Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_027699422.1 TT13_RS07580 phosphate acetyltransferase
Query= metacyc::MONOMER-13062 (328 letters) >NCBI__GCF_000691805.2:WP_027699422.1 Length = 324 Score = 406 bits (1044), Expect = e-118 Identities = 212/324 (65%), Positives = 253/324 (78%) Query: 1 MDLFESLKSKIKDRKIKLVFPEGEDERIISAASRLANDDLAIPVLLGNEAEIKKTADALN 60 M+LFE L +KI ++ LVFPEGED RI AA RLA + L P+LLG +EI TA + Sbjct: 1 MELFEQLSAKILNQGKILVFPEGEDVRIQGAAIRLAANGLVKPILLGVASEIAATAASHG 60 Query: 61 VSLDGIEIVDIENVPGEVRQQMVQAIVERRKGKTTADQAAQWLKDPNYFGTTMVYMDDVD 120 L IEI+D P + + MV+A+VERR GKT A AA+WLKD NYFGT +VY+ D Sbjct: 61 FDLSSIEIIDPAQYPSDKFEAMVEALVERRNGKTDAVTAAKWLKDVNYFGTMLVYLGQAD 120 Query: 121 GMVSGAAHPTGDTVRPALQIIKTKPGVNLISGSFVMQKGDQRYLFADCAININPNETQLA 180 GMVSGA HPTGDTVRPALQI+KTKPG + ISG+FVMQK DQRY+FAD AINI+ + +A Sbjct: 121 GMVSGATHPTGDTVRPALQIVKTKPGSSRISGAFVMQKADQRYIFADAAINIDIDAQTMA 180 Query: 181 EIAVESGKTARLFDIDPRVALLSFSTNGSAKSPEVEKVHNATKLAQEMDPAMPIDGEMQF 240 EIAV+S +TA++F IDP+VA+LSFST GSAK+P+V+KV ATKLAQ P + IDGE+QF Sbjct: 181 EIAVQSAQTAKVFGIDPKVAMLSFSTKGSAKAPQVDKVAEATKLAQVAAPELLIDGELQF 240 Query: 241 DAAFVPAVAKAKYSDSKVAGHATVFVFPELQSGNIGYKIAQRMGGFEAIGPILQGLNKPV 300 DAAFV +VA AK +SKVAG A VFVFP+LQSGNIGYKIAQR+GGFEAIGP+LQGL KP+ Sbjct: 241 DAAFVESVAAAKAPNSKVAGQANVFVFPDLQSGNIGYKIAQRLGGFEAIGPVLQGLAKPI 300 Query: 301 SDLSRGCNAEDVYKVSIITATQAL 324 SDLSRG N EDVYKV+IITA QAL Sbjct: 301 SDLSRGANEEDVYKVAIITAAQAL 324 Lambda K H 0.315 0.133 0.369 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: 340 Number of extensions: 7 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: 328 Length of database: 324 Length adjustment: 28 Effective length of query: 300 Effective length of database: 296 Effective search space: 88800 Effective search space used: 88800 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: 48 (23.1 bits)
Align candidate WP_027699422.1 TT13_RS07580 (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.2191886.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-115 371.1 0.9 2.9e-115 370.9 0.9 1.0 1 NCBI__GCF_000691805.2:WP_027699422.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000691805.2:WP_027699422.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 370.9 0.9 2.9e-115 2.9e-115 1 304 [] 18 320 .. 18 320 .. 0.97 Alignments for each domain: == domain 1 score: 370.9 bits; conditional E-value: 2.9e-115 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvsk..diekyverlyek 71 +v+PEg++ r+ Aa+ la +++++++ll+ +e+ + +a++ +l++++++dp ++ + e ve+l+e+ NCBI__GCF_000691805.2:WP_027699422.1 18 LVFPEGEDVRIQGAAIRLAANGLVKPILLGVASEIAA-TAASHGFDLSSIEIIDPAQYPsdKFEAMVEALVER 89 69*************************9999888887.78888999999***999987522689********* PP TIGR00651 72 rkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeee 144 r k + +a++ l+D ++++++lv+lg+adg+vsGa + t +t+rpalqi+kt++g++ +s+ f+m+k ++ NCBI__GCF_000691805.2:WP_027699422.1 90 RNGK-TDAVTAAKWLKDVNYFGTMLVYLGQADGMVSGATHPTGDTVRPALQIVKTKPGSSRISGAFVMQKADQ 161 ****.8999999************************************************************* PP TIGR00651 145 vlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdll 217 +++faD a+++d +a+ +AeiA+qsa++ak +g ++pkva+ls+stkgs+k+ +v+kv+eA+k+++ +p+ll NCBI__GCF_000691805.2:WP_027699422.1 162 RYIFADAAINIDIDAQTMAEIAVQSAQTAKVFG-IDPKVAMLSFSTKGSAKAPQVDKVAEATKLAQVAAPELL 233 *********************************.*************************************** PP TIGR00651 218 ldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRG 290 +dGelqfDaA+ve+va+ kap+s+vag+anvfvFPdL++GnigYki+qRl+++eaiGP+lqGlakP++DLsRG NCBI__GCF_000691805.2:WP_027699422.1 234 IDGELQFDAAFVESVAAAKAPNSKVAGQANVFVFPDLQSGNIGYKIAQRLGGFEAIGPVLQGLAKPISDLSRG 306 ************************************************************************* PP TIGR00651 291 asvedivnvviita 304 a+ ed+++v+iita NCBI__GCF_000691805.2:WP_027699422.1 307 ANEEDVYKVAIITA 320 ************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (324 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: 24.23 // [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