Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate BPHYT_RS22635 BPHYT_RS22635 dihydrodipicolinate synthase
Query= BRENDA::A9CFV4 (303 letters) >FitnessBrowser__BFirm:BPHYT_RS22635 Length = 301 Score = 130 bits (328), Expect = 3e-35 Identities = 90/285 (31%), Positives = 137/285 (48%), Gaps = 2/285 (0%) Query: 3 FEGIYTPAITPLGHDGEIDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDLAA 62 +EG+ T D IDR +E+ ++A V GII+ GS GE + E+ + Sbjct: 5 WEGVLPAVTTKFNADFSIDRAWTGKNIEAQIDAGVDGIIVCGSLGEASTLSLDEKLQVLD 64 Query: 63 YARQVIGTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTERENAVHALA 122 A + R+P+++ T D+ A+A GA +V L RE H + Sbjct: 65 IAVEASRGRVPVLLTIAENSTLDACRQAEAGSRHGAAGYMVLPGLRYLSDRRETLHHFRS 124 Query: 123 VDRAANLPIMLYNYPARMGVVMGEEYFSRVGKSKNVVAIKESSGDMGNL-HLLARKFPQI 181 V A+ LP+M+YN P GV M + F+ + K +VAIKES GD+ + L+ + Sbjct: 125 VADASALPLMIYNNPLAYGVDMTPDMFAEIADEKKIVAIKESCGDVRRVTDLINVVGDRF 184 Query: 182 ALSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAMLPLM 241 A+ CG D+ A+E GA WV PRE VA+Y+ + ++ RAI PL+ Sbjct: 185 AILCGVDNLAMEAILMGAHGWVAGLVCAFPRETVAIYKLLKAGR-IEEARAIYRWFAPLL 243 Query: 242 DFLECGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQTVV 286 K VQ+IK I+GL VR P PL DE++ ++ ++ Sbjct: 244 ALDVSAKLVQNIKLAEAIVGLGTEPVRPPRLPLAGDERKAVEALI 288 Lambda K H 0.320 0.135 0.397 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: 219 Number of extensions: 10 Number of successful extensions: 3 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: 303 Length of database: 301 Length adjustment: 27 Effective length of query: 276 Effective length of database: 274 Effective search space: 75624 Effective search space used: 75624 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: 48 (23.1 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