Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_013553394.1 NITSA_RS02185 homoserine O-acetyltransferase
Query= SwissProt::B9L9I6 (368 letters) >NCBI__GCF_000186245.1:WP_013553394.1 Length = 368 Score = 513 bits (1320), Expect = e-150 Identities = 245/367 (66%), Positives = 300/367 (81%), Gaps = 1/367 (0%) Query: 1 MKIETKIAKFTKPLYLESGRILEPWQIIYETYGELNEKKDNVILITHALSGSHHAAGMYE 60 MKIET FT PLYLESGRILEP++I YETYGELNE KDNVIL+ HALSGSHHAAG+YE Sbjct: 1 MKIETHTTHFTSPLYLESGRILEPYEIRYETYGELNEAKDNVILVCHALSGSHHAAGLYE 60 Query: 61 GDRKPGWWDGLIGDGKAIDTTKYFVISTNVIGSCFGSTSPMSPIHPGSSERYRLKFPVVT 120 G+RKPGWWD LIG GK IDT +YFV+ TNVIGSCFGST PMSP +P S E YRLKFPVVT Sbjct: 61 GERKPGWWDALIGPGKGIDTDRYFVVCTNVIGSCFGSTGPMSPQYP-SEEPYRLKFPVVT 119 Query: 121 IKDMVKAQKILLDSLGIRHLKAIVGGSMGGMQALRFAVDFPGFCENIIPIATTYQTKPYV 180 IKDM++AQ+ LL LGI H+KAIVGGSMGGMQAL+FAVD+PGF ++IIP+ATTY T+P+V Sbjct: 120 IKDMIRAQRQLLSHLGIHHVKAIVGGSMGGMQALQFAVDYPGFADHIIPLATTYATRPWV 179 Query: 181 IAINKSMIEAIRADSEFKNGNYDPDIIKQNGLKGLAAARMIGYLNYISPKTFERKFGREY 240 IA NK +EAIR D F NGNY PD K++G GLA R+ G+++Y+SP++ +RKFGR Y Sbjct: 180 IAFNKVAVEAIRRDPRFDNGNYAPDAFKEHGCDGLAVGRIAGHISYLSPQSMDRKFGRNY 239 Query: 241 VKTDGMFELFGRFQVESYLEYNGAMFPKWFDPLSYIYILKAISLFDISRGFVSLEDAFSQ 300 V TDG+FELFGR++VE Y+EYN A F + FDPLSY+YI+KAI+ F++SRG+ SL DA S+ Sbjct: 240 VATDGLFELFGRYEVERYMEYNTANFSRIFDPLSYLYIVKAINTFNLSRGYDSLHDAVSR 299 Query: 301 IKDKLHLISFSGDTLFFPEEMRDIKNYMDKVGGKCNYFEINSDYGHDSFLVELEKFDFII 360 I+ ++HLISF+GD LFFPEEM + + + G +Y EI SDYGHD+FLVE++KFDFII Sbjct: 300 IRAQVHLISFAGDYLFFPEEMEHLAKMLRRNGQAHSYHEIESDYGHDAFLVEVDKFDFII 359 Query: 361 SDILKGE 367 +IL+ E Sbjct: 360 REILEEE 366 Lambda K H 0.322 0.141 0.422 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: 521 Number of extensions: 20 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: 368 Length of database: 368 Length adjustment: 30 Effective length of query: 338 Effective length of database: 338 Effective search space: 114244 Effective search space used: 114244 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 bits)
Align candidate WP_013553394.1 NITSA_RS02185 (homoserine O-acetyltransferase)
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.25488.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-125 402.9 0.0 7e-125 402.7 0.0 1.0 1 lcl|NCBI__GCF_000186245.1:WP_013553394.1 NITSA_RS02185 homoserine O-acety Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013553394.1 NITSA_RS02185 homoserine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 402.7 0.0 7e-125 7e-125 3 350 .. 12 363 .. 10 364 .. 0.96 Alignments for each domain: == domain 1 score: 402.7 bits; conditional E-value: 7e-125 TIGR01392 3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldt 70 ++l+lesG +l+ +e++y+tyG+ln+++dN++lvcHal+gs+h+ag ++ e+k GWWd l+Gpg+ +dt lcl|NCBI__GCF_000186245.1:WP_013553394.1 12 SPLYLESGRILEPYEIRYETYGELNEAKDNVILVCHALSGSHHAAGLYEGERKpGWWDALIGPGKGIDT 80 789*********************************************999888*************** PP TIGR01392 71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139 +ryfvvc+Nv+Gsc GstgP+s + +++py+ +fP+vti+D+++aq++ll +Lg+++++a+vGgS+GG lcl|NCBI__GCF_000186245.1:WP_013553394.1 81 DRYFVVCTNVIGSCFGSTGPMSPQYPSEEPYRLKFPVVTIKDMIRAQRQLLSHLGIHHVKAIVGGSMGG 149 ************************999****************************************** PP TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee...qPekGLalAR 205 mqal++a++yp ++++i++lat+ ++ ++ iafn+v+ +ai+ Dp + +G+ya + + GLa+ R lcl|NCBI__GCF_000186245.1:WP_013553394.1 150 MQALQFAVDYPGFADHIIPLATTYATRPWVIAFNKVAVEAIRRDPRFDNGNYAPDAfkeHGCDGLAVGR 218 ****************************************************99765347789****** PP TIGR01392 206 mlalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdl 274 ++++Y+s +s++++fgr+ +++ ++l +++ve y++y++ +f + Fd sYl++ ka++t++l lcl|NCBI__GCF_000186245.1:WP_013553394.1 219 IAGHISYLSPQSMDRKFGRNYVATDG-LFELFGRYEVERYMEYNTANFSRIFDPLSYLYIVKAINTFNL 286 ********************999966.667899************************************ PP TIGR01392 275 argrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekek 341 +rg dsl++a+++i+a+v ++++ D lf +ee e+lak l++++++ y+eies++GHDaFl+e +k lcl|NCBI__GCF_000186245.1:WP_013553394.1 287 SRG-YDSLHDAVSRIRAQVHLISFAGDYLFFPEEMEHLAKMLRRNGQAhsYHEIESDYGHDAFLVEVDK 354 ***.8*************************************99887779******************* PP TIGR01392 342 veelirefl 350 ++ +ire+l lcl|NCBI__GCF_000186245.1:WP_013553394.1 355 FDFIIREIL 363 *****9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (368 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: 12.12 // [ok]
This GapMind analysis is from Apr 10 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