Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate SM_b21532 SM_b21532 phosphate acetyltransferase
Query= BRENDA::Q5LMK3 (337 letters) >FitnessBrowser__Smeli:SM_b21532 Length = 330 Score = 328 bits (842), Expect = 9e-95 Identities = 184/327 (56%), Positives = 215/327 (65%) Query: 6 PIDLLLSDPPARRATVALSEGSDPRVVAGALAAHSAGIADVILVGQAAEIRAALKAQGAP 65 P+D ++ V L EG DPR+VAGA+ A G+A + LVG I L A A Sbjct: 3 PLDRIIDAARKAPRHVVLPEGEDPRIVAGAVQARREGLAAITLVGNREVITQRLAALDAI 62 Query: 66 ADSLTIHDPDSSPLTAEFAAAYYGLRRHKGVSEAAALAAVRTPLVYAAMLVRGDHAVGTV 125 I DP SPLT +FA AY RR KGV AAA AAV +PL +AAM+VR A GTV Sbjct: 63 PQEFRIEDPACSPLTDDFATAYLERRRSKGVDAAAARAAVLSPLTFAAMMVREGIADGTV 122 Query: 126 GGAVATTSDVVRTAIQVIGAAPGAAMVSSFFLMYPPEAATAHARAMLYSDSGLVIDPSVA 185 GGAVATT+D VR A+QVIG APG +VSSFFLM E A A +++D GLV+DP A Sbjct: 123 GGAVATTADTVRAALQVIGRAPGVGLVSSFFLMMLCEPHHARKGAFVFADCGLVVDPDAA 182 Query: 186 ELAAIAAASAASCRALLRAEPKIAMLSFSTKGSARHPHVSKVTDALARLRADHPDLDADG 245 LA IA SA S L K+AMLSFST GSA H VSKV +A R PDL DG Sbjct: 183 GLADIARMSAKSYEMLAGERAKVAMLSFSTGGSAAHERVSKVVEATGMARRAEPDLIIDG 242 Query: 246 ELQFDAAFVPSVGASKAPGSDVAGQANVMIFPNLDAGNIGYKITQRLGGYTAIGPVLQGL 305 ELQFD+AFV +V +KAP S + G+ANV +FPNLDA NIGYKI QR+GG TAIGP+LQGL Sbjct: 243 ELQFDSAFVEAVCLTKAPHSALRGEANVFVFPNLDAANIGYKIAQRIGGATAIGPILQGL 302 Query: 306 AKPANDLSRGCVAGDVTQMIAVTVLQA 332 ++PANDLSRGC A DV MIAVTV+QA Sbjct: 303 SRPANDLSRGCTAADVFHMIAVTVVQA 329 Lambda K H 0.317 0.130 0.362 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: 285 Number of extensions: 5 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: 337 Length of database: 330 Length adjustment: 28 Effective length of query: 309 Effective length of database: 302 Effective search space: 93318 Effective search space used: 93318 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: 49 (23.5 bits)
Align candidate SM_b21532 SM_b21532 (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.18008.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-110 352.8 0.0 1.1e-109 352.6 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SM_b21532 SM_b21532 phosphate acetyltransf Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SM_b21532 SM_b21532 phosphate acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 352.6 0.0 1.1e-109 1.1e-109 1 304 [] 18 326 .. 18 326 .. 0.98 Alignments for each domain: == domain 1 score: 352.6 bits; conditional E-value: 1.1e-109 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrkh 74 +vlPEg+++r++ a + ++++a+ +l++n e +++ + + ++ ++ ++edp s+ +++++ ++ e+r+ lcl|FitnessBrowser__Smeli:SM_b21532 18 VVLPEGEDPRIVAGAVQARREGLAAITLVGNREVITQ-RLAALDAIPQEFRIEDPACSPLTDDFATAYLERRRS 90 79********************999888887777666.999********************************* PP TIGR00651 75 kGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee..... 143 kGv+ ++ar ++ ++++aa++v+ g adg+v Gav tta+t+r+alq+i++++gv lvss+f+m + e lcl|FitnessBrowser__Smeli:SM_b21532 91 KGVDAAAARAAVLSPLTFAAMMVREGIADGTVGGAVATTADTVRAALQVIGRAPGVGLVSSFFLMMLCEphhar 164 *****************************************************************999999999 PP TIGR00651 144 .evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdl 216 + +vfaDC ++vdP+a LA+iA saks ++l +e kva+ls+st+gs++ e v kv+eA+ +++ epdl lcl|FitnessBrowser__Smeli:SM_b21532 165 kGAFVFADCGLVVDPDAAGLADIARMSAKSYEMLAGERAKVAMLSFSTGGSAAHERVSKVVEATGMARRAEPDL 238 99************************************************************************ PP TIGR00651 217 lldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRG 290 +dGelqfD+A+ve v kap+s+++g+anvfvFP+Lda nigYki+qR+++a+aiGPilqGl++P nDLsRG lcl|FitnessBrowser__Smeli:SM_b21532 239 IIDGELQFDSAFVEAVCLTKAPHSALRGEANVFVFPNLDAANIGYKIAQRIGGATAIGPILQGLSRPANDLSRG 312 ************************************************************************** PP TIGR00651 291 asvedivnvviita 304 +++ d+++++++t+ lcl|FitnessBrowser__Smeli:SM_b21532 313 CTAADVFHMIAVTV 326 ***********995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (330 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: 00:00:00.02 # Mc/sec: 3.60 // [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