Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate 353218 BT3692 phosphate acetyltransferase (NCBI ptt file)
Query= metacyc::PTACLOS-MONOMER (333 letters) >FitnessBrowser__Btheta:353218 Length = 339 Score = 329 bits (843), Expect = 7e-95 Identities = 175/331 (52%), Positives = 235/331 (70%), Gaps = 2/331 (0%) Query: 1 MDLIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELN 60 ++LI I AK D++RI+L EG E+R L AA++I+ + +A+L+L+G +I E A + Sbjct: 2 LNLINQIVARAKADRQRIVLPEGTEERTLKAANQILTDEVADLILLGKPAEINELAVKWG 61 Query: 61 L-DISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRDPLYFATMALKDGYVD 119 L +ISKA I+DPETS K E YA+ ELRK KGMTIE++ ++ DPL++ + +K G D Sbjct: 62 LGNISKATIIDPETSPKHEEYAQLLCELRKKKGMTIEEARQLTNDPLFYGCLMIKSGDAD 121 Query: 120 GMVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNP 179 G ++GA +TTG++LRP LQIIKTAPG+ VSG +++ +YG+ G+L+ D AV P P Sbjct: 122 GQLAGARNTTGNVLRPALQIIKTAPGITCVSGAMLLLTHAPEYGKNGILVMGDVAVTPVP 181 Query: 180 TSDELADIAITTAETARKLCNVE-PKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDL 238 ++LA IA+ TA+TA+ + +E PKVAMLSFST GSAK E+VDKV A +I K+ P L Sbjct: 182 DPNQLAQIAVCTAQTAKAVAGIENPKVAMLSFSTKGSAKHEVVDKVVEATKIAKEMAPTL 241 Query: 239 AIDGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPI 298 +DGE+Q DAA+ EV A KAP S VAG ANVL+ P L+ GNI YKLVQR A AIGPI Sbjct: 242 DLDGEMQADAALVPEVGASKAPGSPVAGEANVLIVPSLEVGNISYKLVQRLGHADAIGPI 301 Query: 299 CQGFAKPINDLSRGCSSEDIVNVVAITVVQA 329 QG A+P+NDLSRGCS ED+ ++AIT QA Sbjct: 302 LQGIARPVNDLSRGCSIEDVYRMIAITANQA 332 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: 308 Number of extensions: 8 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: 339 Length adjustment: 28 Effective length of query: 305 Effective length of database: 311 Effective search space: 94855 Effective search space used: 94855 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 353218 BT3692 (phosphate acetyltransferase (NCBI ptt file))
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.4973.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-111 359.2 0.1 1.2e-111 359.1 0.1 1.0 1 lcl|FitnessBrowser__Btheta:353218 BT3692 phosphate acetyltransfera Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:353218 BT3692 phosphate acetyltransferase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 359.1 0.1 1.2e-111 1.2e-111 1 304 [] 19 329 .. 19 329 .. 0.98 Alignments for each domain: == domain 1 score: 359.1 bits; conditional E-value: 1.2e-111 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrkhkG 76 ivlPEg+eer+lkAa+++++ ++a+ +ll++ +e+++ ++k +++k +++dp++s++ e+y++ l e+rk+kG lcl|FitnessBrowser__Btheta:353218 19 IVLPEGTEERTLKAANQILTDEVADLILLGKPAEINELAVKWGLGNISKATIIDPETSPKHEEYAQLLCELRKKKG 94 8***********************************9777766678999*************************** PP TIGR00651 77 vtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee......evl 146 +t +ear+ +D++ ++ l+++ g adg +Ga +tt ++lrpalqiikt++g+ +vs+ +++ ++ ++l lcl|FitnessBrowser__Btheta:353218 95 MTIEEARQLTNDPLFYGCLMIKSGDADGQLAGARNTTGNVLRPALQIIKTAPGITCVSGAMLLLTHApeygknGIL 170 ***************************************************************9998889999*** PP TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeee.pkvallsystkgsgkgeevekvkeAvkilkekepdllldGe 221 v +D av++ P++++LA+iA+ +a++ak++ ++e pkva+ls+stkgs+k e v+kv+eA+ki+ke +p l ldGe lcl|FitnessBrowser__Btheta:353218 171 VMGDVAVTPVPDPNQLAQIAVCTAQTAKAVAGIEnPKVAMLSFSTKGSAKHEVVDKVVEATKIAKEMAPTLDLDGE 246 ******************************987549**************************************** PP TIGR00651 222 lqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvediv 297 +q DaAlv++v ++kap s+vag+anv++ P+L+ Gni+Yk+vqRl++a+aiGPilqG+a+PvnDLsRG+s+ed++ lcl|FitnessBrowser__Btheta:353218 247 MQADAALVPEVGASKAPGSPVAGEANVLIVPSLEVGNISYKLVQRLGHADAIGPILQGIARPVNDLSRGCSIEDVY 322 **************************************************************************** PP TIGR00651 298 nvviita 304 +++ita lcl|FitnessBrowser__Btheta:353218 323 RMIAITA 329 *****97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (339 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.04 // [ok]
This GapMind analysis is from Sep 17 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