Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 5210463 Shew_2904 2-dehydro-3-deoxyphosphooctonate aldolase (RefSeq)
Query= BRENDA::A0A482F152 (272 letters) >FitnessBrowser__PV4:5210463 Length = 282 Score = 91.7 bits (226), Expect = 2e-23 Identities = 76/266 (28%), Positives = 121/266 (45%), Gaps = 23/266 (8%) Query: 14 RPIDIGSGLTVGGSSVVMMAGPCSVESYEQTRQTAQAIAALGGRVLRGGAFKP------R 67 + I +GS V+ G +ES + Q A+ A + ++ FK R Sbjct: 4 KTIKLGSIEIANDKPFVLFGGMNVLESRDLAMQIAETYAEVTQKLGIPYVFKASFDKANR 63 Query: 68 TAPDSFQGLGIE-GLRILREVADEFNMLVITEALGVDNLDAVVEYADIIQIGSRNMQHFP 126 ++ +S++G G+E GL+I +E+ D FN+ +IT+ V E DIIQ+ + + Sbjct: 64 SSVNSYRGPGMEEGLKIFQEIKDTFNLPLITDVHEPYQCQPVAEVVDIIQLPAFLARQTD 123 Query: 127 LLWEVGGTSIPVLLKRGYMSTVEEWLAAAEHIASRGNEDIILCERG-IRGFDNATRNVLD 185 L+ + T + +K+ E GN++IILCERG G++N ++L Sbjct: 124 LVVAMAKTGAIINVKKPQFLAPHEMRHIITKFNEAGNDEIILCERGSCFGYNNLVVDMLG 183 Query: 186 IGSIALVKAETSYPVIADPSHAT-----------GRVDLVVAAARAGVAAGADGLLVEAH 234 + + ++ YPVI D +HA GR AR+G+A G GL +EAH Sbjct: 184 MDEM----KQSGYPVIFDATHALQRPGGRADSAGGRRAQATELARSGMALGLAGLFIEAH 239 Query: 235 PTPAEALSDSTQQLPLDHLPDLWIQV 260 P P A D LPL L + Q+ Sbjct: 240 PDPDNAKCDGPCALPLHQLENYLTQM 265 Lambda K H 0.318 0.134 0.387 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: 151 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: 272 Length of database: 282 Length adjustment: 25 Effective length of query: 247 Effective length of database: 257 Effective search space: 63479 Effective search space used: 63479 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 (21.7 bits) S2: 47 (22.7 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