Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 7024978 Shewana3_2149 phosphogluconate dehydratase (RefSeq)
Query= curated2:B1I250 (569 letters) >FitnessBrowser__ANA3:7024978 Length = 608 Score = 237 bits (605), Expect = 9e-67 Identities = 181/522 (34%), Positives = 258/522 (49%), Gaps = 46/522 (8%) Query: 33 KPFVAIANSFAEIVPGHAHLNEFVKEIKEAVRE-------AGGVPFEFNTLALCDGIAMN 85 K + I +F +++ H + + +K+A +E AGGVP A+CDG+ Sbjct: 65 KANIGIITAFNDMLSAHQPYETYPELLKKACQEVGSVAQVAGGVP------AMCDGVTQG 118 Query: 86 HPGMRYSLPSRELVADSVETMVQGHRFDGLICIPNCDKIVPGMLMAAVRL-NIPTIFVSG 144 PGM SL SRE++A + + + FDG + + CDKIVPG+L+ A+ ++P +FV Sbjct: 119 QPGMELSLLSREVIAMATAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPA 178 Query: 145 GPMKAGRAKDGRPIDLISVFEGIGAFRAGKIDAGDLLELEQAACPGYGSCAGMFTANSMN 204 GPMK+G + F GK+D LLE E + G+C TANS Sbjct: 179 GPMKSGIPNKEKA-------RIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQ 231 Query: 205 CLCEALGLALPGNGTILAVDPRRSELKKWAGRQIVELIKRDLRPR---DIVTPEAIDNAF 261 + E +GL LPG+ + DP R L K A +Q+ L + + ++V +++ N Sbjct: 232 LMLEVMGLQLPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSVVNGI 291 Query: 262 ALDVAMGGSTNTILHLLAVAQEAGINYPLKRVNLISARTPTLCKISPASSLHIEDVDRAG 321 +A GGSTN +H++A A+ AGI + +S P L ++ P I AG Sbjct: 292 VALLATGGSTNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAG 351 Query: 322 GVSAVLGELSRKPGLLNLDCLTVTGETL-----------GE---TVGQVQSLDPRVIRGV 367 G++ ++ EL GLL+ D TV G L GE G SLD V+ V Sbjct: 352 GMAFLIKEL-LDAGLLHEDVNTVAGFGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTSV 410 Query: 368 EEPLSPVGGLKVLFGSLAPEGAVVKTAAVVPQMMRHQGPAVVFNSEAEASAAILGGRIKH 427 P GGLK+L G+L AV+K +AV + + PAVV + + + A G + Sbjct: 411 ATPFQNNGGLKLLKGNLG--RAVIKVSAVQEKHRVVEAPAVVIDDQNKLDALFKSGALDR 468 Query: 428 GDVVVIRFEGPKGGPGFMEMLGPTAALVGM-GLGESVALVTDGRFSG--GTRGACIGHVC 484 VVV++ +GPK G E+ T L + G VAL+TDGR SG G A I H+ Sbjct: 469 DCVVVVKGQGPKAN-GMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAI-HLT 526 Query: 485 PEAASGGPIALIKDGDLISYDLEAGTLELLVPQEELAARKAA 526 PEA GG IA ++DGDLI D G L LLV ELAAR AA Sbjct: 527 PEAIDGGLIAKVQDGDLIRVDALTGELSLLVSDAELAARTAA 568 Lambda K H 0.319 0.138 0.409 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: 856 Number of extensions: 52 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: 569 Length of database: 608 Length adjustment: 37 Effective length of query: 532 Effective length of database: 571 Effective search space: 303772 Effective search space used: 303772 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