G A Sbjct: 9 LVADIGGTNARFALADTADSSPLLEDSIREFPVVDFPSLGDAARHYLQEVDAEASRGVFA 68 Query: 63 IACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGA 122 +A + GD +TNH W S + LGFS L +INDF A +MAI +L+ + ++Q GGA Sbjct: 69 VAGRVDGDEARITNHPWVISRSRTAAMLGFSELHLINDFAAQAMAISLLQPKDVVQIGGA 128 Query: 123 E---PVEGKPI--AVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEIL 177 G P V G GTGLGV LV R L EGGHV F P + EE ILEIL Sbjct: 129 SWSPRRSGAPANYGVIGPGTGLGVGGLVIRHDRCFPLETEGGHVSFPPGTPEEIRILEIL 188 Query: 178 RAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLF 237 G VS ER++ GPGLVN++RA+ + P +LKP D+T RA A RA+ LF Sbjct: 189 SETFGRVSNERLICGPGLVNIHRAVCEMAGFDPGHLKPADVTARAGAGD-PQAMRAVDLF 247 Query: 238 CVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVY 297 C I G G+L L G + GVF+ GG+VPR LE + SGFR FE KGRF + +P Sbjct: 248 CAIFGAIAGDLVLIQGAWDGVFLTGGLVPRMLESLQHSGFRQRFEHKGRFSSIMGRVPSL 307 Query: 298 LIVHDNPGLLGSGAH 312 ++H NPGLLG+ A+ Sbjct: 308 AVIHPNPGLLGAAAY 322 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: 346 Number of extensions: 15 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: 321 Length of database: 335 Length adjustment: 28 Effective length of query: 293 Effective length of database: 307 Effective search space: 89951 Effective search space used: 89951 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 WP_057508150.1 ABB28_RS08110 (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.12899.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-87 277.6 0.0 8.2e-87 277.3 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057508150.1 ABB28_RS08110 glucokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057508150.1 ABB28_RS08110 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 277.3 0.0 8.2e-87 8.2e-87 1 315 [] 9 320 .. 9 320 .. 0.93 Alignments for each domain: == domain 1 score: 277.3 bits; conditional E-value: 8.2e-87 TIGR00749 1 lvgdiGGtnarlalv...evapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPii 66 lv+diGGtnar+al +++p + ++++ + dfpsl ++ r yl+e e g fa+a+ + lcl|NCBI__GCF_001431535.1:WP_057508150.1 9 LVADIGGTNARFALAdtaDSSPLLEDSIREFPVVDFPSLGDAARHYLQEVDAEASR---GVFAVAGRVD 74 89************98888999999**************************99988...********** PP TIGR00749 67 gdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakvee..saaia...i 130 gd r+tn+ W +s +++ l++++l+lindfaa+a+ai+ l+ +d++q+gga + s+a a + lcl|NCBI__GCF_001431535.1:WP_057508150.1 75 GDEARITNHPWVISRSRTAAMLGFSELHLINDFAAQAMAISLLQPKDVVQIGGASWSPrrSGAPAnygV 143 *****************************************************9866511444333449 PP TIGR00749 131 lGaGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliye 199 +G+GtGlGv l+ + +r l +eGghv+f P ++ei +le+l + +grvs er++ G+Glv+i++ lcl|NCBI__GCF_001431535.1:WP_057508150.1 144 IGPGTGLGVGGLVIRH-DRCFPLETEGGHVSFPPGTPEEIRILEILSETFGRVSNERLICGPGLVNIHR 211 99*********99955.566689********************************************** PP TIGR00749 200 alskrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGG 268 a+ + + +lk+ d++ +a +g+ + a ra++lf++i+Ga+ag+l l ga Gv+++GG lcl|NCBI__GCF_001431535.1:WP_057508150.1 212 AVCEMA------GFDPGHLKPADVTARAGAGD-PQAMRAVDLFCAIFGAIAGDLVLIQGAWDGVFLTGG 273 *98776......5566889*********9996.78999******************************* PP TIGR00749 269 ivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 +vPr++e l++s+fr++fe kGr+ ++++ +P v++ ++GllGa+ lcl|NCBI__GCF_001431535.1:WP_057508150.1 274 LVPRMLESLQHSGFRQRFEHKGRFSSIMGRVPSLAVIHPNPGLLGAA 320 *********************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (335 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.10 // [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