Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate PfGW456L13_4990 Phosphate acetyltransferase (EC 2.3.1.8)
Query= SwissProt::Q9I5A5 (704 letters) >lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 Phosphate acetyltransferase (EC 2.3.1.8) Length = 706 Score = 1080 bits (2792), Expect = 0.0 Identities = 556/699 (79%), Positives = 616/699 (88%), Gaps = 8/699 (1%) Query: 1 MHTFFIAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDLGPERSSELVARTH 60 M TFFIAPT FGVGLTSISLGL+R LERAGLKVGFFKPIAQ HPGD GPERS+ELVARTH Sbjct: 8 MQTFFIAPTDFGVGLTSISLGLVRTLERAGLKVGFFKPIAQPHPGDTGPERSTELVARTH 67 Query: 61 GLDTPKPLPLAQVERMLGDGQLDELLEEIISLYQRAAADKDVVIVEGMVPTRHASYAARV 120 GL P+PL LA VERMLGDGQLDELLEEII+LYQ+AA KDV+IVEGMVPTR ASYAARV Sbjct: 68 GLKPPQPLGLAHVERMLGDGQLDELLEEIITLYQQAAIGKDVLIVEGMVPTRSASYAARV 127 Query: 121 NFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRGEADAA 180 N HLAKSLDAEVILVSAPENE LTEL+ R+E+QAQLFGGP+DPKVLGVILNKV+ Sbjct: 128 NLHLAKSLDAEVILVSAPENEVLTELSGRVELQAQLFGGPKDPKVLGVILNKVK------ 181 Query: 181 NAEDGVADFARRLTEHSPLLRD-DFRLIGCIPWQDELNAARTRDIADLLSARVINAGDYE 239 E+ + FA RL EHSPLLR DFRL+GCIP+Q ELNA RTRD+ADL+ A+V+NAGDYE Sbjct: 182 -TEESMEAFATRLKEHSPLLRSGDFRLLGCIPFQPELNAPRTRDVADLMGAQVLNAGDYE 240 Query: 240 QRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGVPLAGLLLCSDFP 299 RR+ KI++CAR + NTV+LLKPGVLVVTPGDRDDIILA SLAA+NGVPLAGLLL SD Sbjct: 241 TRRMTKIIICARTMRNTVELLKPGVLVVTPGDRDDIILAVSLAALNGVPLAGLLLTSDTL 300 Query: 300 PDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRERAERVTEFVAGHID 359 PDPRIM+LCRGALQ GLPVLSV+TGSYDTA LN +NKEIP+DDRERAE +T+F+AGH+D Sbjct: 301 PDPRIMDLCRGALQAGLPVLSVSTGSYDTANLLNGLNKEIPIDDRERAEIITDFIAGHLD 360 Query: 360 FEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAAAICQARGIAR 419 WL QRCGTPRE+RLSP FRYQ++QRAQ A KRIVLPEGSEP TVQAAAICQARGIAR Sbjct: 361 ANWLHQRCGTPREMRLSPAVFRYQLIQRAQAANKRIVLPEGSEPLTVQAAAICQARGIAR 420 Query: 420 CVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRKGKGLNAPMAEQQLE 479 CVLLAKPE+VQAVA+AQGI LP GLEIIDPDL+R+RYVEPMV LRK K LNAPMAEQQLE Sbjct: 421 CVLLAKPEDVQAVARAQGIELPPGLEIIDPDLIRERYVEPMVALRKSKSLNAPMAEQQLE 480 Query: 480 DSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV 539 D+VV+ TMMLALDEVDGLVSG I+TTA+TIRPALQLIKTAPG LVSSVFFML P++VLV Sbjct: 481 DTVVIGTMMLALDEVDGLVSGVINTTANTIRPALQLIKTAPGCTLVSSVFFMLFPEEVLV 540 Query: 540 YGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSGVDVDKVREATRL 599 YGDC +NP PSAS+LAEIA+QSA SA AFGI RVAMISYS+G+S SG +V+KVREAT L Sbjct: 541 YGDCVMNPHPSASELAEIALQSADSAAAFGITPRVAMISYSSGESASGEEVEKVREATLL 600 Query: 600 AREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNTGNTTYKAVQRSA 659 A EQ+ LLIDGPLQYDAAA SV RQ APNS VAG+ATV++FPDLNTGNTT+KAVQRSA Sbjct: 601 AHEQQHSLLIDGPLQYDAAANESVARQLAPNSQVAGRATVYVFPDLNTGNTTHKAVQRSA 660 Query: 660 DCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698 DCVS+GPMLQGLRKPVNDL RGA V+DIVYTIALTAIQA Sbjct: 661 DCVSLGPMLQGLRKPVNDLPRGAQVDDIVYTIALTAIQA 699 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: 1413 Number of extensions: 54 Number of successful extensions: 3 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: 706 Length adjustment: 39 Effective length of query: 665 Effective length of database: 667 Effective search space: 443555 Effective search space used: 443555 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: 54 (25.4 bits)
Align candidate PfGW456L13_4990 (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.22912.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-118 382.1 0.0 1.5e-118 381.6 0.0 1.2 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 Phosphate acetyltransferase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 Phosphate acetyltransferase (EC 2.3.1.8) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 381.6 0.0 1.5e-118 1.5e-118 1 304 [] 396 696 .. 396 696 .. 0.98 Alignments for each domain: == domain 1 score: 381.6 bits; conditional E-value: 1.5e-118 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvved 54 ivlPEgse+ +++Aaa+++ ++ia++vll++ e+++++ +a++++l g ++++d lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 396 IVLPEGSEPLTVQAAAICQARGIARCVLLAKPEDVQAVaRAQGIELPPG-LEIID 449 8************************************978999999876.67788 PP TIGR00651 55 pdvskdiekyverlyekrkhkGvtekeareqlrDevslaallvelgeadglvsGa 109 pd+ +e+yve ++ +rk k ++ +a++ql+D+v++++++++l+e+dglvsG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 450 PDLI--RERYVEPMVALRKSKSLNAPMAEQQLEDTVVIGTMMLALDEVDGLVSGV 502 8888..8************************************************ PP TIGR00651 110 vsttaktlrpalqiiktlegvklvssvfimekeeevlvfaDCavavdPnaeeLAe 164 +tta+t+rpalq+ikt++g lvssvf+m +eevlv++DC ++++P+a eLAe lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 503 INTTANTIRPALQLIKTAPGCTLVSSVFFMLFPEEVLVYGDCVMNPHPSASELAE 557 ******************************************************* PP TIGR00651 165 iAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219 iAlqsa+sa ++g + p+va++sys++ s++geevekv+eA+ +++e++ ll+d lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 558 IALQSADSAAAFG-ITPRVAMISYSSGESASGEEVEKVREATLLAHEQQHSLLID 611 *************.***************************************** PP TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiG 274 G+lq+DaA e+va++ ap+s+vag+a+v+vFPdL++Gn++ k+vqR+ad ++G lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 612 GPLQYDAAANESVARQLAPNSQVAGRATVYVFPDLNTGNTTHKAVQRSADCVSLG 666 ******************************************************* PP TIGR00651 275 PilqGlakPvnDLsRGasvedivnvviita 304 P+lqGl+kPvnDL RGa+v+div+++++ta lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 667 PMLQGLRKPVNDLPRGAQVDDIVYTIALTA 696 ****************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (706 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 13.13 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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