Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate Ac3H11_604 L-arabonate dehydratase (EC 4.2.1.25)
Query= curated2:Q8TW40 (549 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_604 Length = 577 Score = 348 bits (892), Expect = e-100 Identities = 215/541 (39%), Positives = 306/541 (56%), Gaps = 16/541 (2%) Query: 15 HRALLRACGLTDEEMD-RPFVAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVET 73 +R+ ++ G+ D D RP + + NT+SE+ P + H K+ E VK GI AGG P E Sbjct: 24 YRSWMKNQGIPDHAFDGRPVIGICNTWSELTPCNAHFRKIAEHVKRGIYEAGGFPVEFPV 83 Query: 74 IALCDGIAMNTPGMKYSLPSRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARL 133 + + T ++ +R L + +E I + D V +V CDK P LM AA Sbjct: 84 FSNGESNLRPT-----AMLTRNLASMDVEEAIRGNPIDAVVLLVGCDKTTPALLMGAASC 138 Query: 134 DLPAAIVTGGPMEPGCVDGERVDLIDA-FEAVGAYEEGEISEEELEELEQRACPGPGSCA 192 D+PA +VTGGPM G +DG+ + A + + + GEI+E + E G+C Sbjct: 139 DVPAIVVTGGPMLNGKLDGKDIGSGTAVWRLHESLKAGEINEHQFFAAEAGMSRSAGTCN 198 Query: 193 GMFTANTMACMTEVLGMSEFNCAATPATEAEKLRVAKLTGMRIVEAIEEGITARDVLTRE 252 M TA+TMACM E LG S + AA PA +A + +A ++G RIVE EG+T +LTRE Sbjct: 199 TMGTASTMACMAESLGTSLPHNAAIPAVDARRYVLAHMSGKRIVEMAHEGLTLSKILTRE 258 Query: 253 AFLDAIRVDMALGGSTNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGPYTMR 312 AF +AIR + A+GGSTN V+HL AIA V+L L+D+ + R TP L ++P G + M Sbjct: 259 AFENAIRTNAAIGGSTNAVIHLKAIAGRIGVQLDLEDWTRIGRGTPTLVDLQPSGRFLME 318 Query: 313 DLYEAGGVPAVMKELADD---LHLDRIDFAGRSMRERVERTEVKDREVIRPKEDPVHEEG 369 + Y AGG+PAV++ L ++ H + + G+S+ + V + EVIRP +P+ +G Sbjct: 319 EFYYAGGLPAVLRRLGENNLLPHPNALTVNGKSLWDNVREAPQYNDEVIRPISNPLIADG 378 Query: 370 GIVVLYGNLAPKGAVIKTAALSEEMYEHEGPAVVFDSEEEATEAILGG--DIDPGDVVVI 427 GI +L GNLAP+GAV+K +A S E+ +H G AVVF++ E E I+ DID V+V+ Sbjct: 379 GICILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLEHYKERIVDENLDIDASCVMVL 438 Query: 428 RYEGPAGGPGMREM--LTPTAALCGMGLDDSVALVTDGRFSGGTRGPCVGHVSPEAYRGG 485 + GP G PGM E+ + L G+ D V ++D R SG G V HV+PEA GG Sbjct: 439 KNCGPKGYPGMAEVGNMGLPPKLLRQGVKDMVR-ISDARMSGTAYGTVVLHVAPEAAAGG 497 Query: 486 PIAVVEEGDTIRLDVRERRLEVDVEDEELEARLEEW-EPPEDEVTGYLRRYRELVRGADE 544 P+A V +GD I LD RL +D+ DEEL ARL + GY R Y + V AD+ Sbjct: 498 PLAAVRDGDFIELDCENGRLHLDISDEELAARLAALANTDQGGRGGYQRLYVDHVLQADD 557 Query: 545 G 545 G Sbjct: 558 G 558 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: 831 Number of extensions: 38 Number of successful extensions: 7 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: 577 Length adjustment: 36 Effective length of query: 513 Effective length of database: 541 Effective search space: 277533 Effective search space used: 277533 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 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