Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate GFF2220 HP15_2174 6-phosphogluconate dehydratase
Query= curated2:B7JJG8 (557 letters) >FitnessBrowser__Marino:GFF2220 Length = 610 Score = 249 bits (636), Expect = 2e-70 Identities = 169/546 (30%), Positives = 277/546 (50%), Gaps = 45/546 (8%) Query: 12 KAPHRSLLKATGLK---------DED----FDKPFIAICNSFIEIIPGHKHLNEFGKLVK 58 ++PHRS L L D+D +K +A+ ++ +++ H+ +F +++ Sbjct: 37 QSPHRSSLSCGNLAHGFAACNQGDKDTLKFMNKANVAMVTAYNDMLSAHQPYEKFPDIIR 96 Query: 59 EAVRAAGMVP-FEFNTIGVDDGIAMGHIGMRYSLPSREIIADSVETVVNAHWFDGMICIP 117 EA R G V T + DG+ G GM SL SR+ IA S ++ + FD + + Sbjct: 97 EAARGMGSVAQVAGGTPAMCDGVTQGQPGMELSLFSRDTIAMSTAVALSHNMFDATLLLG 156 Query: 118 NCDKITPGMMMAALRIN-IPTVFVSGGPMAAGKTSKGDVVDLSSVFEGVGAYQSGKISEE 176 CDKI PG+++ +L +PT+ + GPM +G +K + + + Y GK+ +E Sbjct: 157 ICDKIVPGLLIGSLSFGYLPTILLPAGPMPSGLPNK----EKQRIRQ---LYAEGKVGKE 209 Query: 177 ELKDIEDHGCPSCGSCSGMFTANSMNCLCEVLGLALPGNGSILAIDPRREELIKQAAEKL 236 EL + E S G+C+ TANS L EV+GL +PG+ + P R+EL + A E++ Sbjct: 210 ELLEAESKSYHSPGTCTFYGTANSNQLLVEVMGLHMPGSAFVNPNTPLRDELTRAATEQV 269 Query: 237 KILIER---DIKPRDIVTEEAIDDAFALDMAMGGSTNTVLHTLALAQEAGLDYDMNRIDA 293 L + ++ D+V E++I +A + GGSTN +H +A+A+ AG+ D N Sbjct: 270 IRLSKPHGGELGLGDMVDEKSIVNALVALLVTGGSTNHTIHWIAIARAAGIIIDWNDYAE 329 Query: 294 VSRRVPHLCKVSPASNWHMEDIDRAGGISAILKEMSRKEGVLHLDRITATGQTLRENIAH 353 +S VP + ++ P + AGG +++E+ G +H D T G L Sbjct: 330 LSSVVPSMTRIYPNGQEDVNAFHEAGGTPFLIRELL-SGGYVHNDVNTVVGYGLERYTEM 388 Query: 354 AEIKDKE--------------VIHSLENPHSEEGGLRILKGNLAKDGAVIKSGATEVIRF 399 E+ D++ V+ + P + +GGLR+L GNL + + + A E + Sbjct: 389 PELSDEQLVWKPAPEKSLRPDVLSPVAEPFAPDGGLRVLDGNLGRGVIKVSAVAPEHRKV 448 Query: 400 EGPCVIFNSQDEALAGIMLGKVKKGDVVIIRYEGPRGGPGMPEM--LAPTSAIAGMGLGA 457 E P V+FN Q+E A G + + +VI+R++GP+ GMPE+ L P + G Sbjct: 449 EAPAVVFNDQNELKAAFEAGDLDRDCIVIVRFQGPKSN-GMPELHKLTPYLGVL-QDRGF 506 Query: 458 DVALLTDGRFSGASRGISVG-HISPEAAAGGTIALLEQGDIVCIDVEERLLEVRVSDEEL 516 V L+TDGR SGAS + H+ PEA GG +A ++ GD+VC+D E +L +R+ D+E Sbjct: 507 KVGLVTDGRMSGASGKVPAAIHVYPEALDGGPLAKVKNGDMVCLDAESGVLAIRLDDQEF 566 Query: 517 DKRKKE 522 R+ E Sbjct: 567 AGRESE 572 Lambda K H 0.318 0.137 0.400 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: 798 Number of extensions: 47 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: 557 Length of database: 610 Length adjustment: 36 Effective length of query: 521 Effective length of database: 574 Effective search space: 299054 Effective search space used: 299054 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 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