Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_012966677.1 FERP_RS11085 threonine synthase
Query= curated2:Q58860 (405 letters) >NCBI__GCF_000025505.1:WP_012966677.1 Length = 404 Score = 296 bits (757), Expect = 1e-84 Identities = 164/393 (41%), Positives = 253/393 (64%), Gaps = 10/393 (2%) Query: 4 RCIKCGKTYDVDEIIYTCE-CGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVK 62 +C CGK + E +YTC+ C G LE++YD+E IK+ VS+EK+ K +WRY ++LPV Sbjct: 7 KCRICGKEFPA-EALYTCDNCFGPLEVVYDWEWIKENVSKEKIEKGPKTLWRYKDFLPV- 64 Query: 63 DESKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGV 122 E++ V L G T + NL + LG+K LY+ ++ NPT SFKDR ++V VT+A E G+ Sbjct: 65 -EAEPVDLGAGYTRFIKAENLGEVLGLKNLYLLDDSTNPTYSFKDRVVSVAVTKAKEFGM 123 Query: 123 EVVGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDA 182 + +GCASTGN + SLAA++A++ + +P G + K+ QA+ +GAKVI+V+G +DDA Sbjct: 124 KALGCASTGNLAGSLAAHAAKAKLPAYIFVPAG-IEKNKIIQALVHGAKVIEVEGTYDDA 182 Query: 183 LDMVKQLAKEKLIYLLNSIN--PFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISA 240 + ++A+E + +IN P+ EG KT+A+E ++L W++PD+V+VP+ + + A Sbjct: 183 NRLATEVAEEHPDWGFVNINLRPYYAEGSKTLAYETAERLGWELPDQVVVPMASGALLCA 242 Query: 241 IWKGFKEFEITGIIDELPKM-TGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIGN 299 I +GFK+ G++DE + G Q +G PIV A K K + P + +TI ++ IGN Sbjct: 243 IHRGFKDLIRVGLVDEKDVVFNGCQPEGF-PIVRAV-KEGKPVTPIREIKTIVHSLAIGN 300 Query: 300 PVNAPKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEGI 359 P + A + I SGGYAE +D E++EA KLLA+ EGIF E A ++AGLK+L+EEG Sbjct: 301 PADGIFAKEIIEKSGGYAEDPSDLEVIEAVKLLAKTEGIFTELAGGVTVAGLKRLVEEGR 360 Query: 360 IDRDERIVCITTGHGLKDPDAAIRASEEPIKIE 392 ID+ + +V TG+GLK +A + E ++I+ Sbjct: 361 IDKSDVVVIYLTGNGLKTSEALVDYLETTVRIK 393 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: 529 Number of extensions: 29 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: 405 Length of database: 404 Length adjustment: 31 Effective length of query: 374 Effective length of database: 373 Effective search space: 139502 Effective search space used: 139502 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 WP_012966677.1 FERP_RS11085 (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.29005.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-99 316.9 0.0 9.2e-99 316.7 0.0 1.0 1 lcl|NCBI__GCF_000025505.1:WP_012966677.1 FERP_RS11085 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025505.1:WP_012966677.1 FERP_RS11085 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 316.7 0.0 9.2e-99 9.2e-99 2 340 .] 56 380 .. 55 380 .. 0.98 Alignments for each domain: == domain 1 score: 316.7 bits; conditional E-value: 9.2e-99 TIGR00260 2 vryreilevtekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkale 70 +ry+ +l+v +++vdl +g t+++++++l e +g++nly+++++++Pt++FKDr+ v+v++tka+e lcl|NCBI__GCF_000025505.1:WP_012966677.1 56 WRYKDFLPVE-AEPVDLGAGYTRFIKAENLGEVLGLKNLYLLDDSTNPTYSFKDRV---VSVAVTKAKE 120 9********6.*********************************************...********** PP TIGR00260 71 lgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdl 139 g+++++cA++G+++ ++a a+a+ka + +++++P+g i+ k+k+++al+++akv++++G++Dda++l lcl|NCBI__GCF_000025505.1:WP_012966677.1 121 FGMKALGCASTGNLAGSLA-AHAAKAKLPAYIFVPAG-IE--KNKIIQALVHGAKVIEVEGTYDDANRL 185 *******************.*****************.**..*************************** PP TIGR00260 140 vkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekkel 207 +e++e+++ ++++++N++ p++ e++kt+a+e +e+lg+e pd+vvvp++ ++++ ai++Gf+ + ++ lcl|NCBI__GCF_000025505.1:WP_012966677.1 186 ATEVAEEHPDWGFVNINLR-PYYAEGSKTLAYETAERLGWELPDQVVVPMAsGALLCAIHRGFKDLIRV 253 *****************88.*******************************777899************ PP TIGR00260 208 g....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnledl 272 g +++ +++ ++eg +ivr++++++ ++p+++ +T++++++ignp++ a+e++++s+g++ed lcl|NCBI__GCF_000025505.1:WP_012966677.1 254 GlvdeKDVVFNGCQPEGF-PIVRAVKEGKPVTPIREIKTIVHSLAIGNPADGIFAKEIIEKSGGYAEDP 321 ****99***********7.************************************************** PP TIGR00260 273 kesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdpe 340 sd e++ea+k+la++eg+++e +++v+va+lk+lve+g ++d+ vv +ltgn+lk+ e lcl|NCBI__GCF_000025505.1:WP_012966677.1 322 ----SDLEVIEAVKLLAKTEGIFTELAGGVTVAGLKRLVEEG---RIDKS--DVVVIYLTGNGLKTSE 380 ....**************************************...***99..77777*******9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (404 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 13.24 // [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