Align threonine synthase; EC 4.2.3.1 (characterized)
to candidate 351929 BT2401 threonine synthase (NCBI ptt file)
Query= CharProtDB::CH_002114 (428 letters) >lcl|FitnessBrowser__Btheta:351929 BT2401 threonine synthase (NCBI ptt file) Length = 433 Score = 353 bits (907), Expect = e-102 Identities = 192/432 (44%), Positives = 271/432 (62%), Gaps = 6/432 (1%) Query: 1 MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60 MK Y+ S +AV +GL ++GLF P + D + L F + ++ Sbjct: 1 MKYYSTNKQAPMASLQEAVVKGLAADRGLFMPMTIKPLPQEFYDTIDTLSFQEIAYRVAD 60 Query: 61 AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120 AF G++IP + L++ V +F P+ V ++ LELFHGPTLAFKD GGRFMA++L + Sbjct: 61 AFFGEDIPTDTLKQIVYDTLSFDVPLVKVADNIYSLELFHGPTLAFKDVGGRFMARLLGY 120 Query: 121 IA---GDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNI 177 G K V +L ATSGDTG+AVA+ F G+ + V +LYP+GK+S +QEK F TLG NI Sbjct: 121 FIKKEGQKDVNVLVATSGDTGSAVANGFLGVEGIHVYVLYPKGKVSEIQEKQFTTLGQNI 180 Query: 178 ETVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQET 237 + +DG FD CQALVK AF D+EL L L SANSIN++R L Q YYF A AQL + Sbjct: 181 TALEVDGTFDDCQALVKAAFMDKELNEHLSLTSANSINVARFLPQAFYYFYAYAQLKRAG 240 Query: 238 R-NQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQAT 296 + + V+ VPSGNFG++TAGL K +GLPVKRFIAA N ND ++L G+++P+ + AT Sbjct: 241 KADNAVICVPSGNFGNITAGLFGKKMGLPVKRFIAANNRNDIFYQYLQTGKYNPRPSVAT 300 Query: 297 LSNAMDVSQPNNWPRVEELFRRKIWQLK-ELGYAAVDDETTQQTMREL-KELGYTSEPHA 354 ++NAMDV P+N+ RV +L+ + E+ DE ++T++E KE Y +PH Sbjct: 301 IANAMDVGDPSNFARVLDLYGGSHADISAEISGTTYTDEQIRETVKETWKEHHYLLDPHG 360 Query: 355 AVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLP 414 A YRAL++ L GE G+FL TAHPAKF E+VE+I+GE +++P +L E S + Sbjct: 361 ACGYRALQEGLKQGETGVFLETAHPAKFLETVESIIGEAVEIPAKLQEFMKGEKKSLQMT 420 Query: 415 ADFAALRKLMMN 426 +FA +K +++ Sbjct: 421 KEFADFKKYLLS 432 Lambda K H 0.319 0.135 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: 476 Number of extensions: 25 Number of successful extensions: 4 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: 428 Length of database: 433 Length adjustment: 32 Effective length of query: 396 Effective length of database: 401 Effective search space: 158796 Effective search space used: 158796 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 (21.8 bits) S2: 51 (24.3 bits)
Align candidate 351929 BT2401 (threonine synthase (NCBI ptt file))
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.20128.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-96 308.8 0.0 3.2e-96 308.4 0.0 1.0 1 lcl|FitnessBrowser__Btheta:351929 BT2401 threonine synthase (NCBI Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:351929 BT2401 threonine synthase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 308.4 0.0 3.2e-96 3.2e-96 12 335 .. 66 399 .. 56 403 .. 0.92 Alignments for each domain: == domain 1 score: 308.4 bits; conditional E-value: 3.2e-96 TIGR00260 12 ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne...tvlcAtsGdt 84 +++ +l++ ++ ++ ++ + +v n+y +elfhgPtlaFKD+g++f+a ll ++ ++ + vl+AtsGdt lcl|FitnessBrowser__Btheta:351929 66 DIPTDTLKQIVYDTLSFDVPLVKVAD-NIYSLELFHGPTLAFKDVGGRFMARLLGYFIKKEGQkdvNVLVATSGDT 140 578889999***************99.****************************985543333779********* PP TIGR00260 85 gaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNs 157 g+a+a+++ g ++++v+vLyPkgk+s ++ek +t+l +n++ l+++G+FDd+q+lvk++f dke +l l s+Ns lcl|FitnessBrowser__Btheta:351929 141 GSAVANGFLGVEGIHVYVLYPKGKVSEIQEKQFTTLGQNITALEVDGTFDDCQALVKAAFMDKElneHLSLTSANS 216 ************************************************************988778799******* PP TIGR00260 158 inparieaqktyafeiveqlgk.espdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksg 232 in+ar + q y+f + +ql++ + d+ v+ vpsgnfg+i++G + kk++ lp k++iaa++ +di ++l++g lcl|FitnessBrowser__Btheta:351929 217 INVARFLPQAFYYFYAYAQLKRaGKADNAVICVPSGNFGNITAGLFGKKMG-LP-VKRFIAANNRNDIFYQYLQTG 290 **********77777888887758899******************999999.**.9******************** PP TIGR00260 233 dlepkedkeTlstAmdignpsnveralelarrslgnled..lkesvsdeeileaikklaeeegyllephtavavaa 306 + p+ +++T+++Amd+g psn+ r+l+l s +++ + +++ +de+i e++k+ +e++yll+ph+a +++a lcl|FitnessBrowser__Btheta:351929 291 KYNPRPSVATIANAMDVGDPSNFARVLDLYGGSHADISAeiSGTTYTDEQIRETVKETWKEHHYLLDPHGACGYRA 366 ****************************887777766551156699****************************** PP TIGR00260 307 lkklvekg.vs...atadpaKFeevvealtgnk 335 l++ +++g ++ ta+paKF e+ve + g+ lcl|FitnessBrowser__Btheta:351929 367 LQEGLKQGeTGvflETAHPAKFLETVESIIGEA 399 ******997446789************998875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (433 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: 12.47 // [ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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