Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_012759261.1 RLEG_RS19575 dihydroxy-acid dehydratase
Query= curated2:Q8TW40 (549 letters) >NCBI__GCF_000023185.1:WP_012759261.1 Length = 570 Score = 335 bits (858), Expect = 4e-96 Identities = 203/542 (37%), Positives = 303/542 (55%), Gaps = 18/542 (3%) Query: 16 RALLRACGLTDEEMDRPFVAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVETIA 75 +A ++A G +D+ +DRP V + NTYS+ P H ++ ++ EA K G+ + G +P TI+ Sbjct: 23 KAFIKAMGYSDDALDRPIVGIANTYSDFNPCHGNVPQLIEATKRGVMLTGAMPMVFPTIS 82 Query: 76 LCDGIAMNTPGMKYSLPSRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARLDL 135 + + A T S+ R L+A E +I A D V I CDK +P +MAAA ++ Sbjct: 83 IHESFASPT-----SMYLRNLMAMETEEMIRAQPMDAVVLIGGCDKTLPAQIMAAASSEI 137 Query: 136 PAAIVTGGPMEPGCVDGERVDLI-DAFEAVGAYEEGEISEEELEELEQRACPGPGSCAGM 194 PA + GPM G GER+ D G + GEI E E+ E+ + G+C M Sbjct: 138 PAIFLPTGPMAVGHHKGERLGACTDCRRFWGRFRAGEIDEAEIAEVNNKLASSIGTCTVM 197 Query: 195 FTANTMACMTEVLGMSEFNCAATPATEAEKLRVAKLTGMRIVEAI---EEGITARDVLTR 251 TA+TMA +TEV+G+ + PA E+E++R+A+ TG R+ + E T RD+LT Sbjct: 198 GTASTMANLTEVMGLCLPRAGSAPAVESERVRLAEETG-RVAARLAMDEAAPTVRDILTP 256 Query: 252 EAFLDAIRVDMALGGSTNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGPYTM 311 +A + + A+GGSTN V+HL AI + L + + D L R P L ++P G + M Sbjct: 257 QAVRNGLVALQAMGGSTNAVVHLTAITGRLGLRLDMAELDRLGRSIPLLVDLQPSGQHYM 316 Query: 312 RDLYEAGGVPAVMKELADDLHLDRIDFAGRSMRERVER-TEVKDREVIRPKEDPVHEEGG 370 +EAGGVPA++K + ++ G+++ E ++ + + +IR E P+ G Sbjct: 317 EQFHEAGGVPALLKAVRHEIDGSAPTVYGKTIGEIIDAVVDEPGQTIIRTVEKPLKPIGT 376 Query: 371 IVVLYGNLAPKGAVIKTAALSEEMYEHEGPAVVFDSEEEATEAILGGDID--PGDVVVIR 428 I VL+GNLAP+GAVIK +A S+++ +H G AVVFDS E+ T I D+D D++V+R Sbjct: 377 IAVLHGNLAPRGAVIKQSAASKDLLQHIGRAVVFDSVEDMTLRIDSDDLDVHADDILVLR 436 Query: 429 YEGPAGGPGMRE--MLTPTAALCGMGLDDSVALVTDGRFSGGTRGPCVGHVSPEAYRGGP 486 GP G PGM E L L G+ D V ++D R SG G + H++PEA GGP Sbjct: 437 NAGPKGAPGMPEAGYLPIPRKLARQGVKDMVR-ISDARMSGTAFGTIILHIAPEAADGGP 495 Query: 487 IAVVEEGDTIRLDVRERRLEVDVEDEELEARLEEW--EPPEDEVTGYLRRYRELVRGADE 544 +A+V GD IRLDV RR+++D++ E + R+ + P GY R Y+E V ADE Sbjct: 496 LAIVRTGDRIRLDVEGRRIDLDIDQAEFDRRMLDVVNRPSPAPARGYARLYQERVLQADE 555 Query: 545 GA 546 GA Sbjct: 556 GA 557 Lambda K H 0.317 0.137 0.396 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: 788 Number of extensions: 45 Number of successful extensions: 9 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: 549 Length of database: 570 Length adjustment: 36 Effective length of query: 513 Effective length of database: 534 Effective search space: 273942 Effective search space used: 273942 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 (21.6 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