Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_033298495.1 G327_RS0116360 phosphate acetyltransferase
Query= BRENDA::P0A9M8 (714 letters) >NCBI__GCF_000381745.1:WP_033298495.1 Length = 715 Score = 956 bits (2472), Expect = 0.0 Identities = 473/709 (66%), Positives = 582/709 (82%), Gaps = 1/709 (0%) Query: 6 MLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRTGGDAPDQTTTIVRANSSTTT 65 MLIP G+ VG+TSVSLG++RAMER+GV ++ FKPIAQPR G P+++TT +R N S+ T Sbjct: 1 MLIPIGSGVGVTSVSLGMVRAMERQGVAVNFFKPIAQPRPGDTGPERSTTTLR-NGSSLT 59 Query: 66 AAEPLKMSYVEGLLSSNQKDVLMEEIVANYHANTKDAEVVLVEGLVPTRKHQFAQSLNYE 125 EP M Y E L+SS + L+E IV + TK+++V++VEGLVPT KHQFA +NY Sbjct: 60 PPEPFSMKYAENLISSGRTSDLLENIVERFREGTKESDVIIVEGLVPTDKHQFANEINYS 119 Query: 126 IAKTLNAEIVFVMSQGTDTPEQLKERIELTRNSFGGAKNTNITGVIVNKLNAPVDEQGRT 185 IAK L+AE+VFV D+ +QLKER+E+ +SFGG KN I G I+NK+ APVDE ++ Sbjct: 120 IAKALSAEMVFVTHPSNDSSQQLKERMEIAVSSFGGKKNKRIAGCIINKVGAPVDENDKS 179 Query: 186 RPDLSEIFDDSSKAKVNNVDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNATIIN 245 RPDL+E+FD NN++ ++ SPLP+LG +PWS +LIA R D+A HL A ++N Sbjct: 180 RPDLTEMFDIPDGVVNNNLEVLQMFSKSPLPILGCIPWSAELIAPRVKDLATHLEAQVLN 239 Query: 246 EGDINTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIGALLL 305 GD++ RR+ SVTFCARSIP+M+EHF+AGS+LVTS DR DV++AACLA MNG++IG LLL Sbjct: 240 VGDLDNRRLHSVTFCARSIPNMVEHFKAGSMLVTSGDRSDVIIAACLAVMNGMKIGCLLL 299 Query: 306 TGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKVQEYV 365 TG Y + + KLC RA +GLP+ ++ +NTWQT+ LQ FN+E+PVDD ERIEKVQEY+ Sbjct: 300 TGDYPPEEEVMKLCSRAMESGLPILLIKSNTWQTAQRLQHFNMEIPVDDIERIEKVQEYI 359 Query: 366 ANYINADWIESLTATSERSRRLSPPAFRYQLTELARKAGKRIVLPEGDEPRTVKAAAICA 425 A++I+ W+ +LT S +RRLSPPAFRY LTELARK +RIVLPEG+EPRT++AA ICA Sbjct: 360 ASHIDKHWLNTLTEDSSLTRRLSPPAFRYHLTELARKTSQRIVLPEGEEPRTIQAALICA 419 Query: 426 ERGIATCVLLGNPAEINRVAASQGVELGAGIEIVDPEVVRESYVGRLVELRKNKGMTETV 485 +RGIA VLLGNP EI+R+A QG+EL +EI++P V E+YV +VELRK KG+TE V Sbjct: 420 QRGIAKPVLLGNPEEIHRIATQQGIELTDDVEIINPFDVLENYVAPMVELRKAKGLTEVV 479 Query: 486 AREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVFFMLL 545 AREQL+D VVLGT+ML ++EV GLVSGAVHTTANTIRPPLQL+KTAP +SLVSS+FFMLL Sbjct: 480 AREQLQDTVVLGTMMLAENEVAGLVSGAVHTTANTIRPPLQLVKTAPDASLVSSIFFMLL 539 Query: 546 PEQVYVYGDCAINPDPTAEQLAEIAIQSADSAAAFGIEPRVAMLSYSTGTSGAGSDVEKV 605 P+QV VYGDCAINPDPTAEQLA+IAIQSADSA AFGI+P+VAM+SYSTGTSGAGSDVEKV Sbjct: 540 PDQVLVYGDCAINPDPTAEQLADIAIQSADSAIAFGIDPKVAMISYSTGTSGAGSDVEKV 599 Query: 606 REATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGNTTYK 665 REAT++AQ++RPDL+IDGPLQYDAAVM +VA+SKAPNSPVAG+ATVFIFPDLNTGNTTYK Sbjct: 600 REATKIAQDRRPDLLIDGPLQYDAAVMENVAQSKAPNSPVAGKATVFIFPDLNTGNTTYK 659 Query: 666 AVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQSAQQQ 714 AVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQ+ Q + Sbjct: 660 AVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQATQAE 708 