Align threonine synthase; EC 4.2.3.1 (characterized)
to candidate WP_007691417.1 C447_RS04700 threonine synthase
Query= CharProtDB::CH_107419 (405 letters) >NCBI__GCF_000336675.1:WP_007691417.1 Length = 417 Score = 402 bits (1033), Expect = e-116 Identities = 222/399 (55%), Positives = 271/399 (67%), Gaps = 13/399 (3%) Query: 4 LKCIECGAEYSR-DEVIYTCSKCDGLLDVIYDYSSIKIDMEKLKTECPSVWKYAKLLPVE 62 L CIECG + DE Y C CDGLL+ Y+ D VW+YA LP E Sbjct: 20 LACIECGRTLAPFDEPTYRCPDCDGLLEARYEEYPTFEDFSGR-----GVWRYAAALPFE 74 Query: 63 REPVTIQEGGTPLYKCDRLAEKIGIKKLYVKHEGMNPTGSFKDRGMTVGVTKALELGMNT 122 V++ EG TPL++ RL +G++ L VKHEGMNPTGSFKDRGMTVGV A ELG++ Sbjct: 75 -SGVSLPEGDTPLHEVPRLEADVGVRSLRVKHEGMNPTGSFKDRGMTVGVRVAQELGVDR 133 Query: 123 VACASTGNTSAALAIYGAKAGIPVVVLLPAGKVALGKVAQALMHGAKVLSIRGNFDDALA 182 +ACASTGNTSAALA YG +AG+ +VLLPAGKVA GKVAQA +HGA++L + GNFD L Sbjct: 134 LACASTGNTSAALAAYGGRAGVETLVLLPAGKVAAGKVAQAALHGARILEVDGNFDACLD 193 Query: 183 LVRTLCSQEKIYLLNSINPYRLEGQKTIGFEIADQL---DFKVPDRIVLPVGNAGNITAI 239 +V L + + YLLNS+NP+RLEGQKTIGFEI + + PDRIVLPVGNAGN A+ Sbjct: 194 VVAELANMGEAYLLNSLNPFRLEGQKTIGFEILESFLAEYDRYPDRIVLPVGNAGNTAAL 253 Query: 240 YKGFREFKILGITD--SLPKMTGIQAEGSCPIVKAIKSGAPAITPEENPETVATAIRIGN 297 YK FRE G D +P +TG+QAEG+ P+V+AI+ G E+ ET ATAIRIGN Sbjct: 254 YKAFRELVEAGALDEAEVPMLTGVQAEGAAPMVEAIEEGLDDTRRWEDVETRATAIRIGN 313 Query: 298 PVNATKALSAIRESGGTAESVTDEEILAAQKDLARLEGIGVEPASAASVAGLRKLVDMGV 357 PVNA KAL IR +GGTA +V DE I+ AQ+ LA EG+GVEPASAAS+AGLRKL + G Sbjct: 314 PVNARKALPGIRGTGGTAVAVADEAIVDAQRTLAE-EGVGVEPASAASIAGLRKLRESGT 372 Query: 358 IGRDETVVCITTGHLLKDPQTVIDVCEEPTVVDANIDAI 396 + DE VVC+TTGHLLKDP +P V + +AI Sbjct: 373 VDDDEDVVCLTTGHLLKDPDAAAAAGRDPEPVPNDTEAI 411 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: 551 Number of extensions: 34 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 WP_007691417.1 C447_RS04700 (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.1265849.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-92 293.9 0.0 9.1e-92 293.7 0.0 1.0 1 NCBI__GCF_000336675.1:WP_007691417.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000336675.1:WP_007691417.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 293.7 0.0 9.1e-92 9.1e-92 1 340 [] 64 392 .. 64 392 .. 0.96 Alignments for each domain: == domain 1 score: 293.7 bits; conditional E-value: 9.1e-92 TIGR00260 1 vvryreilevtekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgn 73 v+ry+++l+ v+l eg t+l ++p+l++ vg++ l vk+++++Pt++FKDrg ++v++ a+elg+ NCBI__GCF_000336675.1:WP_007691417.1 64 VWRYAAALPFE--SGVSLPEGDTPLHEVPRLEADVGVRSLRVKHEGMNPTGSFKDRG---MTVGVRVAQELGV 131 8********97..99******************************************...************* PP TIGR00260 74 etvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifed 146 + ++cA++G+t+aa+a a+ g+a+v+ +vL+P+gk++ ++k+++a ++a++l+++G+FD+++d+v+e++++ NCBI__GCF_000336675.1:WP_007691417.1 132 DRLACASTGNTSAALA-AYGGRAGVETLVLLPAGKVA--AGKVAQAALHGARILEVDGNFDACLDVVAELANM 201 ****************.********************..********************************** PP TIGR00260 147 keklklnsvNsinparieaqktyafeiveqlgk...espdkvvvpvp.sgnfgailkGflekkelg......l 209 e+++lns N p+r+e+qkt+ fei+e + pd++v+pv+ +gn a++k+f e+ e+g + NCBI__GCF_000336675.1:WP_007691417.1 202 GEAYLLNSLN---PFRLEGQKTIGFEILESFLAeydRYPDRIVLPVGnAGNTAALYKAFRELVEAGaldeaeV 271 *********9...***************9987656689********************************888 PP TIGR00260 210 pieklaiaaegaadivrrflksg.dlepkedkeTlstAmdignpsnveralelarrslgnledlkesvsdeei 281 p + ++++aegaa++v++ ++ d ed+eT +tA++ignp+n+ +al ++r ++g + ++ de+i NCBI__GCF_000336675.1:WP_007691417.1 272 P-MLTGVQAEGAAPMVEAIEEGLdDTRRWEDVETRATAIRIGNPVNARKALPGIRGTGGTAVAV----ADEAI 339 8.899**************8888666677888*****************************999....99999 PP TIGR00260 282 leaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdpe 340 ++a++ la eeg+ +ep++a+++a+l+kl e+g t+d + e+vv+ tg+ lkdp+ NCBI__GCF_000336675.1:WP_007691417.1 340 VDAQRTLA-EEGVGVEPASAASIAGLRKLRESG---TVDDD--EDVVCLTTGHLLKDPD 392 99987765.78**********************...*****..**************97 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 25.42 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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