Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_008623525.1 C943_RS01285 phosphate acetyltransferase
Query= SwissProt::P77844 (329 letters) >NCBI__GCF_000330725.2:WP_008623525.1 Length = 698 Score = 344 bits (883), Expect = 3e-99 Identities = 180/327 (55%), Positives = 234/327 (71%), Gaps = 2/327 (0%) Query: 1 MSAELFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERAT 60 ++ +F+ L+ AR + HIVLPEG D+RIL AA +L+ Q I ++T+LG+ I Sbjct: 370 ITPRMFQYQLVSWARNKKKHIVLPEGIDERILKAADRLVRQGIVNVTLLGNLNDITGTIN 429 Query: 61 ELGLHL--NTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHN 118 LGL L + +++P E++A+ ELRK K++ ++ AR++M D+SYFGTMMVH Sbjct: 430 RLGLQLTQDNCQIIDPHDSIFFEDYAQTLFELRKGKNMPLEVARDLMTDVSYFGTMMVHK 489 Query: 119 GDADGMVSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTA 178 G ADGMVSGA +TTAHTI+P+ Q IKT P S+VSSIF M L R+ FGDCA+N NPTA Sbjct: 490 GHADGMVSGAMHTTAHTIRPALQFIKTKPGISLVSSIFFMCLPDRVTVFGDCAININPTA 549 Query: 179 EQLGEIAVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDG 238 E+L EIA+ SA TA +FGI+PRVA+LSYS+G SG G DV++ A R+ ++ V+G Sbjct: 550 EELAEIAISSADTATKFGIEPRVAMLSYSSGASGTGEDVEKVRTATELVRQNRKDIKVEG 609 Query: 239 PLQFDAAVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGL 298 P+Q+DAAVDP ++KMPDS+VAGQA+V IFPDL GN YK QR A+A+GP+LQGL Sbjct: 610 PIQYDAAVDPLTGKQKMPDSEVAGQASVLIFPDLNTGNNTYKAVQRETGAIAIGPMLQGL 669 Query: 299 NKPVNDLSRGATVPDIVNTVAITAIQA 325 NKPVNDLSRG TV DI NTV ITAIQA Sbjct: 670 NKPVNDLSRGCTVDDIFNTVVITAIQA 696 Lambda K H 0.318 0.134 0.386 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: 537 Number of extensions: 24 Number of successful extensions: 2 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: 329 Length of database: 698 Length adjustment: 33 Effective length of query: 296 Effective length of database: 665 Effective search space: 196840 Effective search space used: 196840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_008623525.1 C943_RS01285 (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.2151942.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-127 410.9 0.0 3.9e-127 409.9 0.0 1.5 1 NCBI__GCF_000330725.2:WP_008623525.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330725.2:WP_008623525.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 409.9 0.0 3.9e-127 3.9e-127 1 304 [] 390 693 .. 390 693 .. 0.98 Alignments for each domain: == domain 1 score: 409.9 bits; conditional E-value: 3.9e-127 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 ivlPEg +er+lkAa l++++i++ +ll+n ++++ + + +++l+ +++++dp+ s e+y+++l+e+r NCBI__GCF_000330725.2:WP_008623525.1 390 IVLPEGIDERILKAADRLVRQGIVNVTLLGNLNDITGTiNRLGLQLTQDNCQIIDPHDSIFFEDYAQTLFELR 462 8*********************************999545556666667899*****999************* PP TIGR00651 73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145 k k + ++ ar+ ++D +++++++v++g+adg+vsGa +tta+t+rpalq ikt++g++lvss+f+m+++++v NCBI__GCF_000330725.2:WP_008623525.1 463 KGKNMPLEVARDLMTDVSYFGTMMVHKGHADGMVSGAMHTTAHTIRPALQFIKTKPGISLVSSIFFMCLPDRV 535 ************************************************************************* PP TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218 vf+DCa++++P+aeeLAeiA++sa++a ++g +ep+va+lsys+++sg ge+vekv+ A++++++ + d+++ NCBI__GCF_000330725.2:WP_008623525.1 536 TVFGDCAININPTAEELAEIAISSADTATKFG-IEPRVAMLSYSSGASGTGEDVEKVRTATELVRQNRKDIKV 607 ********************************.**************************************** PP TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291 +G++q+DaA+ + ++k+p+sevag+a v++FPdL++Gn++Yk+vqR+++a aiGP+lqGl+kPvnDLsRG+ NCBI__GCF_000330725.2:WP_008623525.1 608 EGPIQYDAAVDPLTGKQKMPDSEVAGQASVLIFPDLNTGNNTYKAVQRETGAIAIGPMLQGLNKPVNDLSRGC 680 ************************************************************************* PP TIGR00651 292 svedivnvviita 304 +v+di+n+v+ita NCBI__GCF_000330725.2:WP_008623525.1 681 TVDDIFNTVVITA 693 ***********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (698 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: 39.83 // [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