Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate HSERO_RS22480 HSERO_RS22480 dihydroxy-acid dehydratase
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__HerbieS:HSERO_RS22480 Length = 594 Score = 281 bits (718), Expect = 7e-80 Identities = 193/573 (33%), Positives = 301/573 (52%), Gaps = 30/573 (5%) Query: 2 KRSDVFLRPEYAPHRALWRAS----GLIDEELR--RPLIGVANSWNEIVP-GHVHLDKVA 54 + D F P++ AL+ G+ EELR RP+IG+A S ++I P +HL+ +A Sbjct: 12 RSQDWFDNPDHIDMTALYLERFMNYGITAEELRSGRPIIGIAQSGSDISPCNRIHLE-LA 70 Query: 55 EAVKAGIRMAGGTPLEFGTIAVCDGIAMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVV 114 + V+ GIR AGG P+EF + + + +L VEI+ + +DAVV Sbjct: 71 KRVRDGIRDAGGIPMEFPLHPIFENCRRPTAAIDRNL----AYLGLVEIL-HGYPIDAVV 125 Query: 115 MVTNCDKITPGFLLAAARLEVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTE 174 + T CDK TP ++AAA +++P I+++GGPM+ G E + + + L+ G + Sbjct: 126 LTTGCDKTTPSQIMAAATVDIPAIVLSGGPMLDGWMDGELVGSGSAIWKGRKLLSAGSID 185 Query: 175 ELRKLEESALPGP--GSCAGLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGM 232 + LE +A P G C + TA+TMN ++EA+G+ L G S +PA R A TG Sbjct: 186 NEKFLEIAAASAPSSGHCNTMGTASTMNAMAEALGMSLTGCSAIPAPYRERGQMAYETGR 245 Query: 233 RIVKMVEEGLTPDKILTRKALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEI 292 RIV M E L P ILTR A +AI V+ A+GGSTN+ H+ A+A G++L E + + Sbjct: 246 RIVGMAYEDLRPSAILTRDAFLDAIVVNAAIGGSTNAQPHIMAMARHAGVELQSEDWMKY 305 Query: 293 SRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAA 352 VP + ++ P+G++ RAGG+PA++ EL +AG + + +T TGKT+ EN++ A Sbjct: 306 GYDVPLLLNMQPAGKYLGERFHRAGGVPAIMWELQQAGKLRAERITATGKTMAENLQGRA 365 Query: 353 VLDREVIRPLDNPYSPFGGLAILKGSLAPNGAVVKASAVKRELWK-----------FKGV 401 DRE+I P P G +LKG+L + A++K S + + F+ Sbjct: 366 SNDREMIYPFAAPLRERAGFLVLKGNLF-DFAIMKTSVISETFRERYLSTPGQENIFECR 424 Query: 402 ARVFDREEDAVKAIRGG--EIEPGTVIVIRYEGPRGGPGMREMLTATAAVMALGLG-DKV 458 A VFD +D I +I+ T++ IR GP G PG E++ + G + Sbjct: 425 AVVFDGSDDYHARINDPALKIDENTLLAIRGAGPVGWPGSAEVVNMQPPDALIKRGVSTL 484 Query: 459 ALVTDGRFSGATRGPAIGHVSPEAAAGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEER 518 + DGR SG + P+I + SPE+A GG +A ++DGD + ID+ ++LV E+EL R Sbjct: 485 PTLGDGRQSGTSDSPSILNASPESAVGGGLAYLRDGDRVRIDLNTGECNMLVSEEELARR 544 Query: 519 RARWKPKVKPLRRGILRRYAKMALSADKGGALE 551 ++ P V P + Y + G +E Sbjct: 545 KSEGIPPVPPSQTPWQEIYRSTVGQLETGACME 577 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: 787 Number of extensions: 35 Number of successful extensions: 5 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: 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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