Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_013553440.1 NITSA_RS02420 threonine ammonia-lyase
Query= curated2:Q9K7E3 (354 letters) >NCBI__GCF_000186245.1:WP_013553440.1 Length = 403 Score = 70.5 bits (171), Expect = 7e-17 Identities = 80/302 (26%), Positives = 133/302 (44%), Gaps = 25/302 (8%) Query: 30 NTPLIPLENLSKEWGVKAYVKYEGANPTGSFKDRGMVMAVAKAKEEGSRTIICASTGNTS 89 +TP+ LS+ G + Y+K E TGSFK RG +A EEG R + A++ Sbjct: 20 HTPMAYAPILSELSGYEIYLKKENLQRTGSFKLRGAFNKIASLVEEGRRNGVVAASAGNH 79 Query: 90 AAAAAYGAR-AGLRCIVVIPEGKIALGKLAQAVMYGAEVLEIKGNFDHALDIVRSISEKE 148 A A+ AR G+ +V+PE L K+ GAEV+ N+D A ++++ Sbjct: 80 AQGVAFAARYFGIDGTIVMPE-STPLTKVMGVQELGAEVILKGSNYDEAYAYAVEYAKEK 138 Query: 149 PITLVNSVNPYRI-EGQKTSAFEICDALGQAPDVLAIPVGNAGNITAYWKGFKEYHEKKG 207 V+ + GQ T E+ + + D + IPVG G I+ K Sbjct: 139 GKDFVHPFADEEVMAGQGTIMLEMLEEEPEL-DAVVIPVGGGGLISGCAVAAKSLS---- 193 Query: 208 TGLPQMR--GFEAEGAAAIVRNQVIEEP------ETIATAIRIGNPASWTYAVEAAAESN 259 P+M+ G + GA A+ + +P TIA I + + + T +E + Sbjct: 194 ---PEMKVIGVASAGAPAMKLSYDAGKPIDTTGVRTIADGIAVRDTSPVT--LEYIRKYV 248 Query: 260 GKIDEVTDEEILAAYQLLAQKEGVFAEPASCASIAG-LRKQIASGEIKKGSTVVCVLTGN 318 ++ V ++EI A L +++ + E A +A L K + ++ KGS + VL+G Sbjct: 249 DEMKLVGEDEIANAILFLLERQKLTVEGAGAVGVAAILHKHL---DLPKGSRIGIVLSGG 305 Query: 319 GL 320 + Sbjct: 306 NI 307 Lambda K H 0.313 0.132 0.378 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: 279 Number of extensions: 13 Number of successful extensions: 1 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: 354 Length of database: 403 Length adjustment: 30 Effective length of query: 324 Effective length of database: 373 Effective search space: 120852 Effective search space used: 120852 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 bits)
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