Align threonine deaminase (EC 4.3.1.19) (characterized)
to candidate WP_057508536.1 ABB28_RS10275 serine dehydratase
Query= reanno::Korea:Ga0059261_3694 (420 letters) >NCBI__GCF_001431535.1:WP_057508536.1 Length = 320 Score = 167 bits (424), Expect = 3e-46 Identities = 109/310 (35%), Positives = 158/310 (50%), Gaps = 3/310 (0%) Query: 16 QPLPVTLADVQAAAARIMGAVVHTPTLHSKTLSDLTGATVYLKFENLQFTAAYKERGALN 75 + LP V AAARI TP L S+TL L GA + K E+LQ + A+K RGA N Sbjct: 3 EALPPPAQAVLEAAARIAPHAAVTPVLRSQTLDALAGAQLAFKAEHLQRSGAFKFRGACN 62 Query: 76 TLLQLDDAARAKGVIAASAGNHAQGLAYHGNRLGIPVTIVMPKSTPTVKVMQTESHGATI 135 + L GV+ S+GNH LA GI +V+P K+ HGAT+ Sbjct: 63 AVWSLSADRAPAGVVTHSSGNHGAALALAARTRGIACHVVVPDGAVAAKLANIARHGATL 122 Query: 136 ILEGETFDEAYAHARQLEASNGYTFVHPFDDPRIIAGQGTVFLEMLADAPAIDTLIVPIG 195 T A Q++A G T VHP+ D +IAGQGT LE+L D ++VP+G Sbjct: 123 WRCAPTIAAREAVCAQVQADTGATLVHPYADAAVIAGQGTAVLELLQAEGPFDVVVVPVG 182 Query: 196 GGGLISG-ALTVAKAADKPIEVVGVQAELFPSMFNRFTGAHE-PIGGDTLAEGIAVKEPG 253 GGGL +G AL + + + V+ A + + G DT+ +G+ G Sbjct: 183 GGGLAAGTALALQQVSPHTRLVLAEPAGAADTARSLQAGERRIDFVPDTVCDGLR-GTLG 241 Query: 254 GLTAQIVEALVDEIMLVSERSLEEAVSLLLQIEKTVVEGAGAAGLAALMTQPERFRGKTV 313 Q+++A E+++V + + A+ LL Q+ K VE + A LAA++ QP+RF G V Sbjct: 242 APNFQLLQAAGAEVIVVDDAATVAAMRLLWQVLKQTVEPSSAIALAAVLAQPQRFAGLRV 301 Query: 314 GVILTGGNID 323 G++L+GGN+D Sbjct: 302 GLVLSGGNVD 311 Lambda K H 0.319 0.135 0.374 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: 2 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: 420 Length of database: 320 Length adjustment: 30 Effective length of query: 390 Effective length of database: 290 Effective search space: 113100 Effective search space used: 113100 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: 49 (23.5 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