Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_043530028.1 JH15_RS10540 phosphate acetyltransferase
Query= SwissProt::Q9I5A5 (704 letters) >NCBI__GCF_000759345.1:WP_043530028.1 Length = 727 Score = 791 bits (2042), Expect = 0.0 Identities = 417/713 (58%), Positives = 524/713 (73%), Gaps = 21/713 (2%) Query: 3 TFFIAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDLGPERSSELVARTHGL 62 T + PT G GLTS LGL++AL+ GLK GF KP Q GP+RSS LVAR L Sbjct: 12 TLLMVPTAVGTGLTSACLGLIKALDSIGLKAGFLKPFMQQELNGPGPDRSSALVARAMNL 71 Query: 63 DTPKPLPLAQVERMLGDGQLDELLEEIISLYQRAAADK----DVVIVEGMVPTRHASYAA 118 P +P ++ER L + +LDELLE ++ L+Q+AA D+ D+V+VEG+V T H++YA Sbjct: 72 SPPPSIPQERIERALREDKLDELLETVVELHQQAADDENIEQDIVVVEGLVSTEHSTYAN 131 Query: 119 RVNFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRG--- 175 ++N HLA +LDA +I V + EL ++++I A+ FGG + LG IL +++ Sbjct: 132 QLNAHLAHALDARIIFVGTGDYHAPRELAEQLDIHARSFGGLASARTLGCILMRMKHLPN 191 Query: 176 ---------EADAANAEDGVADFARRLTEHSPLLRDD-FRLIGCIPWQDELNAARTRDIA 225 A +A +D + RR ++P L D F +IG +P+ D L+ R RD+A Sbjct: 192 ATSEIPIAPGAGSAPLDDALVTELRR---YAPALATDRFHMIGVVPFSDTLSVPRIRDVA 248 Query: 226 DLLSARVINAGDYEQRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMN 285 + A+ +N GD + RRV LC R + + + KPG L+VT GDRDDI+LAA+L MN Sbjct: 249 AAVGAKWLNEGDADSRRVLATSLCGRRAAHALDVFKPGSLIVTSGDRDDILLAAALVTMN 308 Query: 286 GVPLAGLLLCSDFPPDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRE 345 G PLAG++L + + P+ +++ C AL+ GLPV++V T S++T +L+RM+ EIPVDD E Sbjct: 309 GTPLAGVMLTNGYLPNQAMIDACTPALKTGLPVMAVETNSFNTVQDLSRMSNEIPVDDLE 368 Query: 346 RAERVTEFVAGHIDFEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRT 405 RA++V FVAGHID +WLK RLSP AFR+Q+VQ+AQ+A KRIVLPEG+EPRT Sbjct: 369 RADQVARFVAGHIDLQWLKDHLSRGYPRRLSPSAFRHQLVQKAQQAKKRIVLPEGNEPRT 428 Query: 406 VQAAAICQARGIARCVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRK 465 ++AAA+CQ RG+A CVLLAK EEV+ VA+ +GI LP LEIIDPD + YV MVE R+ Sbjct: 429 IEAAALCQRRGLAHCVLLAKREEVENVARTRGIDLPADLEIIDPDSIYMNYVAAMVERRR 488 Query: 466 GKGLNAPMAEQQLEDSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLV 525 GK LN PMAE QL+D+VVL TMML +VDGLVSGA+HTTA+T+RPA QLIKTAP Y LV Sbjct: 489 GK-LNEPMAEAQLQDTVVLGTMMLYQGDVDGLVSGAVHTTANTVRPAFQLIKTAPDYRLV 547 Query: 526 SSVFFMLLPDQVLVYGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSG 585 SS+FFMLLP+QV+VYGDCAVNPDP+ +LAEIA+QSA SA AFGI A+VAMISYSTG+SG Sbjct: 548 SSIFFMLLPEQVVVYGDCAVNPDPNPEELAEIAIQSARSAIAFGIEAKVAMISYSTGESG 607 Query: 586 SGVDVDKVREATRLAREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDL 645 SG DVDKVREATR+ARE+ P+LLIDGPLQYDAAAI SVGRQKAP+SPVAGQATVF+FPDL Sbjct: 608 SGSDVDKVREATRIARERAPELLIDGPLQYDAAAIDSVGRQKAPDSPVAGQATVFVFPDL 667 Query: 646 NTGNTTYKAVQRSADCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698 NTGNTTYKAVQRSA VSVGPMLQGL KPVNDLSRGALV+DIVYTIALTAIQA Sbjct: 668 NTGNTTYKAVQRSAKVVSVGPMLQGLNKPVNDLSRGALVDDIVYTIALTAIQA 720 Lambda K H 0.319 0.136 0.388 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: 1343 Number of extensions: 62 Number of successful extensions: 5 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: 704 Length of database: 727 Length adjustment: 39 Effective length of query: 665 Effective length of database: 688 Effective search space: 457520 Effective search space used: 457520 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: 55 (25.8 bits)
Align candidate WP_043530028.1 JH15_RS10540 (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.2174619.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-126 405.8 0.0 1e-125 405.2 0.0 1.3 1 NCBI__GCF_000759345.1:WP_043530028.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000759345.1:WP_043530028.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.2 0.0 1e-125 1e-125 1 304 [] 418 717 .. 418 717 .. 0.97 Alignments for each domain: == domain 1 score: 405.2 bits; conditional E-value: 1e-125 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 ivlPEg+e+r+++Aaal++++++a++vll++ ee++++ ++++++l + ++++dpd+ +yv +++e+r NCBI__GCF_000759345.1:WP_043530028.1 418 IVLPEGNEPRTIEAAALCQRRGLAHCVLLAKREEVENVaRTRGIDLPAD-LEIIDPDSI--YMNYVAAMVERR 487 8******************************999999867888888765.555666665..589********* PP TIGR00651 73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145 + k ++e +a+ ql+D+v+l+++++++g +dglvsGav+tta+t+rpa+q+ikt++ +lvss+f+m ++e+v NCBI__GCF_000759345.1:WP_043530028.1 488 RGK-LNEPMAEAQLQDTVVLGTMMLYQGDVDGLVSGAVHTTANTVRPAFQLIKTAPDYRLVSSIFFMLLPEQV 559 ***.********************************************************************* PP TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218 +v++DCav++dPn+eeLAeiA+qsa sa ++g +e kva++syst+ sg+g++v+kv+eA++i++e++p+ll+ NCBI__GCF_000759345.1:WP_043530028.1 560 VVYGDCAVNPDPNPEELAEIAIQSARSAIAFG-IEAKVAMISYSTGESGSGSDVDKVREATRIARERAPELLI 631 ********************************.**************************************** PP TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291 dG+lq+DaA +++v ++kap+s+vag+a+vfvFPdL++Gn++Yk+vqR+a++ ++GP+lqGl+kPvnDLsRGa NCBI__GCF_000759345.1:WP_043530028.1 632 DGPLQYDAAAIDSVGRQKAPDSPVAGQATVFVFPDLNTGNTTYKAVQRSAKVVSVGPMLQGLNKPVNDLSRGA 704 ************************************************************************* PP TIGR00651 292 svedivnvviita 304 +v+div+++++ta NCBI__GCF_000759345.1:WP_043530028.1 705 LVDDIVYTIALTA 717 ***********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (727 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 35.08 // [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