Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_062735419.1 AYX06_RS08590 phosphate acetyltransferase
Query= BRENDA::C1DQG8 (712 letters) >NCBI__GCF_001580365.1:WP_062735419.1 Length = 697 Score = 407 bits (1046), Expect = e-118 Identities = 275/701 (39%), Positives = 390/701 (55%), Gaps = 43/701 (6%) Query: 14 GLNSISLGLIRALEQAGLKVGFFKPI------AQPFPIDQGRERSCLLVERTLGRSTPEP 67 G + ++LGL +L + ++G+F+P+ A+ + + L ER G Sbjct: 15 GKSLVTLGLADSLFRRTDRLGYFRPVHLGSSPAEDPMVQLMKRNFDLPDERCRGG----- 69 Query: 68 ILLDQVERHLASGETDLLLEEVVSRYQQAAAGKDVVIVEG--MLPTRDSDYSAYLNPLLS 125 + L + LA+G+ D L VS Y + A DV++V+G +L + +N ++ Sbjct: 70 LSLARTRELLAAGDHDELDSMAVSVYGEMARHCDVIVVDGTDLLAHNAATAEFDMNARMA 129 Query: 126 KSLNAEVI-LIAVQGGDGLKQLAERIEI-QAQLFGGIKSPKVLGAIINKIDSGDGIPAFV 183 +L V+ +I + + + IE+ +A+L + I+N+ P +V Sbjct: 130 NNLGTSVLAVIGADESESPEDVLNAIEVTRAELHQA--RCDIFAVIVNRAR-----PEWV 182 Query: 184 ERLKEYLPSLGSTDFQLFGAIPFAEELNALRTRDVAELIGAQVLSAGEAD---RRRVSKI 240 ++L S G ++ E A+ VAEL G + R V + Sbjct: 183 DQLSTNA-SRGVRGLPVY----VIAENAAVAAPTVAELRDRHGFGDGPSAVSLDRDVKGV 237 Query: 241 VLCARAVPSTVPLLQPGVLVVTPGDRDDVILAASLASLNGVKL---AGLLLCSDFMPDPR 297 + A V + L G V+TPGDR D+++A SLAS L +G+LL F + R Sbjct: 238 KIAAMTVAHYLEQLADGDFVITPGDRSDIVVA-SLASALSPALPVPSGMLLTGGFGTEGR 296 Query: 298 IMELCKAALDGGLPVMSVTTGSYDTATNLFALNKETPADDIERATRVTDFIAGHLHPEYL 357 I EL AA PV++ +Y A + + A + E L Sbjct: 297 IQELTAAA---PFPVLTTGLDTYSAARAVSRSRGTLSGAHPRKVAAALGEWARRVDDEEL 353 Query: 358 RSRCSLPRELLLSPPAFRYQLVKSAQEADKRIVLPEGTEPRTIRAAAICQERGIARCVLL 417 SR LPR L +P F ++LV++A+ K IVLPEG +PR +RAA + R +L Sbjct: 354 VSRLDLPRPLRRTPLRFLHELVEAARTQRKNIVLPEGEDPRILRAAEMIHRRNFCDLTIL 413 Query: 418 ARPEEVRAVAREQGITLP---DGLEILD---PESIRAQYIAPMVKMRQSKGLTPEMADEQ 471 P ++ + + +GI L +GL ++D E++R +Y V++R KG+ PE A E+ Sbjct: 414 GDPAKIAGLCQTEGINLDFDDEGLTLIDFEHDEALREKYAGEYVRLRAHKGVQPEAALER 473 Query: 472 LRDTVVLGTMMLALDEVDGLVSGAVHTTANTIRPALQLIKTAPGYNLVSSVFFMLLPDQV 531 + D GTMM+ + +VDG+VSGA HTTANTIRPAL+ +KT+ G +VSSVFFMLL D+V Sbjct: 474 MLDGSYFGTMMVQMGDVDGMVSGAAHTTANTIRPALEFVKTSEGVRIVSSVFFMLLEDRV 533 Query: 532 LVYGDCAVNPNPSAAELAEIALQSAESAVALGVHPRVAMISYSTGDSGSGAEVDKVREAT 591 LVYGDCAVNPNP A +LA+IAL SA +A GV PRVAM+SYSTG SGSG +VDKVR AT Sbjct: 534 LVYGDCAVNPNPDAQQLADIALASARTARQFGVEPRVAMLSYSTGGSGSGQDVDKVRAAT 593 Query: 592 RIAQERAPGLPIDGPLQYDAASVASVGKQKAPNSPVAGQATVFVFPDLNTGNTTYKAVQR 651 I + P L ++GP+QYDAA AS+ K P S VAG+ATVFVFPDLNTGN TYKAVQ+ Sbjct: 594 EIVRAADPELEVEGPIQYDAAVDASIAASKLPGSTVAGRATVFVFPDLNTGNNTYKAVQQ 653 Query: 652 NANCISVGPMLQGLAKPVNDLSRGALVDDIVFTIALTALQA 692 +A ++VGP+LQGL KPVNDLSRG VDDIV T+A+TA+QA Sbjct: 654 SAGAVAVGPVLQGLRKPVNDLSRGCTVDDIVNTVAITAIQA 694 Lambda K H 0.318 