Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate SM_b21508 SM_b21508 dihydrodipicolinate synthetase
Query= BRENDA::Q9I4W3 (292 letters) >FitnessBrowser__Smeli:SM_b21508 Length = 304 Score = 126 bits (317), Expect = 5e-34 Identities = 94/282 (33%), Positives = 135/282 (47%), Gaps = 6/282 (2%) Query: 11 TPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIRRVVDQVKGR 70 TP D G++ D+L++L++ ++I +G+TG A L E + + V+ V GR Sbjct: 16 TPADMDGKVSEDALSRLLERIRVARADSIGLLGSTGAYAFLSRGERRRAVETAVECVGGR 75 Query: 71 IPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRHIAEAVAIPQ 130 +P+I G GA T EA AL AK GAD LL Y T+E +YQHF +A A +P Sbjct: 76 VPLIVGVGALRTDEAQALARDAKEAGADGLLLAPVSYTPLTEEEVYQHFVAVAGASDLPL 135 Query: 131 ILYNVPGRTSCDMLPETVERLSKVPNIIGIK---EATGDLQ-RAKEVIERVGKDFLVYSG 186 +YN PG T E + RLS+VPNI +K A GD + + + F + Sbjct: 136 CIYNNPGTTKFVFSEELIVRLSQVPNIAAVKMPLPADGDFEGEIARLRAKTSAAFAIGYS 195 Query: 187 DDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLHKALFIE 246 D A + +L G SV + P S L AA GD A A I+ PL ALF E Sbjct: 196 GDWGAADALLSGADAWFSVVGGLLPAPASKLARAAKAGDRAEAHRIDMAFQPLW-ALFKE 254 Query: 247 SNPIPVKWALHE-MGLIPEGIRLPLTWLSPRCHEPLRQAMRQ 287 V +A+ +GL P+ L P ++QA+++ Sbjct: 255 FGSFRVMYAIGSILGLFQALPPRPILPLGPGDSVRVKQAVQE 296 Lambda K H 0.319 0.134 0.393 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: 218 Number of extensions: 15 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: 292 Length of database: 304 Length adjustment: 26 Effective length of query: 266 Effective length of database: 278 Effective search space: 73948 Effective search space used: 73948 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