Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate 5209946 Shew_2394 phosphate acetyltransferase (RefSeq)
Query= BRENDA::P0A9M8 (714 letters) >FitnessBrowser__PV4:5209946 Length = 712 Score = 966 bits (2496), Expect = 0.0 Identities = 479/712 (67%), Positives = 590/712 (82%), Gaps = 1/712 (0%) Query: 1 MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRTGGDAPDQTTTIVRAN 60 MSR IMLIP GT VGLTS+SLG++RA+ER GV++ FKPIAQ R P+++TTI+ + Sbjct: 1 MSRNIMLIPNGTGVGLTSISLGMVRALERHGVKVRFFKPIAQQRPTDKGPERSTTIL-SK 59 Query: 61 SSTTTAAEPLKMSYVEGLLSSNQKDVLMEEIVANYHANTKDAEVVLVEGLVPTRKHQFAQ 120 S T EP M++ E L+ ++Q DVLME+I+A +E ++VEGLV TR H F+ Sbjct: 60 SPTVNPLEPFDMAHAEHLIRTDQTDVLMEQIIARATECADPSETLIVEGLVQTRNHPFSD 119 Query: 121 SLNYEIAKTLNAEIVFVMSQGTDTPEQLKERIELTRNSFGGAKNTNITGVIVNKLNAPVD 180 +NYEIAK L+A+I+FV + G +TP L R+E+ N++GG+KN + G I+NK+ APVD Sbjct: 120 DINYEIAKALDADIIFVAAPGNETPTALMNRLEIAHNAWGGSKNKRLIGAIINKIGAPVD 179 Query: 181 EQGRTRPDLSEIFDDSSKAKVNNVDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLN 240 ++GR RPDLSE+FD + + +L S L +LG+VP++ +L+A RA D+A+HL+ Sbjct: 180 DEGRARPDLSEVFDHQDVQRPDAASMFQLPGKSKLRILGSVPYNLNLVAPRASDLAKHLS 239 Query: 241 ATIINEGDINTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEI 300 A IIN G++NTRR++ VTFCARSIP+M+ H + SLLVTS DR DV+V+ACLAAMNGV++ Sbjct: 240 ARIINAGEMNTRRLRKVTFCARSIPNMVTHIKTDSLLVTSGDRSDVIVSACLAAMNGVKV 299 Query: 301 GALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEK 360 GALLLTG YE + I LCE+AF TGLPVF+++TNTWQTSL++Q F+ EVPVDD RIE+ Sbjct: 300 GALLLTGSYEPEPEIMALCEQAFETGLPVFLIDTNTWQTSLNIQRFDHEVPVDDAVRIEE 359 Query: 361 VQEYVANYINADWIESLTATSERSRRLSPPAFRYQLTELARKAGKRIVLPEGDEPRTVKA 420 VQEYVA++I+ W+ES+T S R RLSPPAFRY+LTELAR A K +VLPEGDEPRT++A Sbjct: 360 VQEYVASHIDQSWVESVTMNSPREHRLSPPAFRYKLTELARAAAKTVVLPEGDEPRTIEA 419 Query: 421 AAICAERGIATCVLLGNPAEINRVAASQGVELGAGIEIVDPEVVRESYVGRLVELRKNKG 480 AAICAERGIA CVL+GNP EI R+A+ QGV LG G+EI++PE RE YV +VELR++KG Sbjct: 420 AAICAERGIARCVLIGNPEEIQRIASQQGVTLGEGVEIIEPETARERYVAPMVELRRHKG 479 Query: 481 MTETVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSV 540 MTE VAREQLEDN+VLGT+ML Q EVDG+VSGAV+TTANTIRPPLQLIKTAPGSSLVSS+ Sbjct: 480 MTEVVAREQLEDNMVLGTMMLAQGEVDGIVSGAVNTTANTIRPPLQLIKTAPGSSLVSSI 539 Query: 541 FFMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAAAFGIEPRVAMLSYSTGTSGAGS 600 FFML+P+QV VYGDCAINPDP AEQLA+IAIQSADSAAAFGIEP+VAM+SYSTG+SG GS Sbjct: 540 FFMLMPDQVLVYGDCAINPDPNAEQLADIAIQSADSAAAFGIEPKVAMISYSTGSSGTGS 599 Query: 601 DVEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTG 660 DV+KVREATR+A+EKRP+L+IDGPLQYDAAVM +VA+SKAPNSPVAG+ATVF+FPDLNTG Sbjct: 600 DVDKVREATRIAKEKRPELVIDGPLQYDAAVMPNVAQSKAPNSPVAGQATVFVFPDLNTG 659 Query: 661 NTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQSAQ 712 NTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQ++Q Sbjct: 660 NTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ 711 Lambda K H 0.316 0.131 0.363 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: 1362 Number of extensions: 41 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: 714 Length of database: 712 Length adjustment: 39 Effective length of query: 675 Effective length of database: 673 Effective search space: 454275 Effective search space used: 454275 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 (21.6 bits) S2: 55 (25.8 bits)
Align candidate 5209946 Shew_2394 (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.6510.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-139 448.8 0.1 8.8e-139 448.1 0.1 1.3 1 lcl|FitnessBrowser__PV4:5209946 Shew_2394 phosphate acetyltransf Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209946 Shew_2394 phosphate acetyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 448.1 0.1 8.8e-139 8.8e-139 1 304 [] 406 706 .. 406 706 .. 0.97 Alignments for each domain: == domain 1 score: 448.1 bits; conditional E-value: 8.8e-139 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekrkhkGv 77 +vlPEg+e+r+++Aaa++ae++ia++vl++n ee+++ + ++v l + v++++p++ +e+yv ++e+r+hkG+ lcl|FitnessBrowser__PV4:5209946 406 VVLPEGDEPRTIEAAAICAERGIARCVLIGNPEEIQRIaSQQGVTLG-EGVEIIEPETA--RERYVAPMVELRRHKGM 480 69***********************************7334444444.45778888888..8**************** PP TIGR00651 78 tekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfaDCavav 155 te areql+D+++l+++++++ge+dg+vsGav+tta+t+rp+lq+ikt++g++lvss+f+m +++vlv++DCa+++ lcl|FitnessBrowser__PV4:5209946 481 TEVVAREQLEDNMVLGTMMLAQGEVDGIVSGAVNTTANTIRPPLQLIKTAPGSSLVSSIFFMLMPDQVLVYGDCAINP 558 ****************************************************************************** PP TIGR00651 156 dPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqfDaAlvekva 233 dPnae+LA+iA+qsa+sa ++g +epkva++syst++sg g++v+kv+eA++i+kek+p+l++dG+lq+DaA++++va lcl|FitnessBrowser__PV4:5209946 559 DPNAEQLADIAIQSADSAAAFG-IEPKVAMISYSTGSSGTGSDVDKVREATRIAKEKRPELVIDGPLQYDAAVMPNVA 635 **********************.******************************************************* PP TIGR00651 234 ekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviita 304 ++kap+s+vag+a+vfvFPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kPvnDLsRGa+v+div+++++ta lcl|FitnessBrowser__PV4:5209946 636 QSKAPNSPVAGQATVFVFPDLNTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTA 706 *********************************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (712 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: 20.25 // [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