Align 1-phosphofructokinase (characterized)
to candidate WP_013404313.1 CALHY_RS12555 1-phosphofructokinase
Query= CharProtDB::CH_024159 (312 letters) >NCBI__GCF_000166355.1:WP_013404313.1 Length = 315 Score = 176 bits (447), Expect = 5e-49 Identities = 107/307 (34%), Positives = 169/307 (55%), Gaps = 3/307 (0%) Query: 5 VATITLNPAYDLVGFCPEIERGEVNLVKTTGLHAAGKGINVAKVLKDLGIDVTVGGFLGK 64 + T+TLNPA D+ + E+++G+VN + A GKGINV+KV+K LG GFLG Sbjct: 2 IYTVTLNPAIDMTVYIDELKKGQVNRSNHCLIDAGGKGINVSKVIKSLGGKSIALGFLGN 61 Query: 65 DNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEV-TDFNFSGFEVTPADWERFVT 123 DN+D F + + I F V G TR N+K+ E +V TD N +GFEV D + Sbjct: 62 DNKDWFLKYLKNMQIDYDFIFVDGLTRTNIKIVETAQKVYTDLNQNGFEVKKKDIN-LLF 120 Query: 124 DSLSWLGQFDMVCV-SGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAAPW 182 D + + + D + V SGSLP G + + + + L+ + +I+D+ +AL +G+ P Sbjct: 121 DKIDRIAKTDDIFVLSGSLPPGTDEDVYVELIRMLKRKGAKVIYDADGKALESGVLEKPD 180 Query: 183 LVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLGAEGALWVNASGEWIAKP 242 ++KPN E + + ++ ++ +A L E GI V+IS+G++GA++V + E AK Sbjct: 181 VIKPNIHEFKCLFDVEENDLNSIVSSAKKLIENGIKKVLISMGSKGAVFVTENMELFAKA 240 Query: 243 PSVDVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDRPQLAAM 302 V V ST GAGDSMV + YGL +LA A AA VS+ V ++ ++ Sbjct: 241 AEVKVKSTTGAGDSMVAAISYGLSQNMDDVSIFKLALACAAAKVSKEGVKPPEKNEIEGF 300 Query: 303 MARVDLQ 309 + ++ L+ Sbjct: 301 LEKIKLE 307 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: 227 Number of extensions: 13 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_013404313.1 CALHY_RS12555 (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.2438737.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-106 341.5 0.4 2.2e-106 341.3 0.4 1.0 1 NCBI__GCF_000166355.1:WP_013404313.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166355.1:WP_013404313.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 341.3 0.4 2.2e-106 2.2e-106 1 304 [. 2 306 .. 2 307 .. 0.99 Alignments for each domain: == domain 1 score: 341.3 bits; conditional E-value: 2.2e-106 TIGR03828 1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleee 73 I+TvTlNpaiD+t+ ++el+ g+vnr ++ +dagGKGinV++v+k lg +++algflG+++++ + + l++ NCBI__GCF_000166355.1:WP_013404313.1 2 IYTVTLNPAIDMTVYIDELKKGQVNRSNHCLIDAGGKGINVSKVIKSLGGKSIALGFLGNDNKDWFLKYLKNM 74 9************************************************************************ PP TIGR03828 74 giktdfvevkgetRinvkikes.sgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedl 145 +i+ df+ v+g tR+n+ki+e+ ++ t+ln++G+e+++++++ l++k+++ +k++d++vl+GSlP+g +ed+ NCBI__GCF_000166355.1:WP_013404313.1 75 QIDYDFIFVDGLTRTNIKIVETaQKVYTDLNQNGFEVKKKDINLLFDKIDRIAKTDDIFVLSGSLPPGTDEDV 147 **********************9999************************999******************** PP TIGR03828 146 yaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvli 218 y+eli++l++kgakvi D++g+aL ++ +kp++iKPN +E++ l++ e ++ +++++ a+kl+e+g+++vli NCBI__GCF_000166355.1:WP_013404313.1 148 YVELIRMLKRKGAKVIYDADGKALESGVLEKPDVIKPNIHEFKCLFDVEENDLNSIVSSAKKLIENGIKKVLI 220 ************************************************************************* PP TIGR03828 219 slGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpd 291 s+G++Ga++vt++ +lfaka++++vkst+GAGDsmvA++ ++l+++++ +++la+A++aa++s+eg++ p+ NCBI__GCF_000166355.1:WP_013404313.1 221 SMGSKGAVFVTENMELFAKAAEVKVKSTTGAGDSMVAAISYGLSQNMDDVSIFKLALACAAAKVSKEGVKPPE 293 ************************************************************************* PP TIGR03828 292 ledieelleevki 304 +++ie le++k+ NCBI__GCF_000166355.1:WP_013404313.1 294 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 16.25 // [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