Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate Pf1N1B4_1055 Phosphate acetyltransferase (EC 2.3.1.8)
Query= SwissProt::P77844 (329 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 Length = 422 Score = 266 bits (681), Expect = 5e-76 Identities = 143/330 (43%), Positives = 206/330 (62%), Gaps = 5/330 (1%) Query: 1 MSAELFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERAT 60 +S +F L++RA+A + IVLPEG + + AA + I +L P ++ A Sbjct: 92 LSPAVFRYQLIQRAQAANKRIVLPEGSEPLTVQAAAICQARGIARCVLLAKPADVEAVAR 151 Query: 61 ELGLHLNTAYLVNPLTDPRL--EEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHN 118 G+ L + DP L E + E LRK+KS+ A + ++D GTMM+ Sbjct: 152 AQGIELPPGL---EILDPDLIRERYVEPMVALRKTKSLNAPMAEQQLEDTVVIGTMMLAL 208 Query: 119 GDADGMVSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTA 178 + DG+VSG ++TA+TI+P+ Q+IKT P ++VSS+F M+ + +GDC +NP+P+A Sbjct: 209 DEVDGLVSGVIHSTANTIRPALQLIKTAPGCTLVSSVFFMLFPEEVLVYGDCVMNPHPSA 268 Query: 179 EQLGEIAVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDG 238 +L EIA+ SA +AA FGI PRVA++SYS+G S G +V++ +A A L +DG Sbjct: 269 SELAEIALQSADSAAAFGITPRVAMISYSSGESASGEEVEKVREATLLAHEQQNSLLIDG 328 Query: 239 PLQFDAAVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGL 298 PLQ+DAA + VAR+ P+S VAG+A VF+FPDL GN +K QR+ +++GP+LQGL Sbjct: 329 PLQYDAAANETVARQLAPNSQVAGRATVFVFPDLNTGNTTHKAVQRSADCVSLGPMLQGL 388 Query: 299 NKPVNDLSRGATVPDIVNTVAITAIQAGGR 328 KPVNDL RGA V DIV T+A+TAIQA R Sbjct: 389 RKPVNDLPRGAQVDDIVYTIALTAIQAANR 418 Lambda K H 0.318 0.134 0.386 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: 332 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: 329 Length of database: 422 Length adjustment: 30 Effective length of query: 299 Effective length of database: 392 Effective search space: 117208 Effective search space used: 117208 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: 49 (23.5 bits)
Align candidate Pf1N1B4_1055 (Phosphate acetyltransferase (EC 2.3.1.8))
to HMM TIGR00651 (pta: phosphate acetyltransferase (EC 2.3.1.8))
# 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/TIGR00651.hmm # target sequence database: /tmp/gapView.19346.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00651 [M=304] Accession: TIGR00651 Description: pta: phosphate acetyltransferase 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-118 380.9 0.0 3.2e-118 380.6 0.0 1.1 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 Phosphate acetyltransferase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 Phosphate acetyltransferase (EC 2.3.1.8) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 380.6 0.0 3.2e-118 3.2e-118 1 304 [] 112 412 .. 112 412 .. 0.98 Alignments for each domain: == domain 1 score: 380.6 bits; conditional E-value: 3.2e-118 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiek 63 ivlPEgse+ +++Aaa+++ ++ia++vll++ ++++++ +a++++l g +++ dpd+ +e+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 112 IVLPEGSEPLTVQAAAICQARGIARCVLLAKPADVEAVaRAQGIELPPG-LEILDPDLI--RER 172 8************************************978999999876.678889998..8** PP TIGR00651 64 yverlyekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktl 127 yve ++ +rk+k ++ +a++ql+D+v++++++++l+e+dglvsG ++ta+t+rpalq+ikt+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 173 YVEPMVALRKTKSLNAPMAEQQLEDTVVIGTMMLALDEVDGLVSGVIHSTANTIRPALQLIKTA 236 **************************************************************** PP TIGR00651 128 egvklvssvfimekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystk 191 +g lvssvf+m +eevlv++DC ++++P+a eLAeiAlqsa+sa ++g + p+va++sys++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 237 PGCTLVSSVFFMLFPEEVLVYGDCVMNPHPSASELAEIALQSADSAAAFG-ITPRVAMISYSSG 299 **************************************************.************* PP TIGR00651 192 gsgkgeevekvkeAvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLd 255 s++geevekv+eA+ +++e++ ll+dG+lq+DaA e+va++ ap+s+vag+a+vfvFPdL+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 300 ESASGEEVEKVREATLLAHEQQNSLLIDGPLQYDAAANETVARQLAPNSQVAGRATVFVFPDLN 363 **************************************************************** PP TIGR00651 256 aGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviita 304 +Gn++ k+vqR+ad ++GP+lqGl+kPvnDL RGa+v+div+++++ta lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1055 364 TGNTTHKAVQRSADCVSLGPMLQGLRKPVNDLPRGAQVDDIVYTIALTA 412 ***********************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (422 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.52 // [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