Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate GFF2220 HP15_2174 6-phosphogluconate dehydratase
Query= curated2:B1I250 (569 letters) >FitnessBrowser__Marino:GFF2220 Length = 610 Score = 245 bits (626), Expect = 3e-69 Identities = 188/570 (32%), Positives = 279/570 (48%), Gaps = 53/570 (9%) Query: 12 RAPHRSLLRATGII----------KDEADFQ-KPFVAIANSFAEIVPGHAHLNEFVKEIK 60 ++PHRS L + KD F K VA+ ++ +++ H +F I+ Sbjct: 37 QSPHRSSLSCGNLAHGFAACNQGDKDTLKFMNKANVAMVTAYNDMLSAHQPYEKFPDIIR 96 Query: 61 EAVREAGGVP-FEFNTLALCDGIAMNHPGMRYSLPSRELVADSVETMVQGHRFDGLICIP 119 EA R G V T A+CDG+ PGM SL SR+ +A S + + FD + + Sbjct: 97 EAARGMGSVAQVAGGTPAMCDGVTQGQPGMELSLFSRDTIAMSTAVALSHNMFDATLLLG 156 Query: 120 NCDKIVPGMLMAAVRLN-IPTIFVSGGPMKAGRA-KDGRPIDLISVFEGIGAFRAGKIDA 177 CDKIVPG+L+ ++ +PTI + GPM +G K+ + I + + GK+ Sbjct: 157 ICDKIVPGLLIGSLSFGYLPTILLPAGPMPSGLPNKEKQRIRQL--------YAEGKVGK 208 Query: 178 GDLLELEQAACPGYGSCAGMFTANSMNCLCEALGLALPGNGTILAVDPRRSELKKWAGRQ 237 +LLE E + G+C TANS L E +GL +PG+ + P R EL + A Q Sbjct: 209 EELLEAESKSYHSPGTCTFYGTANSNQLLVEVMGLHMPGSAFVNPNTPLRDELTRAATEQ 268 Query: 238 IVELIK---RDLRPRDIVTPEAIDNAFALDVAMGGSTNTILHLLAVAQEAGINYPLKRVN 294 ++ L K +L D+V ++I NA + GGSTN +H +A+A+ AGI Sbjct: 269 VIRLSKPHGGELGLGDMVDEKSIVNALVALLVTGGSTNHTIHWIAIARAAGIIIDWNDYA 328 Query: 295 LISARTPTLCKISPASSLHIEDVDRAGGVSAVLGELSRKPGLLNLDCLTVTG-------- 346 +S+ P++ +I P + AGG ++ EL G ++ D TV G Sbjct: 329 ELSSVVPSMTRIYPNGQEDVNAFHEAGGTPFLIREL-LSGGYVHNDVNTVVGYGLERYTE 387 Query: 347 ------ETLGETVGQVQSLDPRVIRGVEEPLSPVGGLKVLFGSLAPEGAVVKTAAVVPQM 400 E L +SL P V+ V EP +P GGL+VL G+L V+K +AV P+ Sbjct: 388 MPELSDEQLVWKPAPEKSLRPDVLSPVAEPFAPDGGLRVLDGNLG--RGVIKVSAVAPEH 445 Query: 401 MRHQGPAVVFNSEAEASAAILGGRIKHGDVVVIRFEGPKGGPGFMEMLGPTAAL-VGMGL 459 + + PAVVFN + E AA G + +V++RF+GPK G E+ T L V Sbjct: 446 RKVEAPAVVFNDQNELKAAFEAGDLDRDCIVIVRFQGPKSN-GMPELHKLTPYLGVLQDR 504 Query: 460 GESVALVTDGRFSG--GTRGACIGHVCPEAASGGPIALIKDGDLISYDLEAGTLELLVPQ 517 G V LVTDGR SG G A I HV PEA GGP+A +K+GD++ D E+G L + + Sbjct: 505 GFKVGLVTDGRMSGASGKVPAAI-HVYPEALDGGPLAKVKNGDMVCLDAESGVLAIRLDD 563 Query: 518 EELAARKA------AFTPPLRQGLTGWLAR 541 +E A R++ + + L GW+ R Sbjct: 564 QEFAGRESEKADLTGYHHGYGRELFGWMRR 593 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: 955 Number of extensions: 65 Number of successful extensions: 9 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: 610 Length adjustment: 37 Effective length of query: 532 Effective length of database: 573 Effective search space: 304836 Effective search space used: 304836 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