Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate HSERO_RS00265 HSERO_RS00265 threonine dehydratase
Query= BRENDA::Q74FW6 (402 letters) >FitnessBrowser__HerbieS:HSERO_RS00265 Length = 401 Score = 286 bits (733), Expect = 6e-82 Identities = 168/398 (42%), Positives = 240/398 (60%), Gaps = 7/398 (1%) Query: 7 IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREA 66 I+ A RL+ ++ T + S S+ +G ++ K ENLQ T +FK RGA N + Sbjct: 7 IEAAARRLQGQILETPCVESRTLSQIVGAQVFLKFENLQFTASFKERGACNKLVDVAASG 66 Query: 67 L-AKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFD 125 A+GV+ SAGNHAQGVA+ A LG+P+T+ MP TP K+ TR +GA VVL G + Sbjct: 67 GGARGVVAMSAGNHAQGVAYHAQRLGLPATIVMPRFTPGVKIERTRGFGANVVLHGDTLE 126 Query: 126 EAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIAGI 185 A A + E+ G FVHP+DD ++AGQGT+ LE+++ +PD+ ++V IGGGGL+AG+ Sbjct: 127 AARTHAYELAEKEGLTFVHPYDDEAIIAGQGTVALEMMKAVPDLDCLVVSIGGGGLLAGM 186 Query: 186 ATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPV-TVTLADGIAVKKPGVNTFPII 244 A A R P + I+GV+T P+ + K + PV T+A+GIAV PG T II Sbjct: 187 AVAARAIKPEIEIVGVQTRRFPT---MVNAVKGTEHPVGASTIAEGIAVGTPGTLTRAII 243 Query: 245 RDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTV-CVLSG 303 DE++LV+E +I A++ LLE K LVEGAGA LAAL+ R GK V VLSG Sbjct: 244 AREADELLLVDEGDIEQAVLMLLEIEKTLVEGAGAAGLAALV-RYPDRFRGKRVGLVLSG 302 Query: 304 GNIDVKTISVVVERGLVAAGRYLKLKVELDDLPGALARLATEIAEAKANISIITHDRRSK 363 GNID ++ ++ERG+V AGR ++KV D+PG LAR+ +AEA AN+ + H R Sbjct: 303 GNIDPLLLTAIIERGMVRAGRLARVKVSSRDVPGTLARITGIVAEAGANVDEVHHQRAFT 362 Query: 364 SLPIGKTEVLIELETRGFEHIQEVISHLQGVGYLVDVL 401 L ++ + L+TRG H+ +V+ L+ G+ + L Sbjct: 363 LLAAQNVDIELVLQTRGRPHLAQVLQALRAAGFEAEEL 400 Lambda K H 0.319 0.137 0.383 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: 353 Number of extensions: 14 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: 402 Length of database: 401 Length adjustment: 31 Effective length of query: 371 Effective length of database: 370 Effective search space: 137270 Effective search space used: 137270 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: 50 (23.9 bits)
Align candidate HSERO_RS00265 HSERO_RS00265 (threonine dehydratase)
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.carbon/TIGR01127.hmm # target sequence database: /tmp/gapView.19340.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-126 406.0 2.7 8.7e-126 405.8 2.7 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS00265 HSERO_RS00265 threonine dehydrat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS00265 HSERO_RS00265 threonine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.8 2.7 8.7e-126 8.7e-126 1 378 [. 21 397 .. 21 399 .. 0.97 Alignments for each domain: == domain 1 score: 405.8 bits; conditional E-value: 8.7e-126 TIGR01127 1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklsee.ekkrGvvaasaGnhaqGvalaa 67 tp s tls+i+ga+v+lk enlq t sfk rGa nk+ +++ + rGvva saGnhaqGva+ a lcl|FitnessBrowser__HerbieS:HSERO_RS00265 21 TPCVESRTLSQIVGAQVFLKFENLQFTASFKERGACNKLVDVAASgGGARGVVAMSAGNHAQGVAYHA 88 78999**********************************9988762579******************* PP TIGR01127 68 kvfgikakivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGq 135 ++ g++a+ivmP+++p k++ t+++Ga+v+LhG++++ a +a elae+eg++fvh++dDe +iaGq lcl|FitnessBrowser__HerbieS:HSERO_RS00265 89 QRLGLPATIVMPRFTPGVKIERTRGFGANVVLHGDTLEAARTHAYELAEKEGLTFVHPYDDEAIIAGQ 156 ******************************************************************** PP TIGR01127 136 GtlgleiledlpdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikaves 203 Gt++le+++ +pd+d ++v +GGGGL++G+a+a++ ++pe+ ++Gv+++ p++v+++k ++ lcl|FitnessBrowser__HerbieS:HSERO_RS00265 157 GTVALEMMKAVPDLDCLVVSIGGGGLLAGMAVAARAIKPEIEIVGVQTRRFPTMVNAVKGT--EHPVG 222 ********************************************************98754..44557 PP TIGR01127 204 vktiaDGiavkkpgdltfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvd 271 +tia+Giav +pg+lt i+ De++ vde +i +a+l+Lle +k+++egaGa+g+aa++ lcl|FitnessBrowser__HerbieS:HSERO_RS00265 223 ASTIAEGIAVGTPGTLTRAIIAREADELLLVDEGDIEQAVLMLLEIEKTLVEGAGAAGLAALVRYPDR 290 89*************************************************************97777 PP TIGR01127 272 vkgkkvavvvsGGnidlnllekiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehd 339 gk+v++v+sGGnid+ ll+ iie+g+v+ gr++++++ D PG+L ++++++ae++an+ +++h+ lcl|FitnessBrowser__HerbieS:HSERO_RS00265 291 FRGKRVGLVLSGGNIDPLLLTAIIERGMVRAGRLARVKVSSRDVPGTLARITGIVAEAGANVDEVHHQ 358 ******************************************************************** PP TIGR01127 340 rlskeialgaakvelelevkgkehleellktlrdkgyev 378 r + +a +el l+++g+ hl ++l+ lr+ g+e lcl|FitnessBrowser__HerbieS:HSERO_RS00265 359 RAFTLLAAQNVDIELVLQTRGRPHLAQVLQALRAAGFEA 397 *************************************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (401 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: 10.00 // [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