Align L-threonine dehydratase biosynthetic IlvA; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate AO356_27710 AO356_27710 threonine dehydratase
Query= curated2:P37946 (422 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27710 Length = 333 Score = 230 bits (586), Expect = 5e-65 Identities = 133/331 (40%), Positives = 193/331 (58%), Gaps = 9/331 (2%) Query: 7 ENSLIQ--VKHILKAHQNVKDVVIHTPLQRNDRLSERYECNIYLKREDLQVVRSFKLRGA 64 E +L++ VK IL A V ++ + TPLQ LSE I LKREDLQ SFK+RGA Sbjct: 7 EQTLLEHYVKKILAAP--VYELAVRTPLQAAPALSEALGNRILLKREDLQPTFSFKIRGA 64 Query: 65 YHKMKQLSSEQTENGVVCASAGNHAQGVAFSCKHLGIHGKIFMPSTTPRQKVSQVELFGK 124 Y+K+ L+ EQ GV+ ASAGNHAQGVA + + LGI +I MP TTP+ KV V G Sbjct: 65 YNKLVHLTPEQRARGVITASAGNHAQGVALAARELGISARIVMPVTTPQLKVLGVRNRGA 124 Query: 125 GFIDIILTGDTFDDVYKSAAECCEAESRTFIHPFDDPDVMAGQGTLAVEILNDIDTEPHF 184 + +L GD+F A E E R F+ PFDDPDV+AGQGT+A+EIL Sbjct: 125 ---EALLHGDSFPFALAHALELAEQTGREFVSPFDDPDVIAGQGTVAMEILRQHPGRLDA 181 Query: 185 LFASVGGGGLLSGVGTYLKNVSPDTKVIAVEPAGAASYFESNKAGHVVTLDKIDKFVDGA 244 +F VGGGGL++G+ Y+K + P+ ++I VE +A + AG VTL ++ F DG Sbjct: 182 IFVPVGGGGLIAGIAAYVKYLRPEVRIIGVESQHSACLQAALAAGERVTLPEVGTFADGV 241 Query: 245 AVKKIGEETFRTLETVVDDILLVPEGKVCTSILELYNECAVVAEPAGALSVAALDLY--K 302 AV +IG VD+++ V ++C +I ++Y++ + EP+GAL+VA + Y Sbjct: 242 AVAQIGAHGLDICRFCVDEVMTVSNDQLCAAIKDIYDDTRSITEPSGALAVAGIKQYVAH 301 Query: 303 DQIKGKNVVCVVSGGNNDIGRMQEMKERSLI 333 +G+ +V + SG N + ++ + ER+ + Sbjct: 302 TGARGETLVAIDSGANINFDSLRHVAERAAV 332 Lambda K H 0.318 0.137 0.397 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: 329 Number of extensions: 15 Number of successful extensions: 3 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: 422 Length of database: 333 Length adjustment: 30 Effective length of query: 392 Effective length of database: 303 Effective search space: 118776 Effective search space used: 118776 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate AO356_27710 AO356_27710 (threonine dehydratase)
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.carbon/TIGR01124.hmm # target sequence database: /tmp/gapView.1910357.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-152 492.8 1.0 6.2e-152 492.6 1.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710 AO356_27710 threonine dehydratas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710 AO356_27710 threonine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 492.6 1.0 6.2e-152 6.2e-152 2 321 .. 14 333 .] 13 333 .] 1.00 Alignments for each domain: == domain 1 score: 492.6 bits; conditional E-value: 6.2e-152 TIGR01124 2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqk 64 y+++il a vye av tpl+ a lse l+nr+llkredlqp fsfk+rGaynk+ +l++eq+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710 14 YVKKILAAPVYELAVRTPLQAAPALSEALGNRILLKREDLQPTFSFKIRGAYNKLVHLTPEQR 76 899************************************************************ PP TIGR01124 65 akGviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakak 127 a+Gvi+asaGnhaqGval+a++lG++a ivmp ttp++kv v+++G+e +lhG+++ a a+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710 77 ARGVITASAGNHAQGVALAARELGISARIVMPVTTPQLKVLGVRNRGAEALLHGDSFPFALAH 139 *************************************************************** PP TIGR01124 128 alelaqekgltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkql 190 alela++ g f++pfddp+viaGqGtva+e+lrq+ lda+fvpvGGGGliaG+aa+vk l lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710 140 ALELAEQTGREFVSPFDDPDVIAGQGTVAMEILRQHPGRLDAIFVPVGGGGLIAGIAAYVKYL 202 *************************************************************** PP TIGR01124 191 lpeikvigveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvd 253 +pe+++igve++ sa+l++al+aGerv+l +vG fadGvav ++G++ +++c+ +d++++v lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710 203 RPEVRIIGVESQHSACLQAALAAGERVTLPEVGTFADGVAVAQIGAHGLDICRFCVDEVMTVS 265 *************************************************************** PP TIGR01124 254 tdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvse 316 d++caaikd+++dtr+++ep+Gala+aG+k+yva+ g++++tlvai sGan+nfd+lr+v+e lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710 266 NDQLCAAIKDIYDDTRSITEPSGALAVAGIKQYVAHTGARGETLVAIDSGANINFDSLRHVAE 328 *************************************************************** PP TIGR01124 317 raelG 321 ra +G lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710 329 RAAVG 333 **998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (333 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: 00:00:00.01 # Mc/sec: 16.51 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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