Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_013819383.1 METME_RS13920 phosphate acetyltransferase
Query= SwissProt::P77844 (329 letters) >NCBI__GCF_000214665.1:WP_013819383.1 Length = 710 Score = 358 bits (920), Expect = e-103 Identities = 184/325 (56%), Positives = 240/325 (73%) Query: 1 MSAELFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERAT 60 M+ +FE LL+RA+A+ HIVLPEG ++RIL AA LL +D+ IT+LG+ +I+++ Sbjct: 380 MTPLMFEYDLLQRAKAKKQHIVLPEGTEERILRAAEILLLRDVVRITLLGNEAEIRQKIQ 439 Query: 61 ELGLHLNTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHNGD 120 L L L +++P+T FA+ + E RK K++ D A ++M D+SYFGT+M+H G Sbjct: 440 ALALKLTDVDIIDPMTSELRPLFAQAYFEARKHKNIIYDTAFDLMGDVSYFGTLMIHLGF 499 Query: 121 ADGMVSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQ 180 A+GMVSGA ++T HTI+P+F+IIKT P AS+VSS+F M L R+ +GDCAVNPNP AE+ Sbjct: 500 ANGMVSGAVHSTQHTIRPAFEIIKTKPGASIVSSVFFMCLEDRVLVYGDCAVNPNPNAEE 559 Query: 181 LGEIAVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPL 240 L IAV +A TA F I+P VA+LSYSTG+SG G VD+ +A+ A L P+L ++GP+ Sbjct: 560 LAAIAVSAADTAKMFNIEPFVAMLSYSTGDSGKGEAVDKVREAVKIAHALRPDLKLEGPM 619 Query: 241 QFDAAVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGLNK 300 Q+DAAVD GVA+ K+P S+VAGQA VFIFPDL GN YK QR+ A+AVGPILQGLNK Sbjct: 620 QYDAAVDFGVAKTKLPGSEVAGQATVFIFPDLNTGNNTYKAVQRSSGAIAVGPILQGLNK 679 Query: 301 PVNDLSRGATVPDIVNTVAITAIQA 325 PVNDLSRG TVPDIVNTV ITAIQA Sbjct: 680 PVNDLSRGCTVPDIVNTVIITAIQA 704 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: 558 Number of extensions: 23 Number of successful extensions: 1 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: 710 Length adjustment: 34 Effective length of query: 295 Effective length of database: 676 Effective search space: 199420 Effective search space used: 199420 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_013819383.1 METME_RS13920 (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.18890.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-125 403.7 0.1 3.8e-125 403.3 0.1 1.1 1 lcl|NCBI__GCF_000214665.1:WP_013819383.1 METME_RS13920 phosphate acetyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214665.1:WP_013819383.1 METME_RS13920 phosphate acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 403.3 0.1 3.8e-125 3.8e-125 1 304 [] 400 701 .. 400 701 .. 0.99 Alignments for each domain: == domain 1 score: 403.3 bits; conditional E-value: 3.8e-125 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverly 69 ivlPEg+eer+l+Aa++l+ +++++ +ll+n++e+ + k++ + lkl++v ++dp +s+ + ++++++ lcl|NCBI__GCF_000214665.1:WP_013819383.1 400 IVLPEGTEERILRAAEILLLRDVVRITLLGNEAEIRQ-KIQALALKLTDVDIIDPMTSELRPLFAQAYF 467 8******************************999988.******************************* PP TIGR00651 70 ekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfi 138 e rkhk + +a + + D +++++l+++lg a+g+vsGav++t++t+rpa++iikt++g ++vssvf+ lcl|NCBI__GCF_000214665.1:WP_013819383.1 468 EARKHKNIIYDTAFDLMGDVSYFGTLMIHLGFANGMVSGAVHSTQHTIRPAFEIIKTKPGASIVSSVFF 536 ********************************************************************* PP TIGR00651 139 mekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvk 207 m++e++vlv++DCav+++PnaeeLA iA+++a++ak+++ +ep va+lsyst+ sgkge+v+kv+eAvk lcl|NCBI__GCF_000214665.1:WP_013819383.1 537 MCLEDRVLVYGDCAVNPNPNAEELAAIAVSAADTAKMFN-IEPFVAMLSYSTGDSGKGEAVDKVREAVK 604 **************************************9.***************************** PP TIGR00651 208 ilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPi 276 i++ +pdl+l+G++q+DaA+ va+ k p sevag+a+vf+FPdL++Gn++Yk+vqR+++a a+GPi lcl|NCBI__GCF_000214665.1:WP_013819383.1 605 IAHALRPDLKLEGPMQYDAAVDFGVAKTKLPGSEVAGQATVFIFPDLNTGNNTYKAVQRSSGAIAVGPI 673 ********************************************************************* PP TIGR00651 277 lqGlakPvnDLsRGasvedivnvviita 304 lqGl+kPvnDLsRG++v divn+viita lcl|NCBI__GCF_000214665.1:WP_013819383.1 674 LQGLNKPVNDLSRGCTVPDIVNTVIITA 701 **************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (710 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 16.09 // [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