Align 1-phosphofructokinase (characterized)
to candidate BWI76_RS19730 BWI76_RS19730 1-phosphofructokinase
Query= CharProtDB::CH_024159 (312 letters) >FitnessBrowser__Koxy:BWI76_RS19730 Length = 312 Score = 606 bits (1563), Expect = e-178 Identities = 305/312 (97%), Positives = 307/312 (98%) Query: 1 MSRRVATITLNPAYDLVGFCPEIERGEVNLVKTTGLHAAGKGINVAKVLKDLGIDVTVGG 60 MSRRVATITLNPAYDLVGF PEIERGEVNLV+TTGLHAAGKGINVAKVLKDLGIDVTVGG Sbjct: 1 MSRRVATITLNPAYDLVGFTPEIERGEVNLVRTTGLHAAGKGINVAKVLKDLGIDVTVGG 60 Query: 61 FLGKDNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTPADWER 120 FLGKDNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTP DWER Sbjct: 61 FLGKDNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTPGDWER 120 Query: 121 FVTDSLSWLGQFDMVCVSGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAA 180 FV DSLSWLGQFDMVCVSGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAA Sbjct: 121 FVNDSLSWLGQFDMVCVSGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAA 180 Query: 181 PWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLGAEGALWVNASGEWIA 240 PWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLG EGALWVNASGEWIA Sbjct: 181 PWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLGEEGALWVNASGEWIA 240 Query: 241 KPPSVDVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDRPQLA 300 KPPSV+VVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDR QLA Sbjct: 241 KPPSVEVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDRTQLA 300 Query: 301 AMMARVDLQPFN 312 AMMARVDLQPFN Sbjct: 301 AMMARVDLQPFN 312 Lambda K H 0.319 0.135 0.404 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: 505 Number of extensions: 7 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: 312 Length adjustment: 27 Effective length of query: 285 Effective length of database: 285 Effective search space: 81225 Effective search space used: 81225 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate BWI76_RS19730 BWI76_RS19730 (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.1710.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-105 337.7 0.0 3e-105 337.5 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS19730 BWI76_RS19730 1-phosphofructokin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS19730 BWI76_RS19730 1-phosphofructokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 337.5 0.0 3e-105 3e-105 1 304 [. 5 308 .. 5 309 .. 0.99 Alignments for each domain: == domain 1 score: 337.5 bits; conditional E-value: 3e-105 TIGR03828 1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealle 71 ++T+TlNpa+D++ + e+e+gevn v+++ l+a+GKGinVa+vLk+lg++v++ gflG+++++ +++l++ lcl|FitnessBrowser__Koxy:BWI76_RS19730 5 VATITLNPAYDLVGFTPEIERGEVNLVRTTGLHAAGKGINVAKVLKDLGIDVTVGGFLGKDNQDGFQQLFS 75 68********************************************************************* PP TIGR03828 72 eegiktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvp 142 e gi+++f v+g tRinvk++e++ge+t+ n++G+e+++ ++e+++++ + l + d++ ++GSlP+gv+ lcl|FitnessBrowser__Koxy:BWI76_RS19730 76 ELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTPGDWERFVNDSLSWLGQFDMVCVSGSLPSGVS 146 *********************************************************************** PP TIGR03828 143 edlyaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgv 213 ++++ +++ +lr++ +i+D+s eaL ++lka p+l+KPN++Ele ++gr+l + ++vieaa+ l+e+g+ lcl|FitnessBrowser__Koxy:BWI76_RS19730 147 PEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAAPWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGI 217 *********************************************************************** PP TIGR03828 214 envlislGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaass 284 ++v+islG++Gal+v+++g+++ak+p +ev+stvGAGDsmv+g++++l +s e++lrla+Av+a a+s+ lcl|FitnessBrowser__Koxy:BWI76_RS19730 218 AHVVISLGEEGALWVNASGEWIAKPPSVEVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQ 288 *********************************************************************** PP TIGR03828 285 egtelpdledieelleevki 304 ++++++d+ +++++ ++v++ lcl|FitnessBrowser__Koxy:BWI76_RS19730 289 SNVGITDRTQLAAMMARVDL 308 **************999976 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.52 // [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