0.135 0.379 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: 1157 Number of extensions: 52 Number of successful extensions: 5 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: 712 Length of database: 697 Length adjustment: 39 Effective length of query: 673 Effective length of database: 658 Effective search space: 442834 Effective search space used: 442834 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: 54 (25.4 bits)
Align candidate WP_062735419.1 AYX06_RS08590 (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.2191782.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-124 400.4 0.0 4.2e-124 399.9 0.0 1.2 1 NCBI__GCF_001580365.1:WP_062735419.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001580365.1:WP_062735419.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.9 0.0 4.2e-124 4.2e-124 1 304 [] 385 691 .. 385 691 .. 0.96 Alignments for each domain: == domain 1 score: 399.9 bits; conditional E-value: 4.2e-124 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkv..vved.pdvskdiekyverly 69 ivlPEg+++r+l+Aa+++ +++ + ++l++ +++ +++++nl+ + +++d ++ +eky+ +++ NCBI__GCF_001580365.1:WP_062735419.1 385 IVLPEGEDPRILRAAEMIHRRNFCDLTILGDPAKIAGLcQTEGINLDFDDEglTLIDfEHDEALREKYAGEYV 457 8**********************************998889999988766411344413444458******** PP TIGR00651 70 ekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimeke 142 +r hkGv+ ++a e + D +++++++v++g +dg+vsGa++tta+t+rpal+ +kt egv++vssvf+m +e NCBI__GCF_001580365.1:WP_062735419.1 458 RLRAHKGVQPEAALERMLDGSYFGTMMVQMGDVDGMVSGAAHTTANTIRPALEFVKTSEGVRIVSSVFFMLLE 530 ************************************************************************* PP TIGR00651 143 eevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepd 215 ++vlv++DCav+++P+a++LA+iAl sa +a+++g ep+va+lsyst+gsg+g++v+kv+ A++i++ p+ NCBI__GCF_001580365.1:WP_062735419.1 531 DRVLVYGDCAVNPNPDAQQLADIALASARTARQFG-VEPRVAMLSYSTGGSGSGQDVDKVRAATEIVRAADPE 602 ***********************************.************************************* PP TIGR00651 216 llldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLs 288 l ++G++q+DaA+ +++a++k p s+vag+a+vfvFPdL++Gn++Yk+vq +a+a a+GP+lqGl+kPvnDLs NCBI__GCF_001580365.1:WP_062735419.1 603 LEVEGPIQYDAAVDASIAASKLPGSTVAGRATVFVFPDLNTGNNTYKAVQQSAGAVAVGPVLQGLRKPVNDLS 675 ************************************************************************* PP TIGR00651 289 RGasvedivnvviita 304 RG++v+divn+v+ita NCBI__GCF_001580365.1:WP_062735419.1 676 RGCTVDDIVNTVAITA 691 **************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (697 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 36.15 // [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