Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate AO353_05480 AO353_05480 1-phosphofructokinase
Query= reanno::pseudo5_N2C3_1:AO356_07330 (313 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05480 Length = 313 Score = 510 bits (1313), Expect = e-149 Identities = 260/313 (83%), Positives = 279/313 (89%) Query: 1 MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60 MAKILTLTLNPALDLTV+L LEPGQVNRSDAMH HAAGKG+NVAQVLADLGH LTVSGF Sbjct: 1 MAKILTLTLNPALDLTVQLPHLEPGQVNRSDAMHTHAAGKGINVAQVLADLGHQLTVSGF 60 Query: 61 LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120 LGEDN Q FE LFA+RGFVDAFIRVPGETRSNIKLAE DGRITD+NGPGP+V AAAQQAL Sbjct: 61 LGEDNLQAFEALFAKRGFVDAFIRVPGETRSNIKLAEADGRITDINGPGPVVSAAAQQAL 120 Query: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGP 180 L RL+QI GHD VVVAGSLPRGVS QWL L+ R+K+ GL VALDTSGEALR L+AGP Sbjct: 121 LDRLDQITLGHDAVVVAGSLPRGVSAQWLHGLLLRLKSRGLKVALDTSGEALRAGLSAGP 180 Query: 181 WLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHAS 240 WLIKPNTEEL++AL CE +S AQA+AA RLHA GIEHVVISHGA+GVNWFSVG+A+HA+ Sbjct: 181 WLIKPNTEELSEALDCEAISVAAQAEAASRLHAHGIEHVVISHGAEGVNWFSVGSAMHAT 240 Query: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLAS 300 PP+VSV STVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGI D A LA Sbjct: 241 PPRVSVVSTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIGDAAQLAQ 300 Query: 301 LEQGVRVRPLTEQ 313 LEQ VRVR LTEQ Sbjct: 301 LEQEVRVRLLTEQ 313 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: 422 Number of extensions: 15 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: 313 Length of database: 313 Length adjustment: 27 Effective length of query: 286 Effective length of database: 286 Effective search space: 81796 Effective search space used: 81796 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 AO353_05480 AO353_05480 (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.15181.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-107 344.4 0.5 2.8e-107 344.2 0.5 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480 AO353_05480 1-phosphofructokinas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480 AO353_05480 1-phosphofructokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 344.2 0.5 2.8e-107 2.8e-107 1 305 [] 4 308 .. 4 308 .. 0.99 Alignments for each domain: == domain 1 score: 344.2 bits; conditional E-value: 2.8e-107 TIGR03828 1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgee 65 IlT+TlNpa+D+t++l +le+g+vnr +++++a+GKGinVa+vL++lg++ +++gflG+++ + lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480 4 ILTLTLNPALDLTVQLPHLEPGQVNRSDAMHTHAAGKGINVAQVLADLGHQLTVSGFLGEDNLQA 68 89*************************************************************** PP TIGR03828 66 iealleeegiktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdv 130 +eal++++g+ ++f++v+getR+n+k++e +g+ t++n+pGp +s+++++all++l++ + +d lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480 69 FEALFAKRGFVDAFIRVPGETRSNIKLAEADGRITDINGPGPVVSAAAQQALLDRLDQITLGHDA 133 *********************************************************999***** PP TIGR03828 131 lvlaGSlPrgvpedlyaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrel 195 +v+aGSlPrgv+++++ l+ +l+++g+kv+lDtsgeaL+++l+a p+liKPN+eEl+e+l+ e lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480 134 VVVAGSLPRGVSAQWLHGLLLRLKSRGLKVALDTSGEALRAGLSAGPWLIKPNTEELSEALDCEA 198 ***************************************************************** PP TIGR03828 196 kteeevieaarkllekgvenvlislGadGallvtkegalfakapkievkstvGAGDsmvAgflla 260 + ++ eaa +l+++g+e+v+is Ga+G+ +++ a++a++p+++v+stvGAGDs++Ag+l++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480 199 ISVAAQAEAASRLHAHGIEHVVISHGAEGVNWFSVGSAMHATPPRVSVVSTVGAGDSLLAGMLHG 263 ***************************************************************** PP TIGR03828 261 lekglsleealrlavAvgaaaassegtelpdledieelleevkie 305 l + ++e++lr+a+A++a a+++ g++++d +++++l++ev+++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05480 264 LLSADTPEQTLRTATAIAAMAVTQIGFGIGDAAQLAQLEQEVRVR 308 ******************************************995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (305 nodes) Target sequences: 1 (313 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: 11.29 // [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