Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate 8501128 DvMF_1864 phosphate acetyltransferase (RefSeq)
Query= SwissProt::P77844 (329 letters) >FitnessBrowser__Miya:8501128 Length = 704 Score = 388 bits (996), Expect = e-112 Identities = 194/321 (60%), Positives = 246/321 (76%) Query: 5 LFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGL 64 +FE L++RA+ IVLPEG ++RIL AA L +++ DI +LGD K+ + +ELG+ Sbjct: 377 MFEFNLIERAKQNRMRIVLPEGVEERILRAADILARREVADIILLGDADKVGAKVSELGI 436 Query: 65 HLNTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHNGDADGM 124 L+ ++ P P+ EE+A+ + ELRK K V+I+ AR+ M D++YFGTMMVH GDA+GM Sbjct: 437 ALDGVQIIQPNLSPKFEEYAQAYFELRKHKGVSIERARDTMNDVTYFGTMMVHKGDAEGM 496 Query: 125 VSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEI 184 VSG+ NTTAHTI+P+F+ IKT P S+VSS+FLM L+ R+ AFGDCAVNPNPTAEQL EI Sbjct: 497 VSGSINTTAHTIRPAFEFIKTKPGFSIVSSVFLMCLKDRVLAFGDCAVNPNPTAEQLAEI 556 Query: 185 AVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPLQFDA 244 A+ SA TA FGI+PRVA+LSYSTG+SG G+DV++ I+A A+ PEL ++GPLQ+DA Sbjct: 557 AINSAHTARIFGIEPRVAMLSYSTGSSGKGADVEKVIEATRIAKERAPELLLEGPLQYDA 616 Query: 245 AVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGLNKPVND 304 A+D VAR K+P S VAGQA VFIFPDL GN YK QR A+A+GP+LQGLNKPVND Sbjct: 617 AIDMDVARTKLPGSQVAGQATVFIFPDLNTGNNTYKAVQRAAGAVAIGPVLQGLNKPVND 676 Query: 305 LSRGATVPDIVNTVAITAIQA 325 LSRG TVPDIVNTVAITAIQA Sbjct: 677 LSRGCTVPDIVNTVAITAIQA 697 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: 600 Number of extensions: 18 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: 704 Length adjustment: 34 Effective length of query: 295 Effective length of database: 670 Effective search space: 197650 Effective search space used: 197650 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 8501128 DvMF_1864 (phosphate acetyltransferase (RefSeq))
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.14755.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-133 429.0 0.1 7.7e-133 428.6 0.1 1.2 1 lcl|FitnessBrowser__Miya:8501128 DvMF_1864 phosphate acetyltransf Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501128 DvMF_1864 phosphate acetyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 428.6 0.1 7.7e-133 7.7e-133 1 304 [] 393 694 .. 393 694 .. 0.99 Alignments for each domain: == domain 1 score: 428.6 bits; conditional E-value: 7.7e-133 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrkhkGv 77 ivlPEg eer+l+Aa +la++++a+ +ll++ +++ + k++e+ ++l v++++p++s++ e+y+++++e+rkhkGv lcl|FitnessBrowser__Miya:8501128 393 IVLPEGVEERILRAADILARREVADIILLGDADKVGA-KVSELGIALDGVQIIQPNLSPKFEEYAQAYFELRKHKGV 468 8************************999999888777.9************************************** PP TIGR00651 78 tekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfaDCava 154 + ++ar++++D +++++++v++g a+g+vsG+ +tta+t+rpa++ ikt++g+++vssvf+m+++++vl f+DCav+ lcl|FitnessBrowser__Miya:8501128 469 SIERARDTMNDVTYFGTMMVHKGDAEGMVSGSINTTAHTIRPAFEFIKTKPGFSIVSSVFLMCLKDRVLAFGDCAVN 545 ***************************************************************************** PP TIGR00651 155 vdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqfDaAlvek 231 ++P+ae+LAeiA++sa++a+ +g +ep+va+lsyst++sgkg++vekv eA++i+ke++p+lll+G+lq+DaA+ + lcl|FitnessBrowser__Miya:8501128 546 PNPTAEQLAEIAINSAHTARIFG-IEPRVAMLSYSTGSSGKGADVEKVIEATRIAKERAPELLLEGPLQYDAAIDMD 621 ***********************.***************************************************** PP TIGR00651 232 vaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviita 304 va+ k p s+vag+a+vf+FPdL++Gn++Yk+vqR a+a aiGP+lqGl+kPvnDLsRG++v divn+v+ita lcl|FitnessBrowser__Miya:8501128 622 VARTKLPGSQVAGQATVFIFPDLNTGNNTYKAVQRAAGAVAIGPVLQGLNKPVNDLSRGCTVPDIVNTVAITA 694 ***********************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (704 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: 00:00:00.01 # Mc/sec: 14.54 // [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