Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate GFF723 PGA1_c07380 dihydroxy-acid dehydratase IlvD
Query= curated2:A4YEN4 (557 letters) >FitnessBrowser__Phaeo:GFF723 Length = 571 Score = 349 bits (896), Expect = e-100 Identities = 206/565 (36%), Positives = 324/565 (57%), Gaps = 24/565 (4%) Query: 4 KSRSNKV-YGGYEKAP--NRAFLKAMGLTDDDIS-KPLVGVAVAWNEAGPCNIHLLGLSQ 59 K R N+ YG +K +R+++K G D +P++G+ W+E PCN L L++ Sbjct: 3 KDRRNRAWYGKLDKDGFIHRSWMKNQGFPDHAFDGRPIIGICNTWSELTPCNSGLRDLAE 62 Query: 60 VVKEGIRELGGTPRTFTAPVLIDGIAMGSESMK-YSLVSREVIANTVELTVNGHGYDGFV 118 VK G+ E GG P F PV+ ++G MK +++ R ++A VE ++ +G DG V Sbjct: 63 GVKRGVWEAGGFPVEF--PVM----SLGETQMKPTAMLFRNLLAMDVEESIRAYGIDGVV 116 Query: 119 ALGGCDKTQPGLMMSMARLNIPSVYMYGGTTLPGNFRGRDIAIG-DVYEAVGAFSAGKIT 177 LGGCDKT PG +M A +++P++ + G L G ++G+DI G DV++ A AG++T Sbjct: 117 LLGGCDKTTPGQLMGAASVDLPAIVVSSGPMLNGKWQGKDIGSGTDVWKFSEAVRAGEMT 176 Query: 178 AEDLRIMEDNAIPGPGACGGLYTANTMAMLSEALGLSLPGSSAPPAVSSDRTKFAKETGR 237 +D E G C + TA+TMA L EA+G+SLP ++A PAV + R A TG+ Sbjct: 177 LQDFMAAESGMSRSKGVCMTMGTASTMASLVEAMGMSLPTNAALPAVDARRMALAHLTGK 236 Query: 238 TLMKVMEIGLKPRDILTFEAFENGIALLMASGGSTNGVLHLLAIAHEAGVSLTLDDFDRI 297 +++++E +KP D+LT EAF N I A GGSTN V+HLLA+A G L+LDDFD + Sbjct: 237 RIVEMVEEDIKPSDVLTREAFVNAIMANAAVGGSTNAVVHLLALAGRVGAELSLDDFD-L 295 Query: 298 SKKVPEIVNMKPGGDYVMADLYRVGGTPVILKKLLDRGLLHGDTITVTGKTMAQNLSEYK 357 +P +VN P G Y+M D GG PV+LK+L D G L +T + G +A + Sbjct: 296 GSDIPLLVNCMPSGKYLMEDFCYAGGMPVVLKQLADNGHLRSNTTVLGGDILAY----AE 351 Query: 358 IPEFKHDHIVRDLSNPFLPSGGIRILKGSLAPEGSVVKLSAS--KIKYHRGPARVFNSEE 415 E +D +++ P P+ G+R+L+G+LAP G++VK SA+ + H G A VF + E Sbjct: 352 GAECFNDDVIKSFDEPVKPAAGLRVLRGNLAPNGAIVKPSAATDHLLEHEGVAHVFETIE 411 Query: 416 EAFETVLKK--KINEGDVVVIRYEGPKGGPGMREM--LAVTSAIVGQGLGEKVALVTDGR 471 + + + + + ++V++ GPKG PGM E+ + + +V +G+ + + ++DGR Sbjct: 412 DMKANIDRDDLPVTKDSILVLKGVGPKGYPGMPEVGNMPIPRKLVREGVRDMIR-ISDGR 470 Query: 472 FSGATRGLMVGHVAPEAAVGGPIALIRDGDTIVIDGEKGRLDVELSDQELKSRAKDWTPP 531 SG G ++ HV+PE+ GGP+ L++ GD I + + G LD+ +S++EL +R + W P Sbjct: 471 MSGTAFGTVILHVSPESQAGGPLGLVQTGDRIRVSAKNGTLDLLVSEEELTARREAWQPE 530 Query: 532 EPRYKTGLLAQYAKLVTSSARGAVL 556 Y G Y V + +GA L Sbjct: 531 PLHYTRGYAKLYVDSVLQAEKGADL 555 Lambda K H 0.316 0.137 0.392 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: 876 Number of extensions: 55 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: 557 Length of database: 571 Length adjustment: 36 Effective length of query: 521 Effective length of database: 535 Effective search space: 278735 Effective search space used: 278735 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