Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate 3608428 Dshi_1825 phosphate acetyltransferase (RefSeq)
Query= BRENDA::Q5LMK3 (337 letters) >FitnessBrowser__Dino:3608428 Length = 341 Score = 333 bits (855), Expect = 3e-96 Identities = 183/327 (55%), Positives = 223/327 (68%), Gaps = 1/327 (0%) Query: 6 PIDLLLSDPPARRATVALSEGSDPRVVAGALAAHSAGIADVILVGQAAEIRAAL-KAQGA 64 P+ ++L++ +ALSEG DPRVVA A+ A +A V+LVG A I A L +A GA Sbjct: 3 PLQMILANAARSDRKIALSEGEDPRVVAAAVQARKQRVARVVLVGDRATIVARLAEAGGA 62 Query: 65 PADSLTIHDPDSSPLTAEFAAAYYGLRRHKGVSEAAALAAVRTPLVYAAMLVRGDHAVGT 124 D + +HDP AE AA Y+ LR+HKGV+EA A AA+ P VYAA+LVR HA GT Sbjct: 63 ELDGIDVHDPREDLHRAEMAATYHQLRKHKGVTEADAEAAILNPHVYAALLVRLGHADGT 122 Query: 125 VGGAVATTSDVVRTAIQVIGAAPGAAMVSSFFLMYPPEAATAHARAMLYSDSGLVIDPSV 184 +GGA ATT+++VRTAIQVIG APGA MVSSFFLM + ++++D+GLVIDP+ Sbjct: 123 LGGATATTAEIVRTAIQVIGTAPGAKMVSSFFLMLLCKDHHEKKGGLVFADAGLVIDPTA 182 Query: 185 AELAAIAAASAASCRALLRAEPKIAMLSFSTKGSARHPHVSKVTDALARLRADHPDLDAD 244 AE+A I ASAAS L P++AMLSFST+GSA VSKV +A R P++ D Sbjct: 183 AEMAEIGRASAASLVQLTGETPRVAMLSFSTRGSASGDKVSKVVEATEIFRQLAPEVTVD 242 Query: 245 GELQFDAAFVPSVGASKAPGSDVAGQANVMIFPNLDAGNIGYKITQRLGGYTAIGPVLQG 304 GELQFDAAFVP V +KAP S + G ANV +FPNLD GNI YKI QR+GG AIGP+LQG Sbjct: 243 GELQFDAAFVPEVATAKAPDSAIGGSANVFVFPNLDTGNIAYKIAQRIGGAVAIGPILQG 302 Query: 305 LAKPANDLSRGCVAGDVTQMIAVTVLQ 331 LA PANDLSRGC A DV MIA T Q Sbjct: 303 LALPANDLSRGCSAEDVLHMIATTAAQ 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: 268 Number of extensions: 12 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: 337 Length of database: 341 Length adjustment: 28 Effective length of query: 309 Effective length of database: 313 Effective search space: 96717 Effective search space used: 96717 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 3608428 Dshi_1825 (phosphate acetyltransferase (RefSeq))
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.13378.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-106 340.2 0.1 7.4e-106 340.0 0.1 1.0 1 lcl|FitnessBrowser__Dino:3608428 Dshi_1825 phosphate acetyltransf Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3608428 Dshi_1825 phosphate acetyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 340.0 0.1 7.4e-106 7.4e-106 1 304 [] 18 327 .. 18 327 .. 0.98 Alignments for each domain: == domain 1 score: 340.0 bits; conditional E-value: 7.4e-106 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrkhkGv 77 i l Eg+++rv+ Aa + ++++a+ vl+++ +++v+ a+ +l + v+dp+ ++ + + +++++rkhkGv lcl|FitnessBrowser__Dino:3608428 18 IALSEGEDPRVVAAAVQARKQRVARVVLVGDRATIVARLAEAGGAELDGIDVHDPREDLHRAEMAATYHQLRKHKGV 94 6689************************999999999999999********************************** PP TIGR00651 78 tekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee......evlvf 148 te+ a+ ++ ++ ++aallv+lg+adg+ Ga tta+++r+a+q+i+t++g k+vss+f+m + + + lvf lcl|FitnessBrowser__Dino:3608428 95 TEADAEAAILNPHVYAALLVRLGHADGTLGGATATTAEIVRTAIQVIGTAPGAKMVSSFFLMLLCKdhhekkGGLVF 171 **************************************************************987777888899*** PP TIGR00651 149 aDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqfD 225 aD +++dP+a e+Aei sa+s +l++e p+va+ls+st+gs++g++v kv+eA++i+++ +p++++dGelqfD lcl|FitnessBrowser__Dino:3608428 172 ADAGLVIDPTAAEMAEIGRASAASLVQLTGETPRVAMLSFSTRGSASGDKVSKVVEATEIFRQLAPEVTVDGELQFD 248 ***************************************************************************** PP TIGR00651 226 aAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvvii 302 aA+v++va+ kap+s++ g+anvfvFP+Ld+Gni+Yki+qR+++a aiGPilqGla P nDLsRG+s+ed++++++ lcl|FitnessBrowser__Dino:3608428 249 AAFVPEVATAKAPDSAIGGSANVFVFPNLDTGNIAYKIAQRIGGAVAIGPILQGLALPANDLSRGCSAEDVLHMIAT 325 *************************************************************************9998 PP TIGR00651 303 ta 304 ta lcl|FitnessBrowser__Dino:3608428 326 TA 327 75 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (341 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.59 // [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