Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_028990311.1 G579_RS0111535 threonine ammonia-lyase, biosynthetic
Query= BRENDA::P04968 (514 letters) >NCBI__GCF_000423825.1:WP_028990311.1 Length = 503 Score = 535 bits (1378), Expect = e-156 Identities = 268/498 (53%), Positives = 362/498 (72%), Gaps = 3/498 (0%) Query: 17 LRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTEE 76 +R +L + VY+ A+ TPL+ LS RL N + KRED QPV SFKLRGAY M+A L E Sbjct: 6 IRQILTSRVYDVARETPLEAAANLSRRLHNAVSFKREDLQPVFSFKLRGAYNMIAHLREA 65 Query: 77 QKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANFD 136 ++ GVITASAGNHAQGVAFS+ RLG++A+IVMP T +IKVDAVR +G EV+L G ++ Sbjct: 66 ERTRGVITASAGNHAQGVAFSAQRLGIRAVIVMPQTTPEIKVDAVRAYGAEVVLAGDSYS 125 Query: 137 EAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQD-AHLDRVFVPVGGGGLAAG 195 +AKA L + G T++PPFD P+VIAGQGT+ E+L+Q HLD VFVPVGGGGL AG Sbjct: 126 DAKAHCDRLVAETGLTFIPPFDDPLVIAGQGTIGDEILRQSHGHLDAVFVPVGGGGLIAG 185 Query: 196 VAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLC 255 VA +K LMPQ+++I VE ++ + +L AG + L +VG+FA+GVAV+ +G+ TF + Sbjct: 186 VAGFLKVLMPQVRIIGVEPFEADAMYQSLQAGRRIALDQVGIFADGVAVREVGEHTFAIV 245 Query: 256 QEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHILS 315 ++ +D+II V +D ICAA+KD+F+D RAV EP+GAL++AG+K Y+A + G+RL +LS Sbjct: 246 KDTVDEIIRVSNDEICAAIKDVFDDTRAVMEPAGALSVAGLKAYVAREGVSGQRLVAVLS 305 Query: 316 GANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADAK 375 GAN+NF LR+V+ER ELGEQREAL AVTIPE G+F FC+ +G R +TEFNYR + Sbjct: 306 GANMNFDRLRFVAERAELGEQREALFAVTIPERPGAFRAFCKAIGRRVITEFNYRLSGRD 365 Query: 376 NACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQERL 435 +A IFVG+ ++ ++ + + + L+ GY+ DLSDDEMAKLH+R++VGG E + Sbjct: 366 SAHIFVGIS-TQSRKDARILTETLSRQGYATTDLSDDEMAKLHIRHLVGGHSPEVRNELV 424 Query: 436 YSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHE-PDFETRLNE 494 Y FEFPE PGAL+ FL+ LG +WNISLFHYR+HG D+GRVLA E+ E P+F+ L + Sbjct: 425 YRFEFPERPGALMEFLDKLGGHWNISLFHYRNHGADFGRVLAGIEVPPAELPEFQRFLEQ 484 Query: 495 LGYDCHDETNNPAFRFFL 512 LGY +E NPA++ FL Sbjct: 485 LGYPYAEEGGNPAYQLFL 502 Lambda K H 0.321 0.138 0.403 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: 717 Number of extensions: 29 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: 514 Length of database: 503 Length adjustment: 34 Effective length of query: 480 Effective length of database: 469 Effective search space: 225120 Effective search space used: 225120 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: 52 (24.6 bits)
Align candidate WP_028990311.1 G579_RS0111535 (threonine ammonia-lyase, biosynthetic)
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (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/TIGR01124.hmm # target sequence database: /tmp/gapView.10862.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01124 [M=499] Accession: TIGR01124 Description: ilvA_2Cterm: threonine ammonia-lyase, biosynthetic 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-253 825.4 0.1 8.9e-253 825.2 0.1 1.0 1 lcl|NCBI__GCF_000423825.1:WP_028990311.1 G579_RS0111535 threonine ammonia Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000423825.1:WP_028990311.1 G579_RS0111535 threonine ammonia-lyase, biosynthetic # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 825.2 0.1 8.9e-253 8.9e-253 2 499 .] 5 502 .. 4 502 .. 1.00 Alignments for each domain: == domain 1 score: 825.2 bits; conditional E-value: 8.9e-253 TIGR01124 2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvia 70 ++r+il++rvy++a etple aa+ls+rl+n v +kredlqpvfsfklrGayn++a+l + ++++Gvi+ lcl|NCBI__GCF_000423825.1:WP_028990311.1 5 LIRQILTSRVYDVARETPLEAAANLSRRLHNAVSFKREDLQPVFSFKLRGAYNMIAHLREAERTRGVIT 73 689****************************************************************** PP TIGR01124 71 asaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltf 139 asaGnhaqGva+sa++lG++avivmp+ttpeikvdav+a+G+evvl G++y++aka++ +l e gltf lcl|NCBI__GCF_000423825.1:WP_028990311.1 74 ASAGNHAQGVAFSAQRLGIRAVIVMPQTTPEIKVDAVRAYGAEVVLAGDSYSDAKAHCDRLVAETGLTF 142 ********************************************************************* PP TIGR01124 140 iapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalk 208 i+pfddplviaGqGt++ e+lrq++ +ldavfvpvGGGGliaGva ++k l+p++++igve+ +++a++ lcl|NCBI__GCF_000423825.1:WP_028990311.1 143 IPPFDDPLVIAGQGTIGDEILRQSHGHLDAVFVPVGGGGLIAGVAGFLKVLMPQVRIIGVEPFEADAMY 211 ********************************************************************* PP TIGR01124 209 qaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGa 277 q+l+aG+r+ ldqvG+fadGvav+evG++tf+++k+ +d+i++v de+caaikdvf+dtrav+epaGa lcl|NCBI__GCF_000423825.1:WP_028990311.1 212 QSLQAGRRIALDQVGIFADGVAVREVGEHTFAIVKDTVDEIIRVSNDEICAAIKDVFDDTRAVMEPAGA 280 ********************************************************************* PP TIGR01124 278 lalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevl 346 l++aGlk+yva++g+++++lva+lsGan+nfdrlr+v+eraelGeqreal+avtipe++G+++ f++ + lcl|NCBI__GCF_000423825.1:WP_028990311.1 281 LSVAGLKAYVAREGVSGQRLVAVLSGANMNFDRLRFVAERAELGEQREALFAVTIPERPGAFRAFCKAI 349 ********************************************************************* PP TIGR01124 347 GeraitefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGGraak 415 G r itefnyrl+ +++ahifvG+ ++++++++ l+++l+++gy++ dl+dde+aklh+r+lvGG + + lcl|NCBI__GCF_000423825.1:WP_028990311.1 350 GRRVITEFNYRLSGRDSAHIFVGISTQSRKDARILTETLSRQGYATTDLSDDEMAKLHIRHLVGGHSPE 418 ********************************************************************* PP TIGR01124 416 venerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelgy 484 v+ne +y+fefperpGal++fl++l ++wnislfhyrnhGad+Grvl+g+evp++e ef+ fl++lgy lcl|NCBI__GCF_000423825.1:WP_028990311.1 419 VRNELVYRFEFPERPGALMEFLDKLGGHWNISLFHYRNHGADFGRVLAGIEVPPAELPEFQRFLEQLGY 487 ********************************************************************* PP TIGR01124 485 ryedetenpayrlfl 499 y +e npay+lfl lcl|NCBI__GCF_000423825.1:WP_028990311.1 488 PYAEEGGNPAYQLFL 502 **************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (503 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 7.32 // [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