Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate RR42_RS33075 RR42_RS33075 dihydrodipicolinate synthetase
Query= BRENDA::A9CL97 (313 letters) >FitnessBrowser__Cup4G11:RR42_RS33075 Length = 313 Score = 174 bits (441), Expect = 2e-48 Identities = 106/306 (34%), Positives = 158/306 (51%), Gaps = 2/306 (0%) Query: 1 MDLRGLSPAPVTAFTRDGEVDYAANAKIARWLASMEGVKSLVILGHAGEGTFLTEDERLE 60 ++ G+ PA F D ++ + ARWL GV +L+ GH GE LT ER + Sbjct: 4 INFHGIIPAIAVPFNADYSINEPELRRFARWLGGQAGVTALMTNGHTGEVFSLTPRERAQ 63 Query: 61 LIRVYVDAVGGSLPIIAGITGEGTRVAAAEAKKCKAAGATGALVYPNHGWLRFGFQRGAP 120 + R+ DA G P+I+ + EG A +A K AGA G + P H WLRFGF+ Sbjct: 64 VTRITADATQGICPVISSVVCEGINDAVEQAGWAKEAGAAGLDIMPPHHWLRFGFKPEHC 123 Query: 121 QDRYKAIWEESGLQEILFQYPDVTKASYDLDTQLAIATQPGVVATKNGVRNMKRWYVEIP 180 D + AI + SGL ++ YP T+ SY + +A P V A K G R M ++ +I Sbjct: 124 LDYFNAIGKASGLPLVVHIYPAWTRGSYSSELLAELAKLPYVKAFKMGEREMNKYARDIK 183 Query: 181 ELKNANPNLQVLSCHDEWLLPTMFD-VDGLLVGYGNIAPELLIDLIKAGKAQDYPQARKI 239 E++ A+P +++CHDE+LL +M +DG LVG+ ++ P L+ DL+KA KA D +A ++ Sbjct: 184 EIRAADPTKVLMTCHDEYLLSSMVQGIDGALVGFASLIPGLINDLLKAVKAGDLHEAMRV 243 Query: 240 FEQLLPVTRAVYHRGSHM-EGTVALKLGLVHRGVLDHATIREPLKNLGEKAEQEIFAAFD 298 + P+ AVY G E +K + G+L T+R P I AA + Sbjct: 244 QALINPLKDAVYGAGEPTGEAHGRMKAAMALAGILRDGTVRPPTHAPSAAELAAIRAALE 303 Query: 299 AAGIGR 304 AG+ R Sbjct: 304 HAGVTR 309 Lambda K H 0.319 0.137 0.405 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: 244 Number of extensions: 5 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: 313 Length of database: 313 Length adjustment: 27 Effective length of query: 286 Effective length of database: 286 Effective search space: 81796 Effective search space used: 81796 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: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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