Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_039104752.1 FPB0191_RS06180 phosphate acetyltransferase
Query= BRENDA::Q8ZND6 (714 letters) >NCBI__GCF_000807275.1:WP_039104752.1 Length = 712 Score = 1042 bits (2694), Expect = 0.0 Identities = 519/713 (72%), Positives = 615/713 (86%), Gaps = 2/713 (0%) Query: 1 MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN 60 M+R IMLIPT ++VGLT VSLGVIR+MER+GV++S+FKP+AQP GGD PDQTTT++++N Sbjct: 1 MARTIMLIPTSSNVGLTGVSLGVIRSMERQGVKISLFKPVAQPALGGDRPDQTTTLIQSN 60 Query: 61 STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS 120 +++P+ +PLKMSHVE L+ NQ+DVLMEEIIA + N K +EVVLVEG+VPT + FA Sbjct: 61 TSIPSNKPLKMSHVEKLIGLNQQDVLMEEIIALFAENNKQSEVVLVEGIVPTNNYPFASE 120 Query: 121 LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE 180 LNY IAKTL AEI+FVMS G+DTPEQL ER+E+ RS+FGG KN ITGVIINK+NAP+D Sbjct: 121 LNYNIAKTLGAEIIFVMSMGSDTPEQLKERVEIARSNFGGVKNEKITGVIINKVNAPIDA 180 Query: 181 QGRTRPDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNA 240 Q RPD+S+I+ + K I L++ SPLPVLG +PW+ DL A RAIDMA HL+A Sbjct: 181 QTLARPDVSDIYH-TPKFDGKTITIEDLRQHSPLPVLGCIPWNIDLTACRAIDMANHLSA 239 Query: 241 TIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG 300 IINEG IK RR+K V+FC+RS+P+++ H R +LLVTSADR D++ LA MNG EIG Sbjct: 240 KIINEGGIKQRRIKHVSFCSRSVPNIISHLRPNALLVTSADRADIITTISLAVMNGTEIG 299 Query: 301 ALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV 360 +LLTGGYE+DA ++KLC+ AF TGLPVF V+TNT+QTS++LQ FNLE+PVDD ER++ Sbjct: 300 GVLLTGGYELDANVAKLCKPAFETGLPVFSVDTNTFQTSINLQRFNLEIPVDDKERLDNT 359 Query: 361 QEYVANYVNAEWIESLTATSERS-RRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKA 419 Q +VA+++++EWI++L S R+SPPAFRYQLTE ARKAGK +VLPEGDEPRT+KA Sbjct: 360 QNFVADHIDSEWIKALKNESTSGIARMSPPAFRYQLTEFARKAGKTIVLPEGDEPRTIKA 419 Query: 420 AAICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKG 479 A ICAERGIA CVLLGNPDEI RVAA+QGV LGAGIEI+DPE +RE+YV RLVELRK+KG Sbjct: 420 AVICAERGIAKCVLLGNPDEIKRVAATQGVTLGAGIEIMDPEAIRENYVPRLVELRKNKG 479 Query: 480 MTEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSV 539 MTE +AREQL DNVVLGT+MLE+DEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSV Sbjct: 480 MTEILAREQLADNVVLGTMMLERDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSV 539 Query: 540 FFMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGS 599 FFML+PEQVY+YGDCAINPDP A++LAEIAIQSAD+AIAFGIEP+VAM+SYSTG SG G+ Sbjct: 540 FFMLMPEQVYIYGDCAINPDPNAQELAEIAIQSADTAIAFGIEPKVAMISYSTGNSGQGA 599 Query: 600 DVEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTG 659 DVEKV+EATR+A+EKRPDL+IDGPLQYDAAVM DVAKSKAPNS VAG+ATVFIFPDLNTG Sbjct: 600 DVEKVKEATRIAKEKRPDLLIDGPLQYDAAVMPDVAKSKAPNSQVAGQATVFIFPDLNTG 659 Query: 660 NTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQQ 712 NTTYKAVQRSADL+SIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQA+QQ Sbjct: 660 NTTYKAVQRSADLVSIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQATQQ 712 Lambda K H 0.316 0.131 0.364 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: 1355 Number of extensions: 41 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: 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 WP_039104752.1 FPB0191_RS06180 (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.2188355.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-140 451.3 0.1 1.3e-139 450.9 0.1 1.1 1 NCBI__GCF_000807275.1:WP_039104752.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000807275.1:WP_039104752.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 450.9 0.1 1.3e-139 1.3e-139 1 304 [] 406 706 .. 406 706 .. 0.97 Alignments for each domain: == domain 1 score: 450.9 bits; conditional E-value: 1.3e-139 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 ivlPEg+e+r++kAa ++ae++ia++vll+n +e++++ ++++v l +g +++dp+ +e+yv rl+e+r NCBI__GCF_000807275.1:WP_039104752.1 406 IVLPEGDEPRTIKAAVICAERGIAKCVLLGNPDEIKRVaATQGVTLGAGI-EIMDPEAI--RENYVPRLVELR 475 8************************************9667888887775.56666666..6*********** PP TIGR00651 73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145 k+kG+te areql D+v+l+++++e +e+dglvsGav+tta+t+rp+lq+ikt++g++lvssvf+m +e+v NCBI__GCF_000807275.1:WP_039104752.1 476 KNKGMTEILAREQLADNVVLGTMMLERDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVFFMLMPEQV 548 ************************************************************************* PP TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218 ++++DCa+++dPna+eLAeiA+qsa++a ++g +epkva++syst+ sg+g++vekvkeA++i+kek+pdll+ NCBI__GCF_000807275.1:WP_039104752.1 549 YIYGDCAINPDPNAQELAEIAIQSADTAIAFG-IEPKVAMISYSTGNSGQGADVEKVKEATRIAKEKRPDLLI 620 ********************************.**************************************** PP TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291 dG+lq+DaA++++va++kap+s+vag+a+vf+FPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kPvnDLsRGa NCBI__GCF_000807275.1:WP_039104752.1 621 DGPLQYDAAVMPDVAKSKAPNSQVAGQATVFIFPDLNTGNTTYKAVQRSADLVSIGPMLQGMRKPVNDLSRGA 693 ************************************************************************* PP TIGR00651 292 svedivnvviita 304 +v+div+++++ta NCBI__GCF_000807275.1:WP_039104752.1 694 LVDDIVYTIALTA 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: 00:00:00.00 # Mc/sec: 26.03 // [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