Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate Pf6N2E2_5296 Threonine synthase (EC 4.2.3.1)
Query= curated2:Q58860 (405 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5296 Length = 417 Score = 226 bits (577), Expect = 7e-64 Identities = 141/381 (37%), Positives = 209/381 (54%), Gaps = 10/381 (2%) Query: 4 RCIKCGKTYDVDEIIYTC---ECGGLLEIIYDYEEIKDKVSEEKLRKREI-GVWRYLEYL 59 +C+ C ++Y E+ Y C + G L+ +YDY +K + S + L G+WRY + Sbjct: 11 QCLVCDRSYQPHEVSYYCPHCKVDGALDALYDYPALKREWSRDSLAHDHARGMWRYDRLM 70 Query: 60 PVKDESKIVSLCEGGTPLY-RCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRAN 118 P+ I L G TPLY R L K IK ++VK+E PTGS KDR + V A Sbjct: 71 PLSSTQFIPPLLVGNTPLYSRPELLGKGARIK-VFVKDESRQPTGSLKDRASALAVAHAL 129 Query: 119 ELGVEVVGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGN 178 + G V ASTGN +++LA SA G ++ LP+ KLAQ YGA+++ V G Sbjct: 130 QSGARTVAVASTGNAASALAGMSASLGLHNVIYLPKS-APREKLAQMQGYGAEIVLVDGQ 188 Query: 179 FDDALDMVKQLAKEKLIY-LLNSINPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGN 237 +D+A + +E Y IN + EG+KT+AFE+C+QLNWQVPD V VPVGN Sbjct: 189 YDEAFEQCLNACQEHGWYNRTTGINSYMSEGKKTVAFEMCEQLNWQVPDLVFVPVGNGCI 248 Query: 238 ISAIWKGFKEFEITGIIDELPKMTGIQADGAKPIVEAFRK-RAKDIIPYKNPETIATAIR 296 + +++KGF + G I+ +P++ G+QA+ + + A+R R+ + P ++A++I Sbjct: 249 LGSVYKGFFDLLQLGWIERIPRLIGVQAEHSNFMYRAWRNDRSMQKTERRPPTSLASSIN 308 Query: 297 IGNPVNAPKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLE 356 + P + KA+ A+ +SGG V+D IV A LA G+F E +AS+ AGL K E Sbjct: 309 VALPRDRLKAMRAVTASGGEFICVSDPSIVAAASRLAASTGVFPEAGAASAFAGLLKYAE 368 Query: 357 EGIIDRDERIVCITTGHGLKD 377 D + V + TG GLKD Sbjct: 369 IH-PDTPQTAVILITGSGLKD 388 Lambda K H 0.317 0.137 0.395 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: 405 Number of extensions: 26 Number of successful extensions: 6 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: 405 Length of database: 417 Length adjustment: 31 Effective length of query: 374 Effective length of database: 386 Effective search space: 144364 Effective search space used: 144364 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: 50 (23.9 bits)
Align candidate Pf6N2E2_5296 (Threonine synthase (EC 4.2.3.1))
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.4214.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-56 175.6 0.0 8.7e-56 175.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5296 Threonine synthase (EC 4.2.3.1) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5296 Threonine synthase (EC 4.2.3.1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 175.5 0.0 8.7e-56 8.7e-56 1 339 [. 63 389 .. 63 390 .. 0.91 Alignments for each domain: == domain 1 score: 175.5 bits; conditional E-value: 8.7e-56 TIGR00260 1 vvryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvav 63 ++ry +++ + + + l g+t+l+ p+l + +++vk+++ Pt++ KDr+ a lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5296 63 MWRYDRLMPLSsTQFIPPLLVGNTPLYSRPELLGKGARIKVFVKDESRQPTGSLKDRA---SAL 123 699999999996666678999**********9955555599*****************...99* PP TIGR00260 64 lltkalelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvl 127 ++++al+ g+ tv++A++G+ ++a+a ++++ +++ v+ +Pk ekl++ ++a+++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5296 124 AVAHALQSGARTVAVASTGNAASALA-GMSASLGLHNVIYLPKS-AP--REKLAQMQGYGAEIV 183 **************************.****************9.33..7************** PP TIGR00260 128 aikGdFDdaqdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp. 190 ++G++D+a + + ++++++ + n in + e++kt+afe++eql+++ pd v vpv+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5296 184 LVDGQYDEAFEQCLNACQEHGWY--NRTTGINSYMSEGKKTVAFEMCEQLNWQVPDLVFVPVGn 245 *****************654433..344446699*****************************9 PP TIGR00260 191 sgnfgailkGflekkelg....lpieklaiaaegaadivrrflksgdlepkedk..eTlstAmd 248 + +g+++kGf+ + +lg p + ++++ae ++ ++r+ ++++ +++ e+ l+ +++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5296 246 GCILGSVYKGFFDLLQLGwierIP-RLIGVQAEHSNFMYRAWRNDRSMQKTERRppTSLASSIN 308 9999*****************999.********************9544443333599****** PP TIGR00260 249 ignpsnveralelarrslgnledlkesvsdeeileaikklaeeegyllephtavavaalkklve 312 + p + +a++++ s+g++ + sd +i+ a +la++ g++ e +a a a+l+k +e lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5296 309 VALPRDRLKAMRAVTASGGEFICV----SDPSIVAAASRLAASTGVFPEAGAASAFAGLLKYAE 368 **********************99....********************************9876 PP TIGR00260 313 kgvsatadpaKFeevvealtgnklkdp 339 ++p+ +++v +tg +lkd lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5296 369 ------IHPDTPQTAVILITGSGLKDT 389 ......99**999***********985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (417 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: 11.82 // [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