Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate GFF3782 HP15_3724 1-phosphofructokinase
Query= reanno::psRCH2:GFF3290 (312 letters) >FitnessBrowser__Marino:GFF3782 Length = 321 Score = 271 bits (694), Expect = 1e-77 Identities = 147/309 (47%), Positives = 189/309 (61%) Query: 1 MARVLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGF 60 MAR+LT+TLNPALDL+V+ L LGEVNR+ + AGKG+NVA+VLA LGH +TV G Sbjct: 1 MARILTITLNPALDLSVETAPLALGEVNRTGHTLMEPAGKGINVARVLARLGHSVTVAGL 60 Query: 61 LGEGNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEADGRVTDINGPGLAVSEAQRAEL 120 LG+ N FE+LF A G D FVRV G+ R+N+K+AEA GRVTD+NGPG E L Sbjct: 61 LGDANAAPFERLFEAEGLQDSFVRVPGQNRNNIKIAEAGGRVTDLNGPGFRAPEDALQRL 120 Query: 121 LARLKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRDGLATRP 180 RLK L+P + VV+ GSLP G L+ V LDTSGA L+ G+ P Sbjct: 121 QLRLKSLLPECDAVVIGGSLPDGFPPSGLAILVEQASRADKPVWLDTSGAGLKAGIKAGP 180 Query: 181 WLIKPNEEELAEARGIELSGSSALAAEAQRLQEEGIEHVVVSQGADGVSWFSPGAALHAS 240 + IKPN +EL++ G L +++AA ++ G+ HVVVS GADGV W SP L + Sbjct: 181 YAIKPNTDELSDWAGTPLKDLASVAATVDGIRAGGVSHVVVSMGADGVFWSSPAGILRSR 240 Query: 241 PPKVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITDTAQLAE 300 P V +VSTV AGD+LLAGMLHG+L + L ATA++A+ V +G G Sbjct: 241 VPPVSLVSTVCAGDTLLAGMLHGVLGEQSEDTVLAFATALSAECVQHIGVGDPGAPDFHS 300 Query: 301 LQAAVRLQP 309 L R+QP Sbjct: 301 LLQQTRVQP 309 Lambda K H 0.316 0.132 0.371 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: 292 Number of extensions: 6 Number of successful extensions: 1 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: 312 Length of database: 321 Length adjustment: 27 Effective length of query: 285 Effective length of database: 294 Effective search space: 83790 Effective search space used: 83790 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 GFF3782 HP15_3724 (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.13037.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-93 298.0 0.0 3.7e-93 297.8 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF3782 HP15_3724 1-phosphofructokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF3782 HP15_3724 1-phosphofructokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 297.8 0.0 3.7e-93 3.7e-93 1 304 [. 4 307 .. 4 308 .. 0.99 Alignments for each domain: == domain 1 score: 297.8 bits; conditional E-value: 3.7e-93 TIGR03828 1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleeegi 75 IlT+TlNpa+D+ +e+ l lgevnr+ ++ ++++GKGinVarvL++lg++v++ g+lG ++++++e+l+e+eg+ lcl|FitnessBrowser__Marino:GFF3782 4 ILTITLNPALDLSVETAPLALGEVNRTGHTLMEPAGKGINVARVLARLGHSVTVAGLLGDANAAPFERLFEAEGL 78 89************************************************************************* PP TIGR03828 76 ktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedlyaeli 150 ++ fv+v+g+ R n+ki+e g++t+ln+pG++ e++l++l+ +l++ l+e+d +v++GSlP g p++ +a l+ lcl|FitnessBrowser__Marino:GFF3782 79 QDSFVRVPGQNRNNIKIAEAGGRVTDLNGPGFRAPEDALQRLQLRLKSLLPECDAVVIGGSLPDGFPPSGLAILV 153 *************************************************************************** PP TIGR03828 151 kllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvlislGadGa 225 +++ +++++v lDtsg+ L +++ka p+ iKPN++El++++g+ lk+ ++v ++ +++ gv++v++s+GadG+ lcl|FitnessBrowser__Marino:GFF3782 154 EQASRADKPVWLDTSGAGLKAGIKAGPYAIKPNTDELSDWAGTPLKDLASVAATVDGIRAGGVSHVVVSMGADGV 228 *************************************************************************** PP TIGR03828 226 llvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpdledieelle 300 ++ ++ g l+ + p ++++stv+AGD+++Ag+l+++ ++s++++l++a+A++a+ +++ g++ p d ++ll+ lcl|FitnessBrowser__Marino:GFF3782 229 FWSSPAGILRSRVPPVSLVSTVCAGDTLLAGMLHGVLGEQSEDTVLAFATALSAECVQHIGVGDPGAPDFHSLLQ 303 *************************************************************99888899999999 PP TIGR03828 301 evki 304 ++++ lcl|FitnessBrowser__Marino:GFF3782 304 QTRV 307 9887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (305 nodes) Target sequences: 1 (321 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: 9.15 // [ok]
This GapMind analysis is from Sep 17 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