Align L-threonine dehydratase biosynthetic IlvA; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate Pf6N2E2_802 Threonine dehydratase biosynthetic (EC 4.3.1.19)
Query= curated2:Q02145 (416 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 Length = 335 Score = 230 bits (586), Expect = 5e-65 Identities = 133/313 (42%), Positives = 189/313 (60%), Gaps = 8/313 (2%) Query: 17 VVTKTPLQLDPYLSNKYQANIYLKEENLQKVRSFKLRGAYYSISKLSDEQRSKGVVCASA 76 + +TPLQ P LS I LK E+LQ SFK+RGAY + +L+ EQR++GV+ ASA Sbjct: 26 LAVRTPLQAAPALSEALGNRILLKREDLQPTFSFKIRGAYNKLVQLTPEQRARGVITASA 85 Query: 77 GNHAQGVAFAANQLNISATIFMPVTTPNQKISQVKFFGESHVTIRLIGDTFDESARAAKA 136 GNHAQGVA AA +L ISA+I MPVTTP K+ V+ G + L G++F + A Sbjct: 86 GNHAQGVALAARELGISASIVMPVTTPQLKVLGVRNRGAEAI---LHGESFPFALAHALE 142 Query: 137 FSQDNDKPFIDPFDDENVIAGQGTVALEIFAQAKKQGISLDKIFVQIGGGGLIAGITAYS 196 ++ + F+ PFDD +VIAGQGTVA+EI Q Q LD IFV +GGGGLIAGI AY Sbjct: 143 LAEQSGWEFVSPFDDPDVIAGQGTVAMEILRQHPGQ---LDAIFVPVGGGGLIAGIAAYV 199 Query: 197 KERYPQTEIIGVEAKGATSMKAAYSAGQPVTLEHIDKFADGIAVATVGQKTYQLINDKVK 256 K P+ IIGVE++ + ++AA +AG+ VTL + FADG+AVA +G + V Sbjct: 200 KYLRPEVRIIGVESQHSACLQAALAAGERVTLPEVGTFADGVAVAQIGAHGLDICRFCVD 259 Query: 257 QLLAVDEGLISQTILELYSKLGIVAEPAGATSVAALE--LIKDEIKGKNIVCIISGGNND 314 +++ V + I ++Y + EP+GA +VA ++ + +G+ +V I SG N + Sbjct: 260 EVMTVSNDQLCAAIKDIYDDTRSITEPSGALAVAGIKQYVAGTGARGQTLVAIDSGANIN 319 Query: 315 ISRMQEIEERALV 327 ++ + ERA V Sbjct: 320 FDSLRHVAERAAV 332 Lambda K H 0.317 0.135 0.375 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: 308 Number of extensions: 13 Number of successful extensions: 4 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: 416 Length of database: 335 Length adjustment: 30 Effective length of query: 386 Effective length of database: 305 Effective search space: 117730 Effective search space used: 117730 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 Pf6N2E2_802 (Threonine dehydratase biosynthetic (EC 4.3.1.19))
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.16669.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-153 495.2 1.2 1.2e-152 495.0 1.2 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 Threonine dehydratase biosynthet Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 Threonine dehydratase biosynthetic (EC 4.3.1.19) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 495.0 1.2 1.2e-152 1.2e-152 2 320 .. 14 332 .. 13 334 .. 0.99 Alignments for each domain: == domain 1 score: 495.0 bits; conditional E-value: 1.2e-152 TIGR01124 2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkak 66 y+++il a vye av tpl+ a lse l+nr+llkredlqp fsfk+rGaynk+ ql++eq+a+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 14 YVKKILAAPVYELAVRTPLQAAPALSEALGNRILLKREDLQPTFSFKIRGAYNKLVQLTPEQRAR 78 899************************************************************** PP TIGR01124 67 GviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalel 131 Gvi+asaGnhaqGval+a++lG++a ivmp ttp++kv v+++G+e +lhGe++ a a+alel lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 79 GVITASAGNHAQGVALAARELGISASIVMPVTTPQLKVLGVRNRGAEAILHGESFPFALAHALEL 143 ***************************************************************** PP TIGR01124 132 aqekgltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikv 196 a++ g f++pfddp+viaGqGtva+e+lrq+ +lda+fvpvGGGGliaG+aa+vk l+pe+++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 144 AEQSGWEFVSPFDDPDVIAGQGTVAMEILRQHPGQLDAIFVPVGGGGLIAGIAAYVKYLRPEVRI 208 ***************************************************************** PP TIGR01124 197 igveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaai 261 igve++ sa+l++al+aGerv+l +vG fadGvav ++G++ +++c+ +d++++v d++caai lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 209 IGVESQHSACLQAALAAGERVTLPEVGTFADGVAVAQIGAHGLDICRFCVDEVMTVSNDQLCAAI 273 ***************************************************************** PP TIGR01124 262 kdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvserael 320 kd+++dtr+++ep+Gala+aG+k+yva g++++tlvai sGan+nfd+lr+v+era + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 274 KDIYDDTRSITEPSGALAVAGIKQYVAGTGARGQTLVAIDSGANINFDSLRHVAERAAV 332 ********************************************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (335 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.80 // [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