Align 1-phosphofructokinase; EC 2.7.1.56; Fructose 1-phosphate kinase (uncharacterized)
to candidate WP_009489922.1 C683_RS03170 1-phosphofructokinase
Query= curated2:O31714 (303 letters) >NCBI__GCF_000313915.1:WP_009489922.1 Length = 304 Score = 283 bits (725), Expect = 3e-81 Identities = 139/303 (45%), Positives = 203/303 (66%) Query: 1 MIYTVTLNPSVDYIVHVEDFTVGGLNRSSYDTKYPGGKGINVSRLLKRHHVASKALGFVG 60 MIYT+TLNPS+DY++ ++ +G +NR D K+PGGKGINVSR+L+R + + ALG+VG Sbjct: 1 MIYTITLNPSIDYVIQMDHLELGTVNRMDTDFKFPGGKGINVSRILQRLEIPNTALGYVG 60 Query: 61 GFTGEYIKTFLREENLETAFSEVKGDTRINVKLKTGDETEINGQGPTISDEDFKAFLEQF 120 GFTG +I L +EN+ T F + DTRINVK+K ETEING GP IS+ + + +Q Sbjct: 61 GFTGAFITNELAKENITTDFISIAEDTRINVKIKAQQETEINGAGPMISEAEQQQLFDQL 120 Query: 121 QSLQEGDIVVLAGSIPSSLPHDTYEKIAEACKQQNARVVLDISGEALLKATEMKPFLMKP 180 + + DI+V AGS P +L Y+K+ + ++ A+ V+D +G+ L A +P ++KP Sbjct: 121 SQVTKEDIIVFAGSTPKNLKDGFYQKLIQFVTERGAQFVIDTTGKDLEAALSFRPLVVKP 180 Query: 181 NHHELGEMFGTAITSVEEAVPYGKKLVEQGAEHVIVSMAGDGALLFTNEAVYFANVPKGK 240 N EL E++ T + E+ PY +KL+ +GA+ V++SMAGDGALLF E +YFA K Sbjct: 181 NKDELAELYQTTFETQEDIYPYAQKLMAEGAQQVLISMAGDGALLFEGENIYFAAPLKKP 240 Query: 241 LVNSVGAGDSVVAGFLAGISKQLPLEEAFRLGVTSGSATAFSEELGTEEFVQQLLPEVKV 300 L NSVGAGDS++AGF ++ EAF++GV GSATAFS++L T +F+Q+ EV + Sbjct: 241 LKNSVGAGDSMIAGFTGTYAQTKNPLEAFKMGVACGSATAFSDDLATADFIQECYNEVVI 300 Query: 301 TRL 303 ++ Sbjct: 301 EKI 303 Lambda K H 0.315 0.134 0.372 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: 270 Number of extensions: 8 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: 303 Length of database: 304 Length adjustment: 27 Effective length of query: 276 Effective length of database: 277 Effective search space: 76452 Effective search space used: 76452 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: 42 (22.0 bits) S2: 48 (23.1 bits)
Align candidate WP_009489922.1 C683_RS03170 (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.2375065.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-113 363.0 0.1 6.2e-113 362.8 0.1 1.0 1 NCBI__GCF_000313915.1:WP_009489922.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000313915.1:WP_009489922.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 362.8 0.1 6.2e-113 6.2e-113 1 305 [] 2 301 .. 2 301 .. 0.99 Alignments for each domain: == domain 1 score: 362.8 bits; conditional E-value: 6.2e-113 TIGR03828 1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleee 73 I+T+TlNp+iD++i++++lelg+vnr+ ++ +++gGKGinV+r+L++l+++++alg++Ggftg++i+++l++e NCBI__GCF_000313915.1:WP_009489922.1 2 IYTITLNPSIDYVIQMDHLELGTVNRMDTDFKFPGGKGINVSRILQRLEIPNTALGYVGGFTGAFITNELAKE 74 9************************************************************************ PP TIGR03828 74 giktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedly 146 +i+tdf+ ++++tRinvkik +++et++n++Gp ise+e+++l+++l+ q++++d++v+aGS P+++++ +y NCBI__GCF_000313915.1:WP_009489922.1 75 NITTDFISIAEDTRINVKIK--AQQETEINGAGPMISEAEQQQLFDQLS-QVTKEDIIVFAGSTPKNLKDGFY 144 ********************..8**************************.9********************** PP TIGR03828 147 aelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvlis 219 ++li+ + e+ga++++Dt+g+ L ++l+++pl++KPNk+El+el +++++t+e++ +a+kl+++g+++vlis NCBI__GCF_000313915.1:WP_009489922.1 145 QKLIQFVTERGAQFVIDTTGKDLEAALSFRPLVVKPNKDELAELYQTTFETQEDIYPYAQKLMAEGAQQVLIS 217 ************************************************************************* PP TIGR03828 220 lGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpdl 292 +++dGall++ e+ +fa + k +k++vGAGDsm+Agf+ ++++++++ ea++++vA+g+a+a+s++ l++ NCBI__GCF_000313915.1:WP_009489922.1 218 MAGDGALLFEGENIYFAAPLKKPLKNSVGAGDSMIAGFTGTYAQTKNPLEAFKMGVACGSATAFSDD--LATA 288 *******************************************************************..**** PP TIGR03828 293 edieelleevkie 305 + i+e+++ev ie NCBI__GCF_000313915.1:WP_009489922.1 289 DFIQECYNEVVIE 301 **********986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (305 nodes) Target sequences: 1 (304 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: 14.04 // [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