Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_011812941.1 HHAL_RS00655 threonine synthase
Query= BRENDA::O66740 (352 letters) >NCBI__GCF_000015585.1:WP_011812941.1 Length = 379 Score = 374 bits (960), Expect = e-108 Identities = 186/366 (50%), Positives = 254/366 (69%), Gaps = 22/366 (6%) Query: 3 RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSF 62 R+ G+I +Y LP+ ++ I+ L EGNTPLI+ + +G +Y+K+EGLNPTGSF Sbjct: 6 RYTGLIAKYLDRLPISDDARILGLGEGNTPLIQLTRIPAELGRDVDLYVKFEGLNPTGSF 65 Query: 63 KDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQA 122 KDRGMT+A++KAVE G +A+ICASTGNTSASAAAYAARAG+ +VL+P G +A+GKL+QA Sbjct: 66 KDRGMTMAVTKAVEQGAKAIICASTGNTSASAAAYAARAGISCFVLIPDGKIAMGKLAQA 125 Query: 123 MIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPD 182 +++GA+VL I+G FD + +V+++ E+ P+ IVNS+NPYR++GQKTAAFEI + L APD Sbjct: 126 IMHGAQVLQIRGNFDAGMRLVKELAEHAPLTIVNSINPYRLQGQKTAAFEIIEELERAPD 185 Query: 183 YHFIPVGNAGNITAYWKGF---------------------KIYYEEGKITKLPRMMGWQA 221 YH +PVGNAGNITA+W G+ + Y + + PRM+G+QA Sbjct: 186 YHCLPVGNAGNITAHWIGYSECAGRTGDEQLTAACAFCGGQCRYASALVERRPRMVGYQA 245 Query: 222 EGAAPIVKGYPIKNPQTIATAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIA 281 G+AP ++G P+ P+T+ATAI+IG+P SW A +ESGG D +SD EIL A +++A Sbjct: 246 SGSAPFLRGGPVAEPETVATAIRIGDPQSWDYAQAVREESGGWFDELSDEEILQAQRMLA 305 Query: 282 STEGVFCEPASAASVAGLIKLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPI-TVP 340 EGVFCEPASA SVAG ++ +R G G V CTLTG+GLKDPD A + + TV Sbjct: 306 DHEGVFCEPASATSVAGAMRDIRSGRIPEGSTVVCTLTGHGLKDPDVASAQAGDAVQTVD 365 Query: 341 PDFDEV 346 D+ V Sbjct: 366 ADYQAV 371 Lambda K H 0.317 0.136 0.400 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: 401 Number of extensions: 21 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: 352 Length of database: 379 Length adjustment: 30 Effective length of query: 322 Effective length of database: 349 Effective search space: 112378 Effective search space used: 112378 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_011812941.1 HHAL_RS00655 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))
# 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/TIGR00260.hmm # target sequence database: /tmp/gapView.16330.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00260 [M=340] Accession: TIGR00260 Description: thrC: threonine synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.1e-94 300.3 0.0 1.3e-93 299.8 0.0 1.2 1 lcl|NCBI__GCF_000015585.1:WP_011812941.1 HHAL_RS00655 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015585.1:WP_011812941.1 HHAL_RS00655 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 299.8 0.0 1.3e-93 1.3e-93 2 340 .] 12 351 .. 11 351 .. 0.95 Alignments for each domain: == domain 1 score: 299.8 bits; conditional E-value: 1.3e-93 TIGR00260 2 vryreilevt.ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltka 68 +y l+++ +++++ l eg+t+l++ ++++e+g +lyvk ++++Pt++FKDrg +++++tka lcl|NCBI__GCF_000015585.1:WP_011812941.1 12 AKYLDRLPISdDARILGLGEGNTPLIQLTRIPAELGRdVDLYVKFEGLNPTGSFKDRG---MTMAVTKA 77 67888899999**************************9********************...******** PP TIGR00260 69 lelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaq 137 e+g+++++cA++G+t+a+aa a+a++a+++++vL+P+gki+ +kl++a++++a+vl+i+G+FD+ lcl|NCBI__GCF_000015585.1:WP_011812941.1 78 VEQGAKAIICASTGNTSASAA-AYAARAGISCFVLIPDGKIA--MGKLAQAIMHGAQVLQIRGNFDAGM 143 *********************.********************..************************* PP TIGR00260 138 dlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekk 205 +lvke++e+ + + + Nsinp+r+++qkt+afei+e+l+ ++pd ++pv+ +gn++a + G+ e lcl|NCBI__GCF_000015585.1:WP_011812941.1 144 RLVKELAEHAPLTIV---NSINPYRLQGQKTAAFEIIEELE-RAPDYHCLPVGnAGNITAHWIGYSECA 208 *******77765555...5555*******************.9**********************9976 PP TIGR00260 206 elg.........................lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdi 249 +p ++ + +a g+a+++r g p +++eT++tA++i lcl|NCBI__GCF_000015585.1:WP_011812941.1 209 GRTgdeqltaacafcggqcryasalverRP-RMVGYQASGSAPFLRG----G---PVAEPETVATAIRI 269 44348**********************999.**********776665....5...9************* PP TIGR00260 250 gnpsnveralelarrslgnledlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsat 318 g p ++++a ++ ++s+g +++l sdeeil+a++ la +eg+++ep++a++va+ + + +g + lcl|NCBI__GCF_000015585.1:WP_011812941.1 270 GDPQSWDYAQAVREESGGWFDEL----SDEEILQAQRMLADHEGVFCEPASATSVAGAMRDIRSG---R 331 ***********************....**************************************...* PP TIGR00260 319 adpaKFeevvealtgnklkdpe 340 ++++ ++vv+ ltg++lkdp+ lcl|NCBI__GCF_000015585.1:WP_011812941.1 332 IPEG--STVVCTLTGHGLKDPD 351 ****..**************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 3.16 // [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