Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate WP_090446659.1 BLS63_RS16565 threonine ammonia-lyase, biosynthetic
Query= SwissProt::P25306 (595 letters) >NCBI__GCF_900100495.1:WP_090446659.1 Length = 504 Score = 428 bits (1100), Expect = e-124 Identities = 232/501 (46%), Positives = 319/501 (63%), Gaps = 4/501 (0%) Query: 94 LFQYLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSN 153 L QY+ IL S VYDVA+E+PL+ A++LS+RLG +KRED Q V+SFK+RGAYN ++ Sbjct: 2 LEQYVKKILTSRVYDVAVETPLQAAQQLSERLGNQILLKREDLQPVYSFKIRGAYNKLAQ 61 Query: 154 LSREELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYG 213 L+ EE +GV+TASAGNHAQGVALA + L A IVMP TTP+IK+ VR+ GG VVL+G Sbjct: 62 LTAEEQARGVVTASAGNHAQGVALAAKVLGVKATIVMPKTTPEIKVQGVRSRGGKVVLHG 121 Query: 214 KTFDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLK-DIHAVFIPVGGGG 272 +F EA ++L+L E+ G Y+ P+DDP I GQGT+ EI RQ + A+F+PVGGGG Sbjct: 122 DSFPEALAYSLKLVEEKGYIYVHPYDDPHTIAGQGTVAMEILRQHPGQLDAIFVPVGGGG 181 Query: 273 LIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYT 332 LIAG+A + K + P K+IGVEP + + ++ G RV L V FADGVAVA VGEYT Sbjct: 182 LIAGIAAYVKYLRPEIKVIGVEPDDSNCLQAAMAAGERVVLPQVGLFADGVAVAQVGEYT 241 Query: 333 FAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIV 392 FA C+ +D ++ V+ D I AAIKD+YD+ R+I E +GA+A+AG Y E +V Sbjct: 242 FAICRHHVDEVITVSTDEICAAIKDIYDDTRSITEPAGALAVAGIKKYVEREGCSARVLV 301 Query: 393 AIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRF 452 I SGAN++F +L V E A LG +EA++A + EQ GSFK F +G TE YR+ Sbjct: 302 GIDSGANVNFDRLRHVAERAELGEKREAIIAVTIPEQPGSFKAFCEAIGKRQITEFNYRY 361 Query: 453 TSERKNALILYRVNVDKESD-LEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGG-SANI 510 ++ K A I V E+D ++ ++S ++L+ NEL H++H+VGG +A + Sbjct: 362 HTD-KEAHIFVGVQTHPENDPRAALVASLRSQGFPVVDLTDNELAKLHIRHMVGGHAARV 420 Query: 511 SDEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFK 570 SDE+ F PE+ L FL RWNI++ YRN G + ++ G QVP+AE Sbjct: 421 SDEVVFRFEFPERPGALFNFLQKLGGRWNISMFHYRNHGAADGRVVAGLQVPEAERHLVP 480 Query: 571 NQADKLGYPYELDNYNEAFNL 591 D +GYPY ++ N A+ L Sbjct: 481 AALDAIGYPYWDESDNPAYRL 501 Lambda K H 0.317 0.135 0.382 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: 718 Number of extensions: 31 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: 595 Length of database: 504 Length adjustment: 36 Effective length of query: 559 Effective length of database: 468 Effective search space: 261612 Effective search space used: 261612 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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