Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_010531539.1 ON01_RS13225 phosphate acetyltransferase
Query= metacyc::MONOMER-13062 (328 letters) >NCBI__GCF_000224785.1:WP_010531539.1 Length = 322 Score = 381 bits (978), Expect = e-110 Identities = 187/322 (58%), Positives = 247/322 (76%), Gaps = 2/322 (0%) Query: 2 DLFESLKSKIKDRKIKLVFPEGEDERIISAASRLANDDLAIPVLLGNEAEIKKTADALNV 61 +LFE +K ++ + K+VFPEG DERI++AAS+L + P+LLG++ EIK+ A++ V Sbjct: 3 NLFEEIKDQLANADKKIVFPEGRDERILTAASQLGASGIVTPILLGDKGEIKQQAESAGV 62 Query: 62 SLDGIEIVDIENVPGEVRQQMVQAIVERRKGKTTADQAAQWLKDPNYFGTTMVYMDDVDG 121 ++ E++D + P +M+ V+RRKGK TAD+A Q L D NYFGT +VYMD DG Sbjct: 63 NVSACELIDPHDFPEF--DEMIDVFVKRRKGKVTADEARQTLLDENYFGTMLVYMDKADG 120 Query: 122 MVSGAAHPTGDTVRPALQIIKTKPGVNLISGSFVMQKGDQRYLFADCAININPNETQLAE 181 +VSGAAH T DTVRPALQIIKTK GV SG F+M + D++Y+FADCAIN+NP+ LAE Sbjct: 121 LVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMVRNDEKYVFADCAINVNPDSQDLAE 180 Query: 182 IAVESGKTARLFDIDPRVALLSFSTNGSAKSPEVEKVHNATKLAQEMDPAMPIDGEMQFD 241 IA ES TA+LF +DPR+A+LSFST GSA+S E EKV NA +LA+E + ++ IDGE QFD Sbjct: 181 IAAESANTAKLFRVDPRIAMLSFSTKGSAQSEETEKVVNALELAKEKNASLVIDGEFQFD 240 Query: 242 AAFVPAVAKAKYSDSKVAGHATVFVFPELQSGNIGYKIAQRMGGFEAIGPILQGLNKPVS 301 AAFVP+VA K ++ + G A+VF+FP L++GNIGYKIAQR+G FEA+GPILQGLNKPV+ Sbjct: 241 AAFVPSVAAKKAPNAVIKGDASVFIFPSLEAGNIGYKIAQRLGEFEAVGPILQGLNKPVN 300 Query: 302 DLSRGCNAEDVYKVSIITATQA 323 DLSRGC++EDVY +++ITA QA Sbjct: 301 DLSRGCSSEDVYNLALITAAQA 322 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: 326 Number of extensions: 11 Number of successful extensions: 2 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: 322 Length adjustment: 28 Effective length of query: 300 Effective length of database: 294 Effective search space: 88200 Effective search space used: 88200 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_010531539.1 ON01_RS13225 (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.2211681.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-129 416.6 0.4 4e-129 416.4 0.4 1.0 1 NCBI__GCF_000224785.1:WP_010531539.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010531539.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 416.4 0.4 4e-129 4e-129 1 304 [] 19 319 .. 19 319 .. 0.99 Alignments for each domain: == domain 1 score: 416.4 bits; conditional E-value: 4e-129 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 iv+PEg +er+l Aa++l ++i++++ll++k e+++ +a++ +++ ++++dp+ +++ ++ ++ ++++rk NCBI__GCF_000224785.1:WP_010531539.1 19 IVFPEGRDERILTAASQLGASGIVTPILLGDKGEIKQ-QAESAGVNVSACELIDPHDFPEFDEMIDVFVKRRK 90 8******************************999999.8899999999************************* PP TIGR00651 74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146 k vt ear++l De++++++lv++++adglvsGa+++ta+t+rpalqiikt+egvk +s+vfim +++e + NCBI__GCF_000224785.1:WP_010531539.1 91 GK-VTADEARQTLLDENYFGTMLVYMDKADGLVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMVRNDEKY 162 **.********************************************************************** PP TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219 vfaDCa++v+P++++LAeiA +sa++ak + +p++a+ls+stkgs+++ee+ekv++A++++kek++ l++d NCBI__GCF_000224785.1:WP_010531539.1 163 VFADCAINVNPDSQDLAEIAAESANTAKLFR-VDPRIAMLSFSTKGSAQSEETEKVVNALELAKEKNASLVID 234 *******************************.***************************************** PP TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGas 292 Ge+qfDaA+v++va+kkap+ ++g+a vf+FP+L+aGnigYki+qRl+++ea+GPilqGl+kPvnDLsRG+s NCBI__GCF_000224785.1:WP_010531539.1 235 GEFQFDAAFVPSVAAKKAPNAVIKGDASVFIFPSLEAGNIGYKIAQRLGEFEAVGPILQGLNKPVNDLSRGCS 307 ************************************************************************* PP TIGR00651 293 vedivnvviita 304 ed++n+++ita NCBI__GCF_000224785.1:WP_010531539.1 308 SEDVYNLALITA 319 **********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (322 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: 13.68 // [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