Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate WP_013431307.1 CALKRO_RS12220 1-phosphofructokinase
Query= reanno::psRCH2:GFF3290 (312 letters) >NCBI__GCF_000166775.1:WP_013431307.1 Length = 315 Score = 177 bits (450), Expect = 2e-49 Identities = 103/310 (33%), Positives = 167/310 (53%), Gaps = 1/310 (0%) Query: 4 VLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGFLGE 63 + TVTLNPA+D+TV + L+ G+VNRS+ + A GKG+NV++V+ LG + GFLG Sbjct: 2 IYTVTLNPAIDMTVYIDELKKGQVNRSNHCLIDAGGKGINVSKVIKSLGGKSIALGFLGN 61 Query: 64 GNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEADGRV-TDINGPGLAVSEAQRAELLA 122 N F + +F+ V G TR+N+K+ E +V TD+N G V + L Sbjct: 62 DNKDWFLKYLKDLQLDFDFILVDGLTRTNIKIVETAQKVYTDLNQNGFEVKKKDINLLFE 121 Query: 123 RLKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRDGLATRPWL 182 ++ R+ ++ V++GSLP +D +V+L+ LK G +V D G AL G+ +P + Sbjct: 122 KIDRIAKTDDIFVLSGSLPPSVDEDVYVELIRMLKRKGAKVIYDADGKALESGVLEKPDV 181 Query: 183 IKPNEEELAEARGIELSGSSALAAEAQRLQEEGIEHVVVSQGADGVSWFSPGAALHASPP 242 IKPN E ++ + S++ + A+RL E GI+ V++S GA G + + L A Sbjct: 182 IKPNIHEFKCLFDVDENDLSSIVSSARRLIESGIKKVLISMGAKGAVFVTENMELFAKAA 241 Query: 243 KVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITDTAQLAELQ 302 + +V ST GAGDS++A + +GL + A A AA V + G + ++ Sbjct: 242 EAKVKSTTGAGDSMVAAISYGLSQNMDDISIFKLALACAAAKVSKEGVKAPEKNEIEGFL 301 Query: 303 AAVRLQPLSQ 312 ++L+ L + Sbjct: 302 EKIKLERLGE 311 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: 183 Number of extensions: 7 Number of successful extensions: 2 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: 315 Length adjustment: 27 Effective length of query: 285 Effective length of database: 288 Effective search space: 82080 Effective search space used: 82080 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_013431307.1 CALKRO_RS12220 (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.2182538.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-105 338.2 0.3 2.2e-105 338.0 0.3 1.0 1 NCBI__GCF_000166775.1:WP_013431307.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013431307.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 338.0 0.3 2.2e-105 2.2e-105 1 304 [. 2 306 .. 2 307 .. 0.99 Alignments for each domain: == domain 1 score: 338.0 bits; conditional E-value: 2.2e-105 TIGR03828 1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleee 73 I+TvTlNpaiD+t+ ++el+ g+vnr ++ +dagGKGinV++v+k lg +++algflG+++++ + + l++ NCBI__GCF_000166775.1:WP_013431307.1 2 IYTVTLNPAIDMTVYIDELKKGQVNRSNHCLIDAGGKGINVSKVIKSLGGKSIALGFLGNDNKDWFLKYLKDL 74 9************************************************************************ PP TIGR03828 74 giktdfvevkgetRinvkikes.sgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedl 145 +++ df+ v+g tR+n+ki+e+ ++ t+ln++G+e+++++++ l+ek+++ +k++d++vl+GSlP++v+ed+ NCBI__GCF_000166775.1:WP_013431307.1 75 QLDFDFILVDGLTRTNIKIVETaQKVYTDLNQNGFEVKKKDINLLFEKIDRIAKTDDIFVLSGSLPPSVDEDV 147 **********************9999************************999******************** PP TIGR03828 146 yaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvli 218 y+eli++l++kgakvi D++g+aL ++ +kp++iKPN +E++ l++ + ++ +++++ ar+l+e+g+++vli NCBI__GCF_000166775.1:WP_013431307.1 148 YVELIRMLKRKGAKVIYDADGKALESGVLEKPDVIKPNIHEFKCLFDVDENDLSSIVSSARRLIESGIKKVLI 220 ************************************************************************* PP TIGR03828 219 slGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpd 291 s+Ga+Ga++vt++ +lfaka++ +vkst+GAGDsmvA++ ++l+++++ +++la+A++aa++s+eg+++p+ NCBI__GCF_000166775.1:WP_013431307.1 221 SMGAKGAVFVTENMELFAKAAEAKVKSTTGAGDSMVAAISYGLSQNMDDISIFKLALACAAAKVSKEGVKAPE 293 ************************************************************************* PP TIGR03828 292 ledieelleevki 304 +++ie le++k+ NCBI__GCF_000166775.1:WP_013431307.1 294 KNEIEGFLEKIKL 306 ********99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (305 nodes) Target sequences: 1 (315 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: 19.30 // [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