Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_022603079.1 NSB1T_RS28250 phosphate acetyltransferase
Query= BRENDA::O52593 (332 letters) >NCBI__GCF_000473955.1:WP_022603079.1 Length = 335 Score = 347 bits (889), Expect = e-100 Identities = 178/330 (53%), Positives = 233/330 (70%), Gaps = 3/330 (0%) Query: 1 MSFLEQIIERAKSDVKTIVLPESTDLRVIKAASMIMKKGIAKVVLIGNEKEIKSLAGDID 60 M + QII RAK+D++ IVLPE T+ R +KAA ++ +A + LIGN EI +LA Sbjct: 1 MELMNQIIARAKADMQRIVLPEGTEERTLKAADKLIADKVAHITLIGNPAEIMALAEKHG 60 Query: 61 LEGV---MIEDSLNSEKLEDYANTLYELRKSKGMTIEAARETIKDPLYYGVMMVKKGEAD 117 L+ + +I D N E+ E+YAN L+ELRK KGMT E A + ++DPL+ +M+K G AD Sbjct: 61 LQNIGNAIIVDPKNHERKEEYANLLFELRKKKGMTEEQAAKQVEDPLFLAALMIKSGHAD 120 Query: 118 GMVAGAVNSTANTLRPALQILKTAPGTKLVSSFFVMVVPNCEYGHNGTFVYADCGLVENP 177 G VAGA N+T N LR A QI+KTAPG +VS F+M +PN YG NG V+ADC ++ NP Sbjct: 121 GEVAGAQNTTGNVLRAAFQIVKTAPGVSVVSGAFLMFLPNKNYGENGIMVFADCAVLPNP 180 Query: 178 DADQLSEIAISASKSFEMLVGAKPQVAMLSYSSYGSAKSELTEKVIKATQLAKEKAPHLA 237 +A++L++IA+S + L G +P++AMLS+S+ GSAK E+ +KV++AT++AKE L Sbjct: 181 NAEELAQIAVSTGHTTRTLAGFEPRIAMLSFSTKGSAKHEMVDKVVEATRIAKEMDSSLK 240 Query: 238 IDGELQVDAAIVPEVAKSKAKGSSVAGKANVLIFPDLDAGNIAYKLTQRLAKAEAYGPIT 297 IDGELQ DAAIVP V SKA S +AG ANVL+FP L+ GNI YKL QRLA AEA GPI Sbjct: 241 IDGELQADAAIVPAVGMSKAPDSEIAGNANVLVFPSLETGNITYKLVQRLAGAEAVGPIL 300 Query: 298 QGLARPVNDLSRGCSAEDIVGVAAITAVQA 327 QG+A P+NDLSRGCS EDI + AITA QA Sbjct: 301 QGIAAPINDLSRGCSVEDIYKMVAITANQA 330 Lambda K H 0.313 0.129 0.346 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: 298 Number of extensions: 8 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: 332 Length of database: 335 Length adjustment: 28 Effective length of query: 304 Effective length of database: 307 Effective search space: 93328 Effective search space used: 93328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 bits)
Align candidate WP_022603079.1 NSB1T_RS28250 (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.2109331.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-124 398.8 1.0 1e-123 398.6 1.0 1.0 1 NCBI__GCF_000473955.1:WP_022603079.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000473955.1:WP_022603079.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 398.6 1.0 1e-123 1e-123 1 304 [] 18 327 .. 18 327 .. 0.98 Alignments for each domain: == domain 1 score: 398.6 bits; conditional E-value: 1e-123 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 ivlPEg+eer+lkAa +l+ k+a+ +l++n +e+++ + k+ +++g+ +++dp+ ++ +e+y++ l+e+rk NCBI__GCF_000473955.1:WP_022603079.1 18 IVLPEGTEERTLKAADKLIADKVAHITLIGNPAEIMALAEKHGLQNIGNAIIVDPKNHERKEEYANLLFELRK 90 8************************************8777778899************************** PP TIGR00651 74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee... 143 +kG+te++a++q++D++ laal+++ g+adg+v+Ga++tt ++lr+a+qi+kt++gv++vs+ f+m +++ NCBI__GCF_000473955.1:WP_022603079.1 91 KKGMTEEQAAKQVEDPLFLAALMIKSGHADGEVAGAQNTTGNVLRAAFQIVKTAPGVSVVSGAFLMFLPNkny 163 ******************************************************************9999899 PP TIGR00651 144 ...evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkeke 213 +++vfaDCav ++PnaeeLA+iA+++ +++++l + ep++a+ls+stkgs+k e+v+kv+eA++i+ke NCBI__GCF_000473955.1:WP_022603079.1 164 genGIMVFADCAVLPNPNAEELAQIAVSTGHTTRTLAGFEPRIAMLSFSTKGSAKHEMVDKVVEATRIAKEMD 236 9999********************************************************************* PP TIGR00651 214 pdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnD 286 + l++dGelq DaA+v+ v +kap+se+ag+anv+vFP+L++Gni+Yk+vqRla+aea+GPilqG+a P+nD NCBI__GCF_000473955.1:WP_022603079.1 237 SSLKIDGELQADAAIVPAVGMSKAPDSEIAGNANVLVFPSLETGNITYKLVQRLAGAEAVGPILQGIAAPIND 309 ************************************************************************* PP TIGR00651 287 LsRGasvedivnvviita 304 LsRG+svedi+++v+ita NCBI__GCF_000473955.1:WP_022603079.1 310 LSRGCSVEDIYKMVAITA 327 ****************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (335 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: 23.95 // [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