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: 1303 Number of extensions: 44 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: 714 Length of database: 715 Length adjustment: 39 Effective length of query: 675 Effective length of database: 676 Effective search space: 456300 Effective search space used: 456300 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 WP_033298495.1 G327_RS0116360 (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.2227328.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-134 433.5 0.6 4.2e-134 432.7 0.1 1.6 2 NCBI__GCF_000381745.1:WP_033298495.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000381745.1:WP_033298495.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.6 0.0 0.16 0.16 26 72 .. 322 366 .. 306 376 .. 0.64 2 ! 432.7 0.1 4.2e-134 4.2e-134 1 304 [] 401 701 .. 401 701 .. 0.98 Alignments for each domain: == domain 1 score: -2.6 bits; conditional E-value: 0.16 TIGR00651 26 kvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekr 72 ++ll+++++ ++ a+++++ ++ v+d + +++++y+ ++k+ NCBI__GCF_000381745.1:WP_033298495.1 322 PILLIKSNTWQT--AQRLQHFNMEIPVDDIERIEKVQEYIASHIDKH 366 456666665555..566666666677777777777788887777665 PP == domain 2 score: 432.7 bits; conditional E-value: 4.2e-134 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 ivlPEg+e+r+++Aa ++a+++ia++vll+n ee+++ + ++++l+ ++++ dv e+yv ++e+r NCBI__GCF_000381745.1:WP_033298495.1 401 IVLPEGEEPRTIQAALICAQRGIAKPVLLGNPEEIHRIaTQQGIELTDDVEIINPFDVL---ENYVAPMVELR 470 8************************************9778899998888888888888...*********** PP TIGR00651 73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145 k+kG+te areql+D+v+l++++++ +e+ glvsGav+tta+t+rp+lq++kt++ +lvss+f+m ++++v NCBI__GCF_000381745.1:WP_033298495.1 471 KAKGLTEVVAREQLQDTVVLGTMMLAENEVAGLVSGAVHTTANTIRPPLQLVKTAPDASLVSSIFFMLLPDQV 543 ************************************************************************* PP TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218 lv++DCa+++dP+ae+LA+iA+qsa+sa ++g ++pkva++syst++sg+g++vekv+eA+ki+++++pdll+ NCBI__GCF_000381745.1:WP_033298495.1 544 LVYGDCAINPDPTAEQLADIAIQSADSAIAFG-IDPKVAMISYSTGTSGAGSDVEKVREATKIAQDRRPDLLI 615 ********************************.**************************************** PP TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291 dG+lq+DaA++e+va++kap+s+vagka+vf+FPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kPvnDLsRGa NCBI__GCF_000381745.1:WP_033298495.1 616 DGPLQYDAAVMENVAQSKAPNSPVAGKATVFIFPDLNTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGA 688 ************************************************************************* PP TIGR00651 292 svedivnvviita 304 +v+div+++++ta NCBI__GCF_000381745.1:WP_033298495.1 689 LVDDIVYTIALTA 701 ***********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (715 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: 36.78 // [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