Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 6937660 Sama_1810 phosphogluconate dehydratase (RefSeq)
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__SB2B:6937660 Length = 608 Score = 254 bits (648), Expect = 9e-72 Identities = 179/527 (33%), Positives = 272/527 (51%), Gaps = 37/527 (7%) Query: 21 ASGLIDEELRRPL----IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-A 75 A G D++ R L IG+ ++N+++ H + E +KA G G + A Sbjct: 51 ACGAEDKQSLRQLTKVNIGIVTAFNDMLSAHQPYEHYPELLKAACNEVGSVAQVAGGVPA 110 Query: 76 VCDGIAMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-E 134 +CDG+ G GM SL SREVIA + + + D +++ CDKI PG L+ A Sbjct: 111 MCDGVTQGQPGMELSLLSREVIAMATAVGLSHNMFDGALLLGVCDKIVPGLLIGAMSFGH 170 Query: 135 VPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSCAG 192 +P++ + GPM G+ KE+ R+ EG+ E L + E S+ G+C Sbjct: 171 LPMLFVPAGPMRSGIPNKEKA-------RVRQKFAEGKVDREALLEAEASSYHSAGTCTF 223 Query: 193 LFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPD---KILT 249 TAN+ ++ E MGL LPG+S V + R +K+ ++ ++ E GL +I+ Sbjct: 224 YGTANSNQLVLEVMGLQLPGSSFVNPDDPLRTELSKMAAKQVCRLTENGLQYSPIGEIVN 283 Query: 250 RKALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHF 309 K++ N I +A GGSTN +H+ A A GI + + F E+S VP +A + P+G Sbjct: 284 EKSVVNGIVALLATGGSTNLTMHIVAAARAAGIIINWDDFSELSDAVPLLARVYPNGHAD 343 Query: 310 VVDLDRAGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAV--------------LD 355 + AGG+ ++KEL +AGLIH+D TV G + ++ + LD Sbjct: 344 INHFHAAGGMAFLMKELLDAGLIHEDVNTVAGYGLRRYTQEPRLIDGQLTWVDGPVTSLD 403 Query: 356 REVIRPLDNPYSPFGGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAI 415 +EV+R + P+ GGL ++KG+L AV+K SAV+ + + A V D + Sbjct: 404 QEVLRGVAEPFQSNGGLKLMKGNL--GRAVIKVSAVQEQHRIVEAPAVVIDDQNKLDALF 461 Query: 416 RGGEIEPGTVIVIRYEGPRGGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGP 473 + GE++ V+V++ +GP+ GM E+ T + L G KVAL+TDGR SGA+ + P Sbjct: 462 KAGELDRDCVVVVKGQGPKAN-GMPELHKLTPILGTLQDRGFKVALMTDGRMSGASGKVP 520 Query: 474 AIGHVSPEAAAGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEERRA 520 A H++PEA GG IA VQDGD I I+ L LLV ELE R A Sbjct: 521 AAIHLTPEALDGGLIAKVQDGDLIRINAITGELSLLVSAPELESRTA 567 Lambda K H 0.319 0.138 0.401 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: 799 Number of extensions: 47 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: 552 Length of database: 608 Length adjustment: 36 Effective length of query: 516 Effective length of database: 572 Effective search space: 295152 Effective search space used: 295152 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: 53 (25.0 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