Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate WP_084275803.1 B8779_RS06910 threonine ammonia-lyase
Query= SwissProt::Q9WYJ1 (401 letters) >NCBI__GCF_900176045.1:WP_084275803.1 Length = 403 Score = 369 bits (948), Expect = e-107 Identities = 190/397 (47%), Positives = 282/397 (71%), Gaps = 2/397 (0%) Query: 1 MITLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIA 60 MI L+DI++A + +++V +T AY+ +LS+ G +I+LK ENLQ TG+FK+RGA+NKIA Sbjct: 1 MIALQDIQQAAKRIESVASKTPYAYAPILSKKCGYKIFLKKENLQVTGAFKLRGAFNKIA 60 Query: 61 HLSEEERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILE 120 +S+EE+ RGVVAASAGNHAQGVA ++ F IPATIVMP PL+K+ ++ GA VIL Sbjct: 61 KISQEEKNRGVVAASAGNHAQGVAFSSNYFQIPATIVMPENTPLTKVNGVKSYGASVILH 120 Query: 121 GNIFDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGG 180 G+ +DEAY A++ + FVHPF D V+AGQGTI LEI++ D++ ++VP+GGGG Sbjct: 121 GSNYDEAYAYAVQYAKDHNKTFVHPFADYDVMAGQGTIALEILDQAKDLDAILVPIGGGG 180 Query: 181 LISGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLT 240 LI+G++ AIK +NP++++IGV P+M S + GR T+ADGIAV+ +T Sbjct: 181 LIAGIASAIKQINPKIQIIGVTAAGAPAMRESFQLGRPVDSTQVRTIADGIAVRDTSPVT 240 Query: 241 FELVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVL-NKLDV-KGKKVAI 298 +++ + VD++V V++EEIADAILFLLE K+V EGAGAVGVAA+L KL + + +A+ Sbjct: 241 LKIILETVDDIVEVDDEEIADAILFLLENQKLVVEGAGAVGVAALLYEKLTLPENANIAV 300 Query: 299 VISGGNIDVNMIDRIINKGLVKSGRKVFIETFVMDRPGALKELLGIVAELGANVLSVFHN 358 V+SGGNIDV M+ II KGL+KS RK+ + ++D+PG+L +L I+A + AN++ + ++ Sbjct: 301 VLSGGNIDVTMLSVIIEKGLIKSYRKMKLIVTLVDKPGSLMKLTEILASVSANIVQIGYD 360 Query: 359 RSAKEVPIGFAKIELELETVDEKHVEEIERVLIAKGY 395 R++ + G A + + LET ++H E+I +L G+ Sbjct: 361 RTSANLAYGDANVSIGLETKGKEHQEQIRELLTRHGF 397 Lambda K H 0.317 0.136 0.367 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: 382 Number of extensions: 9 Number of successful extensions: 2 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: 401 Length of database: 403 Length adjustment: 31 Effective length of query: 370 Effective length of database: 372 Effective search space: 137640 Effective search space used: 137640 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_084275803.1 B8779_RS06910 (threonine ammonia-lyase)
to HMM TIGR01127 (ilvA: threonine ammonia-lyase (EC 4.3.1.19))
# 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/TIGR01127.hmm # target sequence database: /tmp/gapView.3434426.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01127 [M=380] Accession: TIGR01127 Description: ilvA_1Cterm: threonine ammonia-lyase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-163 528.9 6.9 4.2e-163 528.7 6.9 1.0 1 NCBI__GCF_900176045.1:WP_084275803.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900176045.1:WP_084275803.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 528.7 6.9 4.2e-163 4.2e-163 1 379 [. 21 400 .. 21 401 .. 1.00 Alignments for each domain: == domain 1 score: 528.7 bits; conditional E-value: 4.2e-163 TIGR01127 1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakvfgik 73 tp++++ +ls+ +g +++lk enlq tG+fk+rGa+nkiak+s+eek+rGvvaasaGnhaqGva++++ f i+ NCBI__GCF_900176045.1:WP_084275803.1 21 TPYAYAPILSKKCGYKIFLKKENLQVTGAFKLRGAFNKIAKISQEEKNRGVVAASAGNHAQGVAFSSNYFQIP 93 899********************************************************************** PP TIGR01127 74 akivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtlgleiledl 146 a+ivmPe +pl+kv+ +ksyGa viLhG+++Deay++a ++a++++++fvh+f D v+aGqGt++leil++ NCBI__GCF_900176045.1:WP_084275803.1 94 ATIVMPENTPLTKVNGVKSYGASVILHGSNYDEAYAYAVQYAKDHNKTFVHPFADYDVMAGQGTIALEILDQA 166 ************************************************************************* PP TIGR01127 147 pdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvktiaDGiavkkpgdl 219 d+d ++vP+GGGGLi+G+asa+k++np++++iGv a +ap++ es++ g++++ ++v+tiaDGiav++++++ NCBI__GCF_900176045.1:WP_084275803.1 167 KDLDAILVPIGGGGLIAGIASAIKQINPKIQIIGVTAAGAPAMRESFQLGRPVDSTQVRTIADGIAVRDTSPV 239 ************************************************************************* PP TIGR01127 220 tfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvd.vkgkkvavvvsGGnidlnll 291 t +i+ e+vD++v+vd+eeia+ail+Lle++k+v+egaGavgvaa+l ek+ +++ ++avv+sGGnid+++l NCBI__GCF_900176045.1:WP_084275803.1 240 TLKIILETVDDIVEVDDEEIADAILFLLENQKLVVEGAGAVGVAALLYEKLTlPENANIAVVLSGGNIDVTML 312 ****************************************************99999**************** PP TIGR01127 292 ekiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlskeialgaakvelelevkgkehl 364 + iiekgL+ks+rk+k+ ++l+DkPG+L+kl+e++a aniv+i +dr+s ++a+g+a+v++ le+kgkeh+ NCBI__GCF_900176045.1:WP_084275803.1 313 SVIIEKGLIKSYRKMKLIVTLVDKPGSLMKLTEILASVSANIVQIGYDRTSANLAYGDANVSIGLETKGKEHQ 385 ************************************************************************* PP TIGR01127 365 eellktlrdkgyevk 379 e++++ l+ +g++++ NCBI__GCF_900176045.1:WP_084275803.1 386 EQIRELLTRHGFRFY 400 ************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (403 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: 00:00:00.00 # Mc/sec: 18.28 // [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