Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_012469280.1 GLOV_RS05950 phosphate acetyltransferase
Query= metacyc::PTACLOS-MONOMER (333 letters) >NCBI__GCF_000020385.1:WP_012469280.1 Length = 333 Score = 327 bits (839), Expect = 2e-94 Identities = 170/331 (51%), Positives = 232/331 (70%), Gaps = 2/331 (0%) Query: 1 MDLIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELN 60 M L++ I + A+++ + ++L E ++R L AA+KI+ EGLA+LV++GD KI+ +A+ Sbjct: 1 MHLVDQIKQKAQKNLQTVVLPESYDERMLYAAEKIVAEGLAKLVILGDPAKIQAEAAAKG 60 Query: 61 LDISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVR--DPLYFATMALKDGYV 118 ++++ E+++P S K + Y DF ELRK KGMT E+++K++ D LY+A M +++G Sbjct: 61 INLAGVELLNPADSPKLDQYIADFVELRKSKGMTAEEAKKLLTADDNLYYAGMMVRNGDA 120 Query: 119 DGMVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPN 178 G V+GA TTG++L+ Q + A G+K VS FF+MI +GE G++LFADCAVNPN Sbjct: 121 GGEVAGATGTTGNVLKAAFQTVGPAAGIKTVSSFFLMITKTPSFGENGIILFADCAVNPN 180 Query: 179 PTSDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDL 238 P + LA+IA+ TA + +VE +V MLSFST GSA VDKV A EI K +PD+ Sbjct: 181 PDAQALAEIAVATAGNCKAFLDVEARVGMLSFSTKGSAAHADVDKVTKAAEIAKTIKPDI 240 Query: 239 AIDGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPI 298 IDGELQ DAA+ +V KAP S VAG ANVL+FPDL GNI YKLV+R A A+A+GPI Sbjct: 241 QIDGELQADAALLPKVGEKKAPGSPVAGKANVLIFPDLDAGNIAYKLVERVAGAEAVGPI 300 Query: 299 CQGFAKPINDLSRGCSSEDIVNVVAITVVQA 329 QG AKP+NDLSRGCS +DIVNVVAIT VQA Sbjct: 301 IQGLAKPVNDLSRGCSVDDIVNVVAITAVQA 331 Lambda K H 0.316 0.134 0.374 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: 313 Number of extensions: 11 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: 333 Length of database: 333 Length adjustment: 28 Effective length of query: 305 Effective length of database: 305 Effective search space: 93025 Effective search space used: 93025 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: 49 (23.5 bits)
Align candidate WP_012469280.1 GLOV_RS05950 (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.22899.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-114 366.4 1.1 7.7e-114 366.2 1.1 1.0 1 lcl|NCBI__GCF_000020385.1:WP_012469280.1 GLOV_RS05950 phosphate acetyltra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020385.1:WP_012469280.1 GLOV_RS05950 phosphate acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 366.2 1.1 7.7e-114 7.7e-114 1 304 [] 18 328 .. 18 328 .. 0.97 Alignments for each domain: == domain 1 score: 366.2 bits; conditional E-value: 7.7e-114 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverly 69 +vlPE+ +er+l Aa++++ +++a+ v+l++ +++++ +a+ ++l+ v++ +p s+++++y+ ++ lcl|NCBI__GCF_000020385.1:WP_012469280.1 18 VVLPESYDERMLYAAEKIVAEGLAKLVILGDPAKIQA-EAAAKGINLAGVELLNPADSPKLDQYIADFV 85 69********************************999.666777888999******************* PP TIGR00651 70 ekrkhkGvtekeareqlr..DevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssv 136 e+rk kG+t +ea++ l+ D++++a ++v+ g a g+v+Ga tt ++l++a+q ++ + g+k+vss+ lcl|NCBI__GCF_000020385.1:WP_012469280.1 86 ELRKSKGMTAEEAKKLLTadDNLYYAGMMVRNGDAGGEVAGATGTTGNVLKAAFQTVGPAAGIKTVSSF 154 ***************9855599*********************************************** PP TIGR00651 137 fimekee......evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeev 199 f+m ++ ++++faDCav+++P+a+ LAeiA+ +a +k++ + e +v +ls+stkgs++ ++v lcl|NCBI__GCF_000020385.1:WP_012469280.1 155 FLMITKTpsfgenGIILFADCAVNPNPDAQALAEIAVATAGNCKAFLDVEARVGMLSFSTKGSAAHADV 223 ****9999999999******************************************************* PP TIGR00651 200 ekvkeAvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRla 268 +kv +A +i+k +pd+++dGelq DaAl++kv ekkap s+vagkanv++FPdLdaGni+Yk+v+R+a lcl|NCBI__GCF_000020385.1:WP_012469280.1 224 DKVTKAAEIAKTIKPDIQIDGELQADAALLPKVGEKKAPGSPVAGKANVLIFPDLDAGNIAYKLVERVA 292 ********************************************************************* PP TIGR00651 269 daeaiGPilqGlakPvnDLsRGasvedivnvviita 304 +aea+GPi+qGlakPvnDLsRG+sv+divnvv+ita lcl|NCBI__GCF_000020385.1:WP_012469280.1 293 GAEAVGPIIQGLAKPVNDLSRGCSVDDIVNVVAITA 328 **********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (333 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.09 // [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