Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_011777975.1 MVAN_RS03535 phosphate acetyltransferase
Query= SwissProt::P77844 (329 letters) >NCBI__GCF_000015305.1:WP_011777975.1 Length = 692 Score = 388 bits (996), Expect = e-112 Identities = 194/327 (59%), Positives = 251/327 (76%) Query: 1 MSAELFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERAT 60 ++ ++F + L+++AR++ IVLPEG+DDRIL AA +LL + + D+TILG+ +++ RA Sbjct: 366 VTPQMFTHQLIEQARSDRKRIVLPEGNDDRILKAAGRLLHRGVADLTILGEEAQVRARAA 425 Query: 61 ELGLHLNTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHNGD 120 ELGL L+TA +++P T + FAEQ+A+LR K VT+++A EI+ D+SYFGTM+VHN Sbjct: 426 ELGLDLSTAVVLDPQTSELCDRFAEQYAKLRAHKGVTVEQAHEIIHDVSYFGTMLVHNDL 485 Query: 121 ADGMVSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQ 180 DGMVSGA +TTAHTI+P+ +II+T P S VSSIFLM L + A+GDCA+ P+PTAEQ Sbjct: 486 VDGMVSGACHTTAHTIRPALEIIRTAPGVSTVSSIFLMCLAHEVLAYGDCAIVPDPTAEQ 545 Query: 181 LGEIAVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPL 240 L +IA+ SA+TAAQFGI+P+VA+LSYSTG SG G+DVD+ A R PEL V+GP+ Sbjct: 546 LADIAISSARTAAQFGIEPKVAMLSYSTGTSGTGADVDKVRKATELVRSRAPELLVEGPI 605 Query: 241 QFDAAVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGLNK 300 Q+DAAV+P VA KMPDS VAG A V IFPDL GN YK QR+ A+A+GP+LQGLNK Sbjct: 606 QYDAAVEPSVAMTKMPDSRVAGHATVLIFPDLNTGNNTYKAVQRSAGAIAIGPVLQGLNK 665 Query: 301 PVNDLSRGATVPDIVNTVAITAIQAGG 327 PVNDLSRGA V DIVNTVAITAIQA G Sbjct: 666 PVNDLSRGALVEDIVNTVAITAIQAQG 692 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: 617 Number of extensions: 21 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: 329 Length of database: 692 Length adjustment: 33 Effective length of query: 296 Effective length of database: 659 Effective search space: 195064 Effective search space used: 195064 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: 51 (24.3 bits)
Align candidate WP_011777975.1 MVAN_RS03535 (phosphate acetyltransferase)
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.36342.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-129 416.2 0.1 6e-129 415.8 0.1 1.2 1 NCBI__GCF_000015305.1:WP_011777975.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000015305.1:WP_011777975.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.8 0.1 6e-129 6e-129 1 304 [] 386 687 .. 386 687 .. 0.99 Alignments for each domain: == domain 1 score: 415.8 bits; conditional E-value: 6e-129 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 ivlPEg++ r+lkAa l+++++a+ ++l++++++ + +a+e+ l+l++ vv dp++s+ ++++e++ ++r NCBI__GCF_000015305.1:WP_011777975.1 386 IVLPEGNDDRILKAAGRLLHRGVADLTILGEEAQVRA-RAAELGLDLSTAVVLDPQTSELCDRFAEQYAKLRA 457 8****************************99988877.9********************************** PP TIGR00651 74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146 hkGvt ++a+e ++D ++++++lv+ + +dg+vsGa +tta+t+rpal+ii+t++gv++vss+f+m++ +evl NCBI__GCF_000015305.1:WP_011777975.1 458 HKGVTVEQAHEIIHDVSYFGTMLVHNDLVDGMVSGACHTTAHTIRPALEIIRTAPGVSTVSSIFLMCLAHEVL 530 ************************************************************************* PP TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219 ++DCa+++dP+ae+LA+iA++sa +a ++g +epkva+lsyst++sg g++v+kv++A+++++ ++p+ll++ NCBI__GCF_000015305.1:WP_011777975.1 531 AYGDCAIVPDPTAEQLADIAISSARTAAQFG-IEPKVAMLSYSTGTSGTGADVDKVRKATELVRSRAPELLVE 602 *******************************.***************************************** PP TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGas 292 G++q+DaA+ ++va k+p+s vag+a+v++FPdL++Gn++Yk+vqR+a+a aiGP+lqGl+kPvnDLsRGa+ NCBI__GCF_000015305.1:WP_011777975.1 603 GPIQYDAAVEPSVAMTKMPDSRVAGHATVLIFPDLNTGNNTYKAVQRSAGAIAIGPVLQGLNKPVNDLSRGAL 675 ************************************************************************* PP TIGR00651 293 vedivnvviita 304 vedivn+v+ita NCBI__GCF_000015305.1:WP_011777975.1 676 VEDIVNTVAITA 687 **********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (692 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: 29.85 // [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