Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_020303665.1 M988_RS06645 phosphate acetyltransferase
Query= BRENDA::Q8ZND6 (714 letters) >NCBI__GCF_001655005.1:WP_020303665.1 Length = 718 Score = 1219 bits (3154), Expect = 0.0 Identities = 618/711 (86%), Positives = 669/711 (94%) Query: 1 MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN 60 MSR IMLIPT TSVGLTSVSLGVIR+ME+KGVRLSVFKPIAQPR GGD+ DQTTTI+RAN Sbjct: 1 MSRTIMLIPTSTSVGLTSVSLGVIRSMEQKGVRLSVFKPIAQPRTGGDSLDQTTTIIRAN 60 Query: 61 STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS 120 S++PAAEPL+MSHVE+LLSSNQ+DVLMEEI+A YH NTKDAEVVLVEGLVPTRKHQFA + Sbjct: 61 SSIPAAEPLRMSHVETLLSSNQQDVLMEEIVARYHENTKDAEVVLVEGLVPTRKHQFANA 120 Query: 121 LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE 180 LNYEIAKTLNAEIVFVM+ G DT Q+ ERIEL RSSFGG+KN NITGVIINKLNAPVD+ Sbjct: 121 LNYEIAKTLNAEIVFVMALGNDTASQVKERIELARSSFGGSKNKNITGVIINKLNAPVDD 180 Query: 181 QGRTRPDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNA 240 QGRTRPDLSEIFDDS+KA V +D A+L +SPLPVLG VPWSF+LIATRAIDMA HL A Sbjct: 181 QGRTRPDLSEIFDDSNKASVANLDTAQLVANSPLPVLGCVPWSFELIATRAIDMANHLKA 240 Query: 241 TIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG 300 I+NEGDIKTRR+KSVTFCARSIPHMLEHFR GSLLVTSADRPDVLVAACLAAMNGVEIG Sbjct: 241 RIVNEGDIKTRRIKSVTFCARSIPHMLEHFRPGSLLVTSADRPDVLVAACLAAMNGVEIG 300 Query: 301 ALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV 360 A+LLTGGY+MD RI+KLCERAF TGLPVFMV+TNTWQTSLSLQSFNLEVP DDH+R+EK+ Sbjct: 301 AILLTGGYDMDERIAKLCERAFQTGLPVFMVDTNTWQTSLSLQSFNLEVPADDHQRVEKL 360 Query: 361 QEYVANYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKAA 420 Q YVA++++++WI+SLTA SERSRRLSPPAFRY+LTELARKA KRVVLPEGDEPRTVKAA Sbjct: 361 QNYVASHIDSKWIDSLTAASERSRRLSPPAFRYELTELARKACKRVVLPEGDEPRTVKAA 420 Query: 421 AICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGM 480 AICAERGIA CVLLGNP+EI RVAA+QGV LG GIEIVDP VVRE YV RLVELRK+KGM Sbjct: 421 AICAERGIAECVLLGNPEEIQRVAAAQGVVLGKGIEIVDPNVVREQYVPRLVELRKNKGM 480 Query: 481 TEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF 540 TE VAREQLEDNVVLGTLMLEQ++VDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF Sbjct: 481 TEVVAREQLEDNVVLGTLMLEQNQVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF 540 Query: 541 FMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSD 600 FMLLP+QV VYGDCAINPDPTAEQL+EIAIQSADSA AFGIEPRVAM+SYSTG SGAGSD Sbjct: 541 FMLLPDQVLVYGDCAINPDPTAEQLSEIAIQSADSAAAFGIEPRVAMISYSTGNSGAGSD 600 Query: 601 VEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGN 660 VEKVREATRLAQEKRPDL+IDGPLQYDAA+MADVAKSKAPNSPVAG+ATVFIFPDLNTGN Sbjct: 601 VEKVREATRLAQEKRPDLIIDGPLQYDAAIMADVAKSKAPNSPVAGKATVFIFPDLNTGN 660 Query: 661 TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ 711 TTYKAVQRSADL+SIGPMLQGMRKPVNDLSRGALVDDIVYT+ALTAIQA+Q Sbjct: 661 TTYKAVQRSADLVSIGPMLQGMRKPVNDLSRGALVDDIVYTVALTAIQAAQ 711 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: 1446 Number of extensions: 44 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: 714 Length of database: 718 Length adjustment: 40 Effective length of query: 674 Effective length of database: 678 Effective search space: 456972 Effective search space used: 456972 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_020303665.1 M988_RS06645 (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.3088462.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-140 451.4 0.1 1.3e-139 450.8 0.1 1.3 1 NCBI__GCF_001655005.1:WP_020303665.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001655005.1:WP_020303665.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 450.8 0.1 1.3e-139 1.3e-139 1 304 [] 406 706 .. 406 706 .. 0.97 Alignments for each domain: == domain 1 score: 450.8 bits; conditional E-value: 1.3e-139 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 +vlPEg+e+r++kAaa++ae++iae+vll+n ee++++ +a++v l g ++++dp+v +e+yv rl+e+r NCBI__GCF_001655005.1:WP_020303665.1 406 VVLPEGDEPRTVKAAAICAERGIAECVLLGNPEEIQRVaAAQGVVLGKG-IEIVDPNVV--REQYVPRLVELR 475 69***********************************966777777665.667777777..7*********** PP TIGR00651 73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145 k+kG+te areql+D+v+l++l++e++++dglvsGav+tta+t+rp+lq+ikt++g++lvssvf+m ++++v NCBI__GCF_001655005.1:WP_020303665.1 476 KNKGMTEVVAREQLEDNVVLGTLMLEQNQVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVFFMLLPDQV 548 ************************************************************************* PP TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218 lv++DCa+++dP+ae+L eiA+qsa+sa ++g +ep+va++syst+ sg+g++vekv+eA+++++ek+pdl + NCBI__GCF_001655005.1:WP_020303665.1 549 LVYGDCAINPDPTAEQLSEIAIQSADSAAAFG-IEPRVAMISYSTGNSGAGSDVEKVREATRLAQEKRPDLII 620 ********************************.**************************************** PP TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291 dG+lq+DaA++++va++kap+s+vagka+vf+FPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kPvnDLsRGa NCBI__GCF_001655005.1:WP_020303665.1 621 DGPLQYDAAIMADVAKSKAPNSPVAGKATVFIFPDLNTGNTTYKAVQRSADLVSIGPMLQGMRKPVNDLSRGA 693 ************************************************************************* PP TIGR00651 292 svedivnvviita 304 +v+div++v++ta NCBI__GCF_001655005.1:WP_020303665.1 694 LVDDIVYTVALTA 706 ***********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (718 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 29.37 // [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