Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_090447850.1 BLS63_RS21525 phosphate acetyltransferase
Query= SwissProt::Q9I5A5 (704 letters) >NCBI__GCF_900100495.1:WP_090447850.1 Length = 697 Score = 1166 bits (3017), Expect = 0.0 Identities = 594/699 (84%), Positives = 644/699 (92%), Gaps = 8/699 (1%) Query: 1 MHTFFIAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDLGPERSSELVARTH 60 MHTFFI+PTGFGVGLTSISLGL+ ALERAGLKVGFFKPIAQ H GD GPERSSEL+ARTH Sbjct: 1 MHTFFISPTGFGVGLTSISLGLVGALERAGLKVGFFKPIAQPHQGDAGPERSSELIARTH 60 Query: 61 GLDTPKPLPLAQVERMLGDGQLDELLEEIISLYQRAAADKDVVIVEGMVPTRHASYAARV 120 GL +PKPL LA VERMLGDGQLDELLEEIISLYQ+AAA KDVVIVEGMVPTR ASYAARV Sbjct: 61 GLHSPKPLALAHVERMLGDGQLDELLEEIISLYQQAAAGKDVVIVEGMVPTRQASYAARV 120 Query: 121 NFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRGEADAA 180 NFHLAKSLDA+VILVSAPE E+L EL DR+EIQAQLFGGP+DPKVLGVI+NKVR Sbjct: 121 NFHLAKSLDADVILVSAPEQESLAELCDRVEIQAQLFGGPKDPKVLGVIINKVR------ 174 Query: 181 NAEDGVADFARRLTEHSPLLR-DDFRLIGCIPWQDELNAARTRDIADLLSARVINAGDYE 239 +EDG F RL EHSPLLR DDFRL+GCIPWQDELNA RTRDIADLL ARV+NAGDYE Sbjct: 175 -SEDGFEAFCERLKEHSPLLRSDDFRLLGCIPWQDELNAPRTRDIADLLGARVLNAGDYE 233 Query: 240 QRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGVPLAGLLLCSDFP 299 QRR+ KI+LCARAV NTVQLLKPG LVVTPGDRDDIILAASLAAMNG+PLAGLLLCSDF Sbjct: 234 QRRILKIMLCARAVANTVQLLKPGTLVVTPGDRDDIILAASLAAMNGMPLAGLLLCSDFV 293 Query: 300 PDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRERAERVTEFVAGHID 359 PDPRIMELCRGALQ GLPV++V+TGSYDTAT+LNR+NKEIPVDD+ERAE+V +FVA HID Sbjct: 294 PDPRIMELCRGALQSGLPVMTVSTGSYDTATDLNRLNKEIPVDDKERAEKVADFVASHID 353 Query: 360 FEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAAAICQARGIAR 419 +WL+ RCGTPRELRLSP AFRYQ+VQRA+ A KRIVLPEGSEPRTV+AAAICQARGIAR Sbjct: 354 HDWLRARCGTPRELRLSPSAFRYQLVQRAKAADKRIVLPEGSEPRTVKAAAICQARGIAR 413 Query: 420 CVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRKGKGLNAPMAEQQLE 479 CVLLAKP+EV+AVA+AQGI LP GLEI+DPDL+R+RYVEPM+ELRKGKGLNAPMA QLE Sbjct: 414 CVLLAKPDEVRAVARAQGIELPPGLEILDPDLIRERYVEPMIELRKGKGLNAPMAFAQLE 473 Query: 480 DSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV 539 D+VVL TMMLALDEVDGLVSGA+HTTA+TIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV Sbjct: 474 DNVVLGTMMLALDEVDGLVSGAVHTTANTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV 533 Query: 540 YGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSGVDVDKVREATRL 599 YGDCAVNPDPSA+ LAEIA+QSAASA AFGIP RVAM+SYSTGDSG+G +V+KVREATRL Sbjct: 534 YGDCAVNPDPSAAQLAEIALQSAASASAFGIPPRVAMLSYSTGDSGTGEEVEKVREATRL 593 Query: 600 AREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNTGNTTYKAVQRSA 659 AR+ P L +DGPLQYDAA I SVGRQKAPNSPVAG+ATVF+FPDLNTGNTTYKAVQRSA Sbjct: 594 ARQLDPQLALDGPLQYDAATIDSVGRQKAPNSPVAGRATVFVFPDLNTGNTTYKAVQRSA 653 Query: 660 DCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698 DCVSVGPMLQGLRKPVNDLSRGALV+DIVYTIALTAIQA Sbjct: 654 DCVSVGPMLQGLRKPVNDLSRGALVDDIVYTIALTAIQA 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: 1464 Number of extensions: 53 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: 697 Length adjustment: 39 Effective length of query: 665 Effective length of database: 658 Effective search space: 437570 Effective search space used: 437570 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 WP_090447850.1 BLS63_RS21525 (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.4929.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-128 412.1 0.0 1.2e-127 411.5 0.0 1.3 1 lcl|NCBI__GCF_900100495.1:WP_090447850.1 BLS63_RS21525 phosphate acetyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090447850.1 BLS63_RS21525 phosphate acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 411.5 0.0 1.2e-127 1.2e-127 1 304 [] 389 689 .. 389 689 .. 0.98 Alignments for each domain: == domain 1 score: 411.5 bits; conditional E-value: 1.2e-127 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverl 68 ivlPEgse+r++kAaa+++ ++ia++vll++ +e+ ++ +a++++l g +++ dpd+ +e+yve + lcl|NCBI__GCF_900100495.1:WP_090447850.1 389 IVLPEGSEPRTVKAAAICQARGIARCVLLAKPDEVRAVaRAQGIELPPG-LEILDPDLI--RERYVEPM 454 8**********************************99978999999876.678889999..8******* PP TIGR00651 69 yekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvf 137 +e+rk kG++ +a ql+D+v+l++++++l+e+dglvsGav+tta+t+rpalq+ikt++g +lvssvf lcl|NCBI__GCF_900100495.1:WP_090447850.1 455 IELRKGKGLNAPMAFAQLEDNVVLGTMMLALDEVDGLVSGAVHTTANTIRPALQLIKTAPGYNLVSSVF 523 ********************************************************************* PP TIGR00651 138 imekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAv 206 +m ++++vlv++DCav++dP+a +LAeiAlqsa+sa ++g + p+va+lsyst+ sg geevekv+eA+ lcl|NCBI__GCF_900100495.1:WP_090447850.1 524 FMLLPDQVLVYGDCAVNPDPSAAQLAEIALQSAASASAFG-IPPRVAMLSYSTGDSGTGEEVEKVREAT 591 ****************************************.**************************** PP TIGR00651 207 kilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGP 275 +++++ p+l+ldG+lq+DaA +++v ++kap+s+vag+a+vfvFPdL++Gn++Yk+vqR+ad ++GP lcl|NCBI__GCF_900100495.1:WP_090447850.1 592 RLARQLDPQLALDGPLQYDAATIDSVGRQKAPNSPVAGRATVFVFPDLNTGNTTYKAVQRSADCVSVGP 660 ********************************************************************* PP TIGR00651 276 ilqGlakPvnDLsRGasvedivnvviita 304 +lqGl+kPvnDLsRGa+v+div+++++ta lcl|NCBI__GCF_900100495.1:WP_090447850.1 661 MLQGLRKPVNDLSRGALVDDIVYTIALTA 689 ***************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (697 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 22.42 // [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