Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_037570494.1 BS73_RS07155 dihydroxy-acid dehydratase
Query= SwissProt::P9WKJ5 (575 letters) >NCBI__GCF_000744815.1:WP_037570494.1 Length = 577 Score = 317 bits (811), Expect = 1e-90 Identities = 208/516 (40%), Positives = 294/516 (56%), Gaps = 33/516 (6%) Query: 41 GMDDEDFA-KPQIGVASSWNEITPCNLSLDRLANAVKEGVFSAGGYPLEFGTISVSDGIS 99 G+ D+ F +PQI +A++ +++TPCN LD +A AV++GV AGG L +S+ + + Sbjct: 33 GLPDDAFTGRPQIAIANTASDLTPCNSHLDEVAAAVRDGVHEAGGIALNLPVVSLGETLL 92 Query: 100 MGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDKSLPGMLMAAARLDLAAVFLY 159 +++ R + A S E +++ +DG+VLL GCDK++P +LMAAA +DL +V + Sbjct: 93 KPT-----AMLWRNMAAMSTEEMLRGNPVDGAVLLGGCDKTIPSLLMAAASVDLPSVVVP 147 Query: 160 AGSILPGRAK---LSDGSERDVTIIDAFEAVGACSRGLMSRADVDAIERAICPGEGACGG 216 G +L G + L G+ D + G +S D A E A+ G C Sbjct: 148 GGPMLTGTFRGRPLGCGT-------DVWRLSEEVRSGELSAEDFTASESAMIRSRGHCNT 200 Query: 217 MYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVELLRRGITARDILTKEA 276 M TA+TM AEALG LPG+A PA D R AR SG+ VE++R +LT+ + Sbjct: 201 MGTASTMGLLAEALGTVLPGTAGIPAPDSRLLRAARESGRLAVEMVRADRRPSTLLTEGS 260 Query: 277 FENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRIGSGVPHLADVKPFGRHVMSD 336 F NAI + A GGSTNAV+HLLAIA + LSL DF RIGSGVP L D++P GR++M D Sbjct: 261 FRNAIVALAALGGSTNAVVHLLAIAGRLGIPLSLDDFDRIGSGVPLLTDLQPAGRYLMED 320 Query: 337 VDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENL--AAITPPDPDGKVLRALANPIHP 394 + GG+ V++ + D LL + LTVTG +A L A I D +V+R P+ P Sbjct: 321 LHRAGGLHAVLREVRD--LLDPEALTVTGRPLAGYLDDARIW----DTEVIRERERPLQP 374 Query: 395 SGGITILHGSLAPEGAVVKTAGFDSDVF--EGTARVFDG---ERAALDALEDGTITVGDA 449 GI +L G+LAP+GAV+K A ++ G A VFD RA +D D + Sbjct: 375 DAGIAVLRGNLAPDGAVIKPAAATPELLSHRGRAMVFDSIEDFRARVDD-PDLDVDADTV 433 Query: 450 VVIRYEGPKGGPGMREM--LAITGAIKGAGLGKDVLLLTDGRFSGGTTGLCVGHIAPEAV 507 +V+R GPKG PGM E+ L + + G+ +D++ + DGR SG G V H+APEA Sbjct: 434 LVLRGCGPKGYPGMPEVSNLPLPPKLLRQGV-RDMVRICDGRMSGTAYGTVVLHVAPEAA 492 Query: 508 DGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQ 543 GGP+AL+R GD I LDVA R L+V E A+R+ Sbjct: 493 AGGPLALIRTGDWIELDVAARTLNVDLPAEELAARK 528 Lambda K H 0.318 0.136 0.393 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: 947 Number of extensions: 49 Number of successful extensions: 6 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: 575 Length of database: 577 Length adjustment: 36 Effective length of query: 539 Effective length of database: 541 Effective search space: 291599 Effective search space used: 291599 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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