Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate AO356_09275 AO356_09275 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::A9CFV4 (303 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_09275 Length = 303 Score = 469 bits (1208), Expect = e-137 Identities = 228/303 (75%), Positives = 266/303 (87%) Query: 1 MKFEGIYTPAITPLGHDGEIDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDL 60 +KFEGIYTPA+TP DGEID F+ VLESL+EA+VHGIIIGGSTGEYYAQTA+ER L Sbjct: 1 LKFEGIYTPAVTPHTPDGEIDWRVFSEVLESLIEAKVHGIIIGGSTGEYYAQTAEERLKL 60 Query: 61 AAYARQVIGTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTERENAVHA 120 AA+AR+VIG+R+ L++GTGA RTED++ +A+ AK I ADAILV++PPYALPT++ENA+HA Sbjct: 61 AAHAREVIGSRVQLIIGTGAIRTEDAVLFAEDAKRIKADAILVTTPPYALPTDQENAIHA 120 Query: 121 LAVDRAANLPIMLYNYPARMGVVMGEEYFSRVGKSKNVVAIKESSGDMGNLHLLARKFPQ 180 L +DRAAN+PIMLYNYP RM V M EEY +RVGKSKNV AIKESSGDMG +HLLAR+FP Sbjct: 121 LTIDRAANMPIMLYNYPGRMCVQMNEEYLARVGKSKNVKAIKESSGDMGRVHLLAREFPH 180 Query: 181 IALSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAMLPL 240 IALSCGWDDQALEFFAWGA+SWVCAGSNFLP+EHVALYEACVVEKNFDKGR IM+AM+PL Sbjct: 181 IALSCGWDDQALEFFAWGARSWVCAGSNFLPKEHVALYEACVVEKNFDKGRQIMSAMMPL 240 Query: 241 MDFLECGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQTVVTTLKRTVAQIASGA 300 M+ L+ GKFVQ IK GCE+ GL G VRAPLRPLNSD+KR+LQTV+ +KRTVA I SGA Sbjct: 241 MNALDGGKFVQCIKFGCELNGLAVGDVRAPLRPLNSDDKRSLQTVIANVKRTVAHITSGA 300 Query: 301 NHA 303 N+A Sbjct: 301 NNA 303 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: 324 Number of extensions: 5 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: 303 Length of database: 303 Length adjustment: 27 Effective length of query: 276 Effective length of database: 276 Effective search space: 76176 Effective search space used: 76176 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 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