Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011883267.1 phosphogluconate dehydratase
Query= curated2:B7JJG8 (557 letters) >NCBI__GCF_000016205.1:WP_011883267.1 Length = 618 Score = 248 bits (632), Expect = 6e-70 Identities = 166/511 (32%), Positives = 262/511 (51%), Gaps = 32/511 (6%) Query: 31 KPFIAICNSFIEIIPGHKHLNEFGKLVKEAVRA-AGMVPFEFNTIGVDDGIAMGHIGMRY 89 +P I I +S+ E++ H +F ++K A R G+ F + DGI G+ GM Sbjct: 68 EPNIGIVSSYNEMLSAHAPYKDFPDIIKAAARENGGVAQFAGGVPAMCDGITQGNAGMEL 127 Query: 90 SLPSREIIADSVETVVNAHWFDGMICIPNCDKITPGMMMAALRI-NIPTVFVSGGPMAAG 148 SL SRE IA + + FD +C+ CDKI PG+++ AL+ ++PT+FV GPM +G Sbjct: 128 SLFSREAIAMGTAIALTHNMFDAALCLGICDKIVPGLLIGALQFGHLPTIFVPAGPMTSG 187 Query: 149 KTSKGDVVDLSSVFEGVGAYQSGKISEEELKDIEDHGCPSCGSCSGMFTANSMNCLCEVL 208 S D + F +G++ + L + E G+C+ TANS L E++ Sbjct: 188 -LSNDDKAKIRQQFA------TGQVGRDALLEAESAAYHGHGTCTFYGTANSNQMLMELM 240 Query: 209 GLALPGNGSILAIDPRREELIKQAAEK-LKILIERD--IKPRDIVTEEAIDDAFALDMAM 265 GL LPG+ + P R+ L QAA + L + +ER ++ E+AI + +A Sbjct: 241 GLHLPGSAFVHPHTPLRDALTAQAARRVLDLTVERGQYTPIGHVIDEKAIVNGIVALLAT 300 Query: 266 GGSTNTVLHTLALAQEAGLDYDMNRIDAVSRRVPHLCKVSPASNWHMEDIDRAGGISAIL 325 GGSTN LH +A+A+ AG+ D N D +S VP L K+ P + AGG++ ++ Sbjct: 301 GGSTNHTLHLVAIARAAGILIDWNDFDELSAVVPLLAKIYPNGKADVNHFHAAGGVAFLV 360 Query: 326 KEMSRKEGVLHLDRITATGQTLRENIAH--------------AEIKDKEVIHSLENPHSE 371 + + + G+LH D T G+ L AE D +V+ S+ P Sbjct: 361 RNLL-EGGLLHEDVTTVAGKGLSHYTQEPKLIDGKLTWVDGTAESHDTKVLRSIREPFQP 419 Query: 372 EGGLRILKGNLAKDGAVIKSGATEVIRFEGPCVIFNSQDEALAGIMLGKVKKGDVVIIRY 431 +GGLR+++G L + I + A E + + P ++F+SQ+ A G++K+ V ++R+ Sbjct: 420 DGGLRLMQGRLGRGVIKISAVAPEHRKVKAPAIVFDSQEAVQAAFDRGELKRDFVAVVRF 479 Query: 432 EGPRGGPGMPEM--LAPTSAIAGMGLGADVALLTDGRFSGASRGI-SVGHISPEAAAGGT 488 +G R GMPE+ L P + G VAL+TDGR SGAS + +V H+SPEA G Sbjct: 480 QGARAN-GMPELHRLTPLLGVL-QDQGFHVALVTDGRMSGASGKVPAVIHVSPEALLAGP 537 Query: 489 IALLEQGDIVCIDVEERLLEVRVSDEELDKR 519 + ++ GD + ID E +L++ + D E R Sbjct: 538 LGKVKTGDTLVIDAEAGVLDIEIDDAEWQVR 568 Lambda K H 0.318 0.137 0.400 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: 778 Number of extensions: 42 Number of successful extensions: 8 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: 557 Length of database: 618 Length adjustment: 37 Effective length of query: 520 Effective length of database: 581 Effective search space: 302120 Effective search space used: 302120 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: 53 (25.0 bits)
This GapMind analysis is from Apr 10 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