Align 1-phosphofructokinase; EC 2.7.1.56; Fructose 1-phosphate kinase (uncharacterized)
to candidate WP_073039722.1 BUB04_RS11760 1-phosphofructokinase
Query= curated2:O51575 (307 letters) >NCBI__GCF_900129305.1:WP_073039722.1 Length = 312 Score = 188 bits (478), Expect = 1e-52 Identities = 107/307 (34%), Positives = 171/307 (55%), Gaps = 5/307 (1%) Query: 1 MIYTLTLNPSVDYKIVLKEFQEESLNYALNNNFFAGGKGINVSTVLKNLGKPSTALGFLG 60 MIYT+TLNP++D +V+ E+ ++AGGKGI+VS V++ L S ALGF+G Sbjct: 1 MIYTVTLNPALDRTLVVDRLVEDDTVRIRKETYYAGGKGIDVSRVIRELEGHSVALGFVG 60 Query: 61 GFTGDYIRFSLDSRGIKNDFIKIKYDTRLNI--KMIANGRETEINANSPDISENEFELLK 118 G+ G ++ L + G+ DF++I +TR NI K GR+ ++A P++ E L Sbjct: 61 GYDGSHLEGLLINAGVLTDFVRIGGETRTNIIVKEAETGRQFVLSAGGPEVRAAEIGELY 120 Query: 119 NKLKNLANNSTLVMSGSVPAALGEDAYNEIANSI-SNDVKLIIDTSGKPLRKILRLNPFL 177 +++ L + +V+SGS+P + + Y ++ + +++D G+ LR+ L P Sbjct: 121 HQILRLPDMEYMVLSGSLPRGVSPNVYGQLVLAARKKGAFVMLDADGEALREALNYRPHC 180 Query: 178 IKPNIYELEDLFNAKFDSTKELIKIGKNLVESGVQNIIISMGSDGAIFIGGKNVAFRAFV 237 IKPN +EL L S +E++ + + GV +++S G DG I G + A +A Sbjct: 181 IKPNRHELSRLVGRDVSSQEEILAACREIHRRGVPLVLVSRGKDGLILSGAEGPAIQAVG 240 Query: 238 PKINFVSTIGAGDSVIAGFVYAFDNGSTLEDSFKFGVAAGTATALK--GNLCEFQDVKKM 295 P + ST+GAGDS +AGF+ A +LE+ + AAGTATA+ LC Q V+++ Sbjct: 241 PAVQVDSTVGAGDSAVAGFILAHSRRQSLEECVRLACAAGTATAMTPGTELCHRQTVEEL 300 Query: 296 LCQIRVE 302 L QI VE Sbjct: 301 LPQIAVE 307 Lambda K H 0.317 0.137 0.381 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: 208 Number of extensions: 8 Number of successful extensions: 3 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: 307 Length of database: 312 Length adjustment: 27 Effective length of query: 280 Effective length of database: 285 Effective search space: 79800 Effective search space used: 79800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
Align candidate WP_073039722.1 BUB04_RS11760 (1-phosphofructokinase)
to HMM TIGR03828 (pfkB: 1-phosphofructokinase (EC 2.7.1.56))
# 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/TIGR03828.hmm # target sequence database: /tmp/gapView.27737.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03828 [M=305] Accession: TIGR03828 Description: pfkB: 1-phosphofructokinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-101 324.9 0.0 2.5e-101 324.7 0.0 1.0 1 lcl|NCBI__GCF_900129305.1:WP_073039722.1 BUB04_RS11760 1-phosphofructokin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900129305.1:WP_073039722.1 BUB04_RS11760 1-phosphofructokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 324.7 0.0 2.5e-101 2.5e-101 1 305 [] 2 307 .. 2 307 .. 0.99 Alignments for each domain: == domain 1 score: 324.7 bits; conditional E-value: 2.5e-101 TIGR03828 1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeieal 69 I+TvTlNpa+D+t+ +++l + + r+++e + agGKGi+V+rv+++l+ ++valgf+Gg g+++e l lcl|NCBI__GCF_900129305.1:WP_073039722.1 2 IYTVTLNPALDRTLVVDRLVEDDTVRIRKETYYAGGKGIDVSRVIRELEGHSVALGFVGGYDGSHLEGL 70 9******************************************************************** PP TIGR03828 70 leeegiktdfvevkgetRinvkikes.sgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSl 137 l + g+ tdfv++ getR+n+ +ke +g+++ l + Gpe++++e+ +l++++ +l++ +++vl+GSl lcl|NCBI__GCF_900129305.1:WP_073039722.1 71 LINAGVLTDFVRIGGETRTNIIVKEAeTGRQFVLSAGGPEVRAAEIGELYHQIL-RLPDMEYMVLSGSL 138 ******************************************************.9************* PP TIGR03828 138 PrgvpedlyaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaar 206 Prgv++++y +l+ ++r+kga v+lD++geaL+++l+++p++iKPN++El++l+gr+++++ee++ a r lcl|NCBI__GCF_900129305.1:WP_073039722.1 139 PRGVSPNVYGQLVLAARKKGAFVMLDADGEALREALNYRPHCIKPNRHELSRLVGRDVSSQEEILAACR 207 ********************************************************************* PP TIGR03828 207 kllekgvenvlislGadGallvtkeg.alfakapkievkstvGAGDsmvAgfllalekglsleealrla 274 +++++gv vl+s+G+dG +l +eg a++a +p+++v stvGAGDs+vAgf+la+++ +slee++rla lcl|NCBI__GCF_900129305.1:WP_073039722.1 208 EIHRRGVPLVLVSRGKDGLILSGAEGpAIQAVGPAVQVDSTVGAGDSAVAGFILAHSRRQSLEECVRLA 276 **********************99954899999************************************ PP TIGR03828 275 vAvgaaaassegtelpdledieelleevkie 305 A+g+a+a+++gtel++++ +eell+++ +e lcl|NCBI__GCF_900129305.1:WP_073039722.1 277 CAAGTATAMTPGTELCHRQTVEELLPQIAVE 307 ****************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (305 nodes) Target sequences: 1 (312 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: 7.26 // [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