Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate WP_086509380.1 BZY95_RS07795 1-phosphofructokinase
Query= reanno::pseudo5_N2C3_1:AO356_07330 (313 letters) >NCBI__GCF_002151265.1:WP_086509380.1 Length = 324 Score = 294 bits (752), Expect = 2e-84 Identities = 170/316 (53%), Positives = 205/316 (64%), Gaps = 4/316 (1%) Query: 1 MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60 MA++LTLTLNPALDL+V L RLEPG VNR+ H AAGKGVNVA+VL LGH +TVSGF Sbjct: 1 MARLLTLTLNPALDLSVSLERLEPGTVNRTHETHLTAAGKGVNVARVLTQLGHDVTVSGF 60 Query: 61 LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120 LG DN F F DAF+RVPGETR N KLAE DGRITD+NGPG +D AA Q L Sbjct: 61 LGADNDGPFLRAFEAMQVEDAFLRVPGETRINAKLAEADGRITDINGPGAAIDEAAWQRL 120 Query: 121 L----ARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVAL 176 L R+ D VV+AGSLP GV+P L L+ R++ GL V +DTSG AL A+ Sbjct: 121 LDGLDTRIGDPRRRPDTVVIAGSLPPGVTPDNLAELVIRLREAGLPVWVDTSGAALDQAI 180 Query: 177 AAGPWLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAA 236 AA P +KPN ELA G + + A+ AA RL+A GIE V+S GA GV W S A Sbjct: 181 AARPTAVKPNELELAAWAGNALDTAEARLTAALRLYAAGIEEAVVSAGAAGVLWVSHRGA 240 Query: 237 LHASPPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTA 296 A PP+VSVASTVGAGD+LLA +LHG++ P+Q LR ATA++A +V +G G Sbjct: 241 WQAMPPRVSVASTVGAGDTLLAALLHGVVCGHPPDQALRLATALSAESVRHLGVGNLHAD 300 Query: 297 LLASLEQGVRVRPLTE 312 L+Q RVR L + Sbjct: 301 DFPQLQQQTRVRRLND 316 Lambda K H 0.317 0.132 0.373 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: 322 Number of extensions: 9 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: 313 Length of database: 324 Length adjustment: 27 Effective length of query: 286 Effective length of database: 297 Effective search space: 84942 Effective search space used: 84942 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_086509380.1 BZY95_RS07795 (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.11409.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-97 311.9 0.0 2.2e-97 311.7 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086509380.1 BZY95_RS07795 1-phosphofructokin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086509380.1 BZY95_RS07795 1-phosphofructokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 311.7 0.0 2.2e-97 2.2e-97 2 304 .. 5 311 .. 4 312 .. 0.98 Alignments for each domain: == domain 1 score: 311.7 bits; conditional E-value: 2.2e-97 TIGR03828 2 lTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeieall 70 lT+TlNpa+D+ ++le+le+g+vnr+++++l a+GKG+nVarvL++lg++v+++gflG+++ ++ + + lcl|NCBI__GCF_002151265.1:WP_086509380.1 5 LTLTLNPALDLSVSLERLEPGTVNRTHETHLTAAGKGVNVARVLTQLGHDVTVSGFLGADNDGPFLRAF 73 7******************************************************************** PP TIGR03828 71 eeegiktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeql....kegdvlvlaG 135 e+ +++++f++v+getRin k++e +g+ t++n+pG++i+e+++++ll+ l++++ ++ d++v+aG lcl|NCBI__GCF_002151265.1:WP_086509380.1 74 EAMQVEDAFLRVPGETRINAKLAEADGRITDINGPGAAIDEAAWQRLLDGLDTRIgdprRRPDTVVIAG 142 ************************************************999988844445679****** PP TIGR03828 136 SlPrgvpedlyaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeeviea 204 SlP+gv++d +ael+ +lre+g++v +Dtsg+aL ++++a+p+ +KPN+ El++++g++l+t e+ ++a lcl|NCBI__GCF_002151265.1:WP_086509380.1 143 SLPPGVTPDNLAELVIRLREAGLPVWVDTSGAALDQAIAARPTAVKPNELELAAWAGNALDTAEARLTA 211 ********************************************************************* PP TIGR03828 205 arkllekgvenvlislGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrl 273 a +l ++g+e++++s Ga+G+l+v++ ga++a +p+++v+stvGAGD+++A++l++++ g+++++alrl lcl|NCBI__GCF_002151265.1:WP_086509380.1 212 ALRLYAAGIEEAVVSAGAAGVLWVSHRGAWQAMPPRVSVASTVGAGDTLLAALLHGVVCGHPPDQALRL 280 ********************************************************************* PP TIGR03828 274 avAvgaaaassegtelpdledieelleevki 304 a+A++a+++ + g++ + +d +l++++++ lcl|NCBI__GCF_002151265.1:WP_086509380.1 281 ATALSAESVRHLGVGNLHADDFPQLQQQTRV 311 **************************99998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (305 nodes) Target sequences: 1 (324 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: 10.29 // [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