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) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4990 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.15914.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: 12.95 // [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