Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate Echvi_3284 Echvi_3284 Homoserine dehydrogenase
Query= BRENDA::D8WXQ2 (413 letters) >FitnessBrowser__Cola:Echvi_3284 Length = 408 Score = 187 bits (474), Expect = 6e-52 Identities = 110/311 (35%), Positives = 172/311 (55%), Gaps = 11/311 (3%) Query: 3 TIHIALLGYGTVGKGVYQTIKTHQKRFKAILGKEVKIEAVLVKNLEKHQLPDPDVILTNK 62 T I L G+G VG+G Y+ K + E ++V+N K + + K Sbjct: 2 TNRIGLFGFGVVGQGYYEIAKNDRPSLLP--------ETIVVQNKNKERPHSLQLSFDPK 53 Query: 63 FEDIISLPKLDVVIDAIVGKQPGFSYLSQAIKRGCHIITANKQMFAHYGRELLSLAEKHG 122 DI++ P D+ I+ I + Y+S +K G +I+ANK+M A + ELL L + +G Sbjct: 54 --DILNTPH-DIGIELISDPIQAYDYVSSLLKSGKKVISANKKMLAAHLPELLELEKSYG 110 Query: 123 VSVGFEATVAGGIPVIQTLRKLLSVNHIKKVHGILNGTSNFILTKMREEGCSFSDALSLA 182 S+ +EA+ A GIP+I L + +HI K+ GILNG+SN+IL+++ ++ S SDA+ LA Sbjct: 111 GSLLYEASAAAGIPIITCLDCHFAGDHISKLQGILNGSSNYILSRLFQDDLSLSDAVKLA 170 Query: 183 QEKGYAEADPTNDVEGFDAFYKAMILSEVVYGKQPDWEKVRKQGISSITLEQIELFSKFG 242 QEKG+AEADPT D+ G D K ILS +G+ ++ G+ + E + L G Sbjct: 171 QEKGFAEADPTLDINGSDVSSKLTILSLHAFGRYIPENEILTIGVQHVHAEDVALAKSLG 230 Query: 243 LRFKHVASLEKTTKGIHCSVKPVLVSSSHPLFHVEDVQNAVSIDADIVGNISLQGPGAGM 302 L+ K +A+++++ G+ + P LV S PLF VE+ NA + + +G QG GAG Sbjct: 231 LKIKLIATVQRSQDGLSMYILPALVGESDPLFLVENEYNAAKVTSHNLGEQFFQGKGAGS 290 Query: 303 FPTASAIVEDL 313 PT +++ DL Sbjct: 291 LPTGASVYADL 301 Lambda K H 0.317 0.135 0.381 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: 406 Number of extensions: 17 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: 413 Length of database: 408 Length adjustment: 31 Effective length of query: 382 Effective length of database: 377 Effective search space: 144014 Effective search space used: 144014 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)
This GapMind analysis is from Apr 09 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