Align Dihydroxy-acid dehydratase 2; DAD 2; EC 4.2.1.9 (uncharacterized)
to candidate WP_012333306.1 M446_RS16850 phosphogluconate dehydratase
Query= curated2:Q5YX61 (629 letters) >NCBI__GCF_000019365.1:WP_012333306.1 Length = 616 Score = 222 bits (566), Expect = 3e-62 Identities = 178/539 (33%), Positives = 253/539 (46%), Gaps = 46/539 (8%) Query: 38 VAVANSFTEFVPGHTHLQPVGRIVGDAIRRAGGIPREFNTI-AVDDGIAMGHQGMLYSLP 96 + + ++ + + H + ++ +A R AGG+ + A+ DGI G GM SL Sbjct: 77 LGIVTAYNDMLSAHRPYERYPDLLREAAREAGGVALVAGGVPAMCDGITQGEAGMELSLF 136 Query: 97 SRDLIADSIEYMVQAHCADALVCISNCDKITPGMLLAAMRLD-IPTVFVSGGPMEGGRAT 155 SRD+IA S + DA V + CDKI PG+++ A+ +P VF+ GPM G Sbjct: 137 SRDVIALSTAVALSHQTFDAAVFLGICDKIVPGLVIGALAFGHLPAVFIPSGPMTSGLPN 196 Query: 156 LADGTVRRLDLITAMSEAVNDATSDADLATIEENACPTCGSCAGMFTANSMNCLVEALGL 215 +R+L A DA LA E ++ G+C TAN+ L+E +GL Sbjct: 197 PEKAKIRQL-------YAEGKVGRDALLAA-ESDSYHGPGTCTFYGTANTNQMLMEMMGL 248 Query: 216 ALPGNGTTLATHTARRDLYEAAGATIMAITRRYYDRDDATVLPRA-IASRAAFDNAMALD 274 LPG R L AA +AIT + LP + AF N + Sbjct: 249 HLPGASFVTPDTPLRDALTRAAAQRALAITALGNE-----YLPVGQLLDERAFANGIVGL 303 Query: 275 LAMGGSTNTVLHLLAAAHEAGLDYTLADIEKRSRAVPCLCKVAPNGSHLMEDVHRAGGIP 334 A GGSTN LHLL A AG+ T D+ + P L +V PNG+ + H AGG+P Sbjct: 304 HATGGSTNHTLHLLPMAAAAGITLTWEDLSDLAEVTPLLARVYPNGTADVNHFHAAGGMP 363 Query: 335 AILGELRRGGHLHTTVRAVHSESLDGWLAEWDVRGPNPAQAAVDLFHAAPGGVRSATAFS 394 ++ EL G LH + V L + R P +A GG+ + Sbjct: 364 FVIRELLGEGLLHADAQTVLGAGLHAY-----TREPVLTEA---------GGLAWREGPA 409 Query: 395 QSARWAALDLDAESGCIRDVAHAYSEDGGLAVLRGNLAVDGAVVKSAGVPADLHVFTGEA 454 +S E+G +R A + GGLAVL GNL AV+K++ V + V A Sbjct: 410 ES---------GETGVLRGAAAPFQPTGGLAVLAGNLG--RAVIKTSAVAPERQVIEAPA 458 Query: 455 VVAESQEEAVTAVLSGRVRPGTVLVIRYEGPR--GGPGMQEMLYPTAYLKGRGLAGSVAV 512 V SQE A +G +R V V+R++GP+ G P + +++ P L+ RG VA+ Sbjct: 459 RVFHSQEALQAAFRAGELRGDVVAVVRFQGPKANGMPELHKLMPPLGVLQDRG--HRVAL 516 Query: 513 VTDGRFSGGSSGL-SIGHVSPEAAAGGTIAAVTDGDPITIDIPSRTLRLEVDDAEIARR 570 VTDGR SG S + S HV+PEAA GG IA + DGD + +D P+ L + V AE A R Sbjct: 517 VTDGRLSGASGKVPSAIHVTPEAAEGGPIARIRDGDVVRVDAPAGRLEVLVPPAEWAAR 575 Lambda K H 0.319 0.134 0.395 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: 1112 Number of extensions: 66 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: 629 Length of database: 616 Length adjustment: 37 Effective length of query: 592 Effective length of database: 579 Effective search space: 342768 Effective search space used: 342768 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 (21.8 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Apr 10 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