Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate AO356_28760 AO356_28760 dihydroxy-acid dehydratase
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28760 Length = 594 Score = 303 bits (776), Expect = 1e-86 Identities = 191/548 (34%), Positives = 301/548 (54%), Gaps = 26/548 (4%) Query: 23 GLIDEELR--RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTIAVCDGI 80 G+ EEL+ RP+IG+A + +++ P + H ++A+ VKAGIR AGG P+EF + + Sbjct: 35 GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94 Query: 81 AMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLEVPVILI 140 + +L VEI+ + LD VV+ T CDK TP L+AAA ++P I++ Sbjct: 95 RRPTAALDRNL----AYLGLVEIL-HGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149 Query: 141 NGGPMMPGVYGKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSCAGLFTANT 198 +GGPM+ G + E I ++ L+ G E ++ +A P G C + TA + Sbjct: 150 SGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALS 209 Query: 199 MNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRKALENAIA 258 MN L+EA+G+ LPG +++PA R A TG RI ++V + + P +I+TR+A ENAIA Sbjct: 210 MNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICELVLQDIRPSQIMTRQAFENAIA 269 Query: 259 VDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGG 318 V ALG S+N HL A+A +G++L L+ + I VP + + P+G++ RAGG Sbjct: 270 VASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGEGFHRAGG 329 Query: 319 IPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLAILKGS 378 +P+V+ EL +AG +H+D TV+G+T+ E V + + +VI P D P G +L G+ Sbjct: 330 VPSVMHELQKAGRLHEDCATVSGRTIGEIVSSSLTSNADVIHPFDTPLKHRAGFIVLSGN 389 Query: 379 LAPNGAVVKASAVKRELWK-----------FKGVARVFDREEDAVKAIRGG--EIEPGTV 425 + A++K S V K F+ A VF+ ED I +I+ + Sbjct: 390 FF-DSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCI 448 Query: 426 IVIRYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAA 483 +VIR G G PG E+ + AA++ G+ D + + DGR SG + P+I ++SPEAA Sbjct: 449 LVIRGVGTVGYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAA 507 Query: 484 AGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGILRRYAKMALS 543 GG +AL+Q D + +D+ R ++LL+D++E+ RR W P + P + Y ++ Sbjct: 508 VGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRRLEWTPNIPPSQTPWQELYRQLVGQ 567 Query: 544 ADKGGALE 551 GG LE Sbjct: 568 LSTGGCLE 575 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: 788 Number of extensions: 37 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 552 Length of database: 594 Length adjustment: 36 Effective length of query: 516 Effective length of database: 558 Effective search space: 287928 Effective search space used: 287928 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