Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate AO356_16680 AO356_16680 phosphate acetyltransferase
Query= SwissProt::Q9I5A5 (704 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_16680 Length = 699 Score = 1066 bits (2758), Expect = 0.0 Identities = 547/699 (78%), Positives = 614/699 (87%), Gaps = 8/699 (1%) Query: 1 MHTFFIAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDLGPERSSELVARTH 60 M TFFIAPT FGVGLTSISLGL+R LERAGLKVGFFKPIAQ HPGD GPERS+ELVARTH Sbjct: 1 MQTFFIAPTDFGVGLTSISLGLVRTLERAGLKVGFFKPIAQPHPGDTGPERSTELVARTH 60 Query: 61 GLDTPKPLPLAQVERMLGDGQLDELLEEIISLYQRAAADKDVVIVEGMVPTRHASYAARV 120 GL P+PL LA VERMLGDGQLDELLEEII+LYQ+AA KDV++VEGMVPTR+ASYAARV Sbjct: 61 GLKPPQPLGLAHVERMLGDGQLDELLEEIITLYQQAAIGKDVLVVEGMVPTRNASYAARV 120 Query: 121 NFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRGEADAA 180 N HLAKSLDAEVILVSAPENE LTEL+ R+E+QAQLFGGP+DPKVLGVILNKVR Sbjct: 121 NLHLAKSLDAEVILVSAPENEVLTELSGRVELQAQLFGGPKDPKVLGVILNKVR------ 174 Query: 181 NAEDGVADFARRLTEHSPLLRD-DFRLIGCIPWQDELNAARTRDIADLLSARVINAGDYE 239 E+ + F+ RL EHSPLLR DFRL+GCIP++ ELNA RTRD+ADL+ A+V+NAGDYE Sbjct: 175 -TEESMEAFSARLKEHSPLLRSGDFRLLGCIPFRPELNAPRTRDVADLMGAQVLNAGDYE 233 Query: 240 QRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGVPLAGLLLCSDFP 299 RR+ I++CAR + NTV+LLKPGVLVVTPGDRDDIILA SLAA+NGVPLAGLLL SD Sbjct: 234 TRRMSNIIICARTMRNTVELLKPGVLVVTPGDRDDIILAVSLAAINGVPLAGLLLTSDTL 293 Query: 300 PDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRERAERVTEFVAGHID 359 PDPRIM+LCRGALQ GLPVLSV+TGSYDTA LN +NKEIP+DDRERAE +T+FVA H+D Sbjct: 294 PDPRIMDLCRGALQAGLPVLSVSTGSYDTANLLNGLNKEIPIDDRERAEIITDFVASHLD 353 Query: 360 FEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAAAICQARGIAR 419 +WL QRCGTPRE+RLSP FRYQ++QRAQ A KRIVLPEGSEP TVQAAAICQARGIAR Sbjct: 354 AKWLHQRCGTPREMRLSPAVFRYQLIQRAQAANKRIVLPEGSEPLTVQAAAICQARGIAR 413 Query: 420 CVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRKGKGLNAPMAEQQLE 479 CVLLAKP +V+AVA+AQGI LP GLEI+DPD +R+RYVEPMV LRK K LNAPMAEQQLE Sbjct: 414 CVLLAKPADVEAVARAQGIELPPGLEILDPDSIRERYVEPMVRLRKSKSLNAPMAEQQLE 473 Query: 480 DSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV 539 D+VV+ TMMLALDEVDGLVSG IH+TA+TIRPALQLIKTAPG +LVSSVFFML P++VLV Sbjct: 474 DTVVIGTMMLALDEVDGLVSGVIHSTANTIRPALQLIKTAPGCSLVSSVFFMLFPEEVLV 533 Query: 540 YGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSGVDVDKVREATRL 599 YGDC +NP PSA++LAEIA+QSA SA AFGI RVAM+SYS+G+S SG +V+KVREAT L Sbjct: 534 YGDCVMNPHPSAAELAEIALQSADSAAAFGITPRVAMLSYSSGESASGEEVEKVREATLL 593 Query: 600 AREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNTGNTTYKAVQRSA 659 A E + LLIDGPLQYDAAA +V RQ APNS VAG+ATVFIFPDLNTGNTT+KAVQRSA Sbjct: 594 AHEAQQGLLIDGPLQYDAAANETVARQLAPNSQVAGRATVFIFPDLNTGNTTHKAVQRSA 653 Query: 660 DCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698 DCVS+GPMLQGLRKPVNDL RGA V+DIVYTIALTAIQA Sbjct: 654 DCVSLGPMLQGLRKPVNDLPRGAQVDDIVYTIALTAIQA 692 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: 1394 Number of extensions: 57 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: 699 Length adjustment: 39 Effective length of query: 665 Effective length of database: 660 Effective search space: 438900 Effective search space used: 438900 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 AO356_16680 AO356_16680 (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.76331.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-118 379.5 0.0 9.5e-118 379.0 0.0 1.2 1 FitnessBrowser__pseudo5_N2C3_1:AO356_16680 Domain annotation for each sequence (and alignments): >> FitnessBrowser__pseudo5_N2C3_1:AO356_16680 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 379.0 0.0 9.5e-118 9.5e-118 1 304 [] 389 689 .. 389 689 .. 0.98 Alignments for each domain: == domain 1 score: 379.0 bits; conditional E-value: 9.5e-118 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyve 66 ivlPEgse+ +++Aaa+++ ++ia++vll++ ++++++ +a++++l g ++ dpd+ +e+yve FitnessBrowser__pseudo5_N2C3_1:AO356_16680 389 IVLPEGSEPLTVQAAAICQARGIARCVLLAKPADVEAVaRAQGIELPPGL-EILDPDSI--RERYVE 452 8************************************9789999998875.56666666..6***** PP TIGR00651 67 rlyekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklv 133 ++ +rk k ++ +a++ql+D+v++++++++l+e+dglvsG ++ta+t+rpalq+ikt++g +lv FitnessBrowser__pseudo5_N2C3_1:AO356_16680 453 PMVRLRKSKSLNAPMAEQQLEDTVVIGTMMLALDEVDGLVSGVIHSTANTIRPALQLIKTAPGCSLV 519 ******************************************************************* PP TIGR00651 134 ssvfimekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeeve 200 ssvf+m +eevlv++DC ++++P+a eLAeiAlqsa+sa ++g + p+va+lsys++ s++geeve FitnessBrowser__pseudo5_N2C3_1:AO356_16680 520 SSVFFMLFPEEVLVYGDCVMNPHPSAAELAEIALQSADSAAAFG-ITPRVAMLSYSSGESASGEEVE 585 ********************************************.********************** PP TIGR00651 201 kvkeAvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRl 267 kv+eA+ +++e + ll+dG+lq+DaA e+va++ ap+s+vag+a+vf+FPdL++Gn++ k+vqR+ FitnessBrowser__pseudo5_N2C3_1:AO356_16680 586 KVREATLLAHEAQQGLLIDGPLQYDAAANETVARQLAPNSQVAGRATVFIFPDLNTGNTTHKAVQRS 652 ******************************************************************* PP TIGR00651 268 adaeaiGPilqGlakPvnDLsRGasvedivnvviita 304 ad ++GP+lqGl+kPvnDL RGa+v+div+++++ta FitnessBrowser__pseudo5_N2C3_1:AO356_16680 653 ADCVSLGPMLQGLRKPVNDLPRGAQVDDIVYTIALTA 689 ***********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (699 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: 40.05 // [ok]
This GapMind analysis is from Apr 09 2024. 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