Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate PfGW456L13_1007 Homoserine O-acetyltransferase (EC 2.3.1.31)
Query= SwissProt::F7XKY8 (492 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1007 Length = 379 Score = 381 bits (978), Expect = e-110 Identities = 189/372 (50%), Positives = 261/372 (70%), Gaps = 6/372 (1%) Query: 5 SLGIVETKYYHLEEELKLESGRKISDVTIAYEAYGTLNRDKNNVILVCHALTGDAHAAGW 64 S+G+V + H E L L GR + + YE YGTLN +N +L+CHAL+G HAAG+ Sbjct: 9 SVGLVTPQVAHFSEPLALACGRSLPAYDLIYETYGTLNATASNAVLICHALSGHHHAAGY 68 Query: 65 HKGDN-KPGWWDILIGPGKCLDTDKYFIVCSNVIGGCRGSTGPSSIDPETGKPYGLSFPV 123 H D+ KPGWWD IGPGK +DT K+F+V N +GGC GSTGPSSI+P+TGKP+G FPV Sbjct: 69 HSADDRKPGWWDSCIGPGKPIDTSKFFVVSLNNLGGCNGSTGPSSINPDTGKPFGADFPV 128 Query: 124 ITIKDMVNAQKKLLDHLGISSIYAVIGGSMGGLQVLQWSVSYPDYINKAIALAASAYSSP 183 +T++D V++Q +L D LGI+ AVIGGS+GG+Q +QWS++YPD I +A+A++ S Sbjct: 129 LTVEDWVHSQARLADRLGIAQFAAVIGGSLGGMQAMQWSITYPDRIRHCLAIASAPKLSA 188 Query: 184 QQIAFNEVARIAIISDPEWNKGNYY-YSRQPSHGLALARMIGHITYLSDESMREKFGREL 242 Q IAFNEVAR AI++DPE++ G++ ++ P GL LARM+GHITYLSD+SM EKFGR L Sbjct: 189 QNIAFNEVARQAILTDPEFHGGSFQEHNVIPKRGLMLARMVGHITYLSDDSMGEKFGRGL 248 Query: 243 QDRDRYNYDL-SMDFQVESYLHYKGRSFTERFDANSYLYITKAVDYFDLTEN--GSLIDG 299 + ++ NYD S++FQVESYL Y+G F+ RFDAN+YL +TKA+DYFD N +L Sbjct: 249 KS-EKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANFDDNLAKT 307 Query: 300 LKDIKAKCLIIAVTSDWLYPPYQSKDIVMALNANNVDVTYREIESNYGHDAFLLEAGQLN 359 + KAK +++ T+DW + P +S+++V AL A DV Y EI++ GHDAFL+ + Sbjct: 308 FEGAKAKFCVMSFTTDWRFSPARSRELVDALMAARKDVCYLEIDAPQGHDAFLIPIPRYL 367 Query: 360 YVIGGFLNNITV 371 G ++N IT+ Sbjct: 368 QAFGNYMNRITL 379 Lambda K H 0.318 0.136 0.405 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: 508 Number of extensions: 26 Number of successful extensions: 5 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: 492 Length of database: 379 Length adjustment: 32 Effective length of query: 460 Effective length of database: 347 Effective search space: 159620 Effective search space used: 159620 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: 51 (24.3 bits)
Align candidate PfGW456L13_1007 (Homoserine O-acetyltransferase (EC 2.3.1.31))
to HMM TIGR01392 (metX: homoserine O-acetyltransferase (EC 2.3.1.31))
# 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.aa/TIGR01392.hmm # target sequence database: /tmp/gapView.30734.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01392 [M=351] Accession: TIGR01392 Description: homoserO_Ac_trn: homoserine O-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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-142 458.1 0.0 1.1e-141 457.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1007 Homoserine O-acetyltransferase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1007 Homoserine O-acetyltransferase (EC 2.3.1.31) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 457.9 0.0 1.1e-141 1.1e-141 3 345 .. 22 369 .. 20 375 .. 0.97 Alignments for each domain: == domain 1 score: 457.9 bits; conditional E-value: 1.1e-141 TIGR01392 3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.. 55 e+l l +G l+ +++ y+tyGtlna +Navl+cHal+g++h+ag+++++d+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1007 22 EPLALACGRSLPAYDLIYETYGTLNATASNAVLICHALSGHHHAAGYHSADDRkp 76 789********************************************99888789 PP TIGR01392 56 GWWdellGpgraldtsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvti 110 GWWd+ +Gpg+++dts++fvv+lN+lG+c+GstgP+sinp+tgkp+ga+fP++t+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1007 77 GWWDSCIGPGKPIDTSKFFVVSLNNLGGCNGSTGPSSINPDTGKPFGADFPVLTV 131 ******************************************************* PP TIGR01392 111 rDlvkaqkalldsLgveklaavvGgSlGGmqalewalsypervkkivvlatsara 165 +D+v+ q++l+d+Lg+ ++aav+GgSlGGmqa++w+++yp+r+++++++a+++++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1007 132 EDWVHSQARLADRLGIAQFAAVIGGSLGGMQAMQWSITYPDRIRHCLAIASAPKL 186 ******************************************************* PP TIGR01392 166 saqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrseesle 219 saq+iafnev+rqail+Dpe+++G+++e++ P++GL lARm++++tY+s++s+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1007 187 SAQNIAFNEVARQAILTDPEFHGGSFQEHNvIPKRGLMLARMVGHITYLSDDSMG 241 ******************************9************************ PP TIGR01392 220 erfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdl 274 e+fgr kse+ ++ ef+vesylryqg++f rFdAn+Yll+tkald++d lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1007 242 EKFGRGLKSEKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDP 296 ********9977777779************************************* PP TIGR01392 275 argrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeie 327 a++ +d+l+++++ +ka+++v+++++D++f++++++el++al aa+++ y ei+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1007 297 AANFDDNLAKTFEGAKAKFCVMSFTTDWRFSPARSRELVDALMAARKDvcYLEID 351 ********************************************999999***** PP TIGR01392 328 seeGHDaFllekekveel 345 ++GHDaFl+ ++ ++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1007 352 APQGHDAFLIPIPRYLQA 369 *********988776665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (379 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.29 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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