Align threonine synthase; EC 4.2.3.1 (characterized)
to candidate WP_011021620.1 MA_RS08365 threonine synthase
Query= CharProtDB::CH_107419 (405 letters) >NCBI__GCF_000007345.1:WP_011021620.1 Length = 405 Score = 798 bits (2061), Expect = 0.0 Identities = 405/405 (100%), Positives = 405/405 (100%) Query: 1 MYHLKCIECGAEYSRDEVIYTCSKCDGLLDVIYDYSSIKIDMEKLKTECPSVWKYAKLLP 60 MYHLKCIECGAEYSRDEVIYTCSKCDGLLDVIYDYSSIKIDMEKLKTECPSVWKYAKLLP Sbjct: 1 MYHLKCIECGAEYSRDEVIYTCSKCDGLLDVIYDYSSIKIDMEKLKTECPSVWKYAKLLP 60 Query: 61 VEREPVTIQEGGTPLYKCDRLAEKIGIKKLYVKHEGMNPTGSFKDRGMTVGVTKALELGM 120 VEREPVTIQEGGTPLYKCDRLAEKIGIKKLYVKHEGMNPTGSFKDRGMTVGVTKALELGM Sbjct: 61 VEREPVTIQEGGTPLYKCDRLAEKIGIKKLYVKHEGMNPTGSFKDRGMTVGVTKALELGM 120 Query: 121 NTVACASTGNTSAALAIYGAKAGIPVVVLLPAGKVALGKVAQALMHGAKVLSIRGNFDDA 180 NTVACASTGNTSAALAIYGAKAGIPVVVLLPAGKVALGKVAQALMHGAKVLSIRGNFDDA Sbjct: 121 NTVACASTGNTSAALAIYGAKAGIPVVVLLPAGKVALGKVAQALMHGAKVLSIRGNFDDA 180 Query: 181 LALVRTLCSQEKIYLLNSINPYRLEGQKTIGFEIADQLDFKVPDRIVLPVGNAGNITAIY 240 LALVRTLCSQEKIYLLNSINPYRLEGQKTIGFEIADQLDFKVPDRIVLPVGNAGNITAIY Sbjct: 181 LALVRTLCSQEKIYLLNSINPYRLEGQKTIGFEIADQLDFKVPDRIVLPVGNAGNITAIY 240 Query: 241 KGFREFKILGITDSLPKMTGIQAEGSCPIVKAIKSGAPAITPEENPETVATAIRIGNPVN 300 KGFREFKILGITDSLPKMTGIQAEGSCPIVKAIKSGAPAITPEENPETVATAIRIGNPVN Sbjct: 241 KGFREFKILGITDSLPKMTGIQAEGSCPIVKAIKSGAPAITPEENPETVATAIRIGNPVN 300 Query: 301 ATKALSAIRESGGTAESVTDEEILAAQKDLARLEGIGVEPASAASVAGLRKLVDMGVIGR 360 ATKALSAIRESGGTAESVTDEEILAAQKDLARLEGIGVEPASAASVAGLRKLVDMGVIGR Sbjct: 301 ATKALSAIRESGGTAESVTDEEILAAQKDLARLEGIGVEPASAASVAGLRKLVDMGVIGR 360 Query: 361 DETVVCITTGHLLKDPQTVIDVCEEPTVVDANIDAIREAIFGKAK 405 DETVVCITTGHLLKDPQTVIDVCEEPTVVDANIDAIREAIFGKAK Sbjct: 361 DETVVCITTGHLLKDPQTVIDVCEEPTVVDANIDAIREAIFGKAK 405 Lambda K H 0.317 0.135 0.389 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: 813 Number of extensions: 27 Number of successful extensions: 1 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: 405 Length adjustment: 31 Effective length of query: 374 Effective length of database: 374 Effective search space: 139876 Effective search space used: 139876 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_011021620.1 MA_RS08365 (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.11819.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-117 378.2 0.0 2.1e-117 378.0 0.0 1.0 1 lcl|NCBI__GCF_000007345.1:WP_011021620.1 MA_RS08365 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007345.1:WP_011021620.1 MA_RS08365 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 378.0 0.0 2.1e-117 2.1e-117 1 339 [. 52 376 .. 52 377 .. 0.99 Alignments for each domain: == domain 1 score: 378.0 bits; conditional E-value: 2.1e-117 TIGR00260 1 vvryreilevtekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkal 69 v++y+++l+v ++v+++eg t+l+++++lae++g+++lyvk+++++Pt++FKDrg ++v++tkal lcl|NCBI__GCF_000007345.1:WP_011021620.1 52 VWKYAKLLPVE-REPVTIQEGGTPLYKCDRLAEKIGIKKLYVKHEGMNPTGSFKDRG---MTVGVTKAL 116 8*********6.*********************************************...********* PP TIGR00260 70 elgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqd 138 elg++tv+cA++G+t+aa+a + +ka++ vvvL+P+gk++ +k+++al+++akvl+i+G+FDda++ lcl|NCBI__GCF_000007345.1:WP_011021620.1 117 ELGMNTVACASTGNTSAALA-IYGAKAGIPVVVLLPAGKVA--LGKVAQALMHGAKVLSIRGNFDDALA 182 ********************.********************..************************** PP TIGR00260 139 lvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekke 206 lv+ +++++++++lns+N p+r+e+qkt+ fei++ql+ + pd++v+pv+ +gn++ai+kGf e+k lcl|NCBI__GCF_000007345.1:WP_011021620.1 183 LVRTLCSQEKIYLLNSIN---PYRLEGQKTIGFEIADQLDFKVPDRIVLPVGnAGNITAIYKGFREFKI 248 *****************9...************************************************ PP TIGR00260 207 lg....lpieklaiaaegaadivrrflksg.dlepkedkeTlstAmdignpsnveralelarrslgnle 270 lg lp ++++i+aeg+ +iv++ + + ++p e++eT++tA++ignp+n+ +al ++r+s+g +e lcl|NCBI__GCF_000007345.1:WP_011021620.1 249 LGitdsLP-KMTGIQAEGSCPIVKAIKSGApAITPEENPETVATAIRIGNPVNATKALSAIRESGGTAE 316 ********.*****************99999************************************** PP TIGR00260 271 dlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdp 339 ++ +deeil a+k la+ eg+ +ep++a++va+l+klv+ g + ++ e+vv++ tg+ lkdp lcl|NCBI__GCF_000007345.1:WP_011021620.1 317 SV----TDEEILAAQKDLARLEGIGVEPASAASVAGLRKLVDMG---VIGRD--ETVVCITTGHLLKDP 376 **....**************************************...*****..*************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (405 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: 7.78 // [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