Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_019865040.1 METMI_RS0104465 phosphogluconate dehydratase
Query= curated2:B7JJG8 (557 letters) >NCBI__GCF_000384075.1:WP_019865040.1 Length = 606 Score = 256 bits (653), Expect = 2e-72 Identities = 188/576 (32%), Positives = 291/576 (50%), Gaps = 47/576 (8%) Query: 12 KAPHRSLLKATGLKD--------EDFD-----KPFIAICNSFIEIIPGHKHLNEFGKLVK 58 K PHRS+L L E D K I I +S+ +++ H+ + L+K Sbjct: 33 KGPHRSVLGCGNLAHGFAACGAGEKLDLAGDKKANIGIISSYNDMLSAHEPYKDAPALIK 92 Query: 59 EAVRAAGMVP-FEFNTIGVDDGIAMGHIGMRYSLPSREIIADSVETVVNAHWFDGMICIP 117 EA+ AAG V F + DGI G GM SL SR++IA S ++ + FDG + + Sbjct: 93 EAISAAGGVAQFAGGVPAMCDGITQGQAGMELSLFSRDVIAMSTAIGLSHNMFDGALYLG 152 Query: 118 NCDKITPGMMMAALRI-NIPTVFVSGGPMAAGKTSKGDVVDLSSVFEGVGAYQSGKISEE 176 CDKI PG++M AL ++P VFV GPM +G T+K Y GKI Sbjct: 153 VCDKIVPGLLMGALSFGHLPAVFVPAGPMPSGITNK-------EKSRARQQYAEGKIGRA 205 Query: 177 ELKDIEDHGCPSCGSCSGMFTANSMNCLCEVLGLALPGNGSILAIDPRREELIKQAAEKL 236 EL + E S G+C+ TANS + E++GL LPG+ + P R+EL K AA ++ Sbjct: 206 ELLESESKSYHSPGTCTFYGTANSNQMMVEMMGLHLPGSSFVNPYTPLRDELTKAAARQV 265 Query: 237 K--ILIERDIKP-RDIVTEEAIDDAFALDMAMGGSTNTVLHTLALAQEAGLDYDMNRIDA 293 + D +P ++ E+AI +A +A GGSTN +H +A+A+ AG+ + N D Sbjct: 266 LKFTALGNDFRPIGHVINEKAILNALIGLLATGGSTNHTMHLVAIARMAGIIINWNDFDN 325 Query: 294 VSRRVPHLCKVSPASNWHMEDIDRAGGISAILKEMSRKEGVLHLDRIT-----ATGQTLR 348 +S+ +P + K+ P + AGG+ ++ E+ K G++H D +T GQ + Sbjct: 326 LSKAIPLITKIYPNGPADVNHFQAAGGMGVLIAELL-KHGMMHEDILTIGDRHGMGQYTQ 384 Query: 349 E----------NIAHAEIKDKEVIHSLENPHSEEGGLRILKGNLAKDGAVIKSGATEVIR 398 E + A D EVI ++E P + GG+ +++GNL + + + + + + Sbjct: 385 EPKIIGGNLVWEASPAASLDTEVIATVEKPFAPGGGIHLIRGNLGRGISKVSAVSEDHQV 444 Query: 399 FEGPCVIFNSQDEALAGIMLGKVKKGDVVIIRYEGPRGGPGMPEMLAPTSAIAGM-GLGA 457 E P V+F+ QDE +A G++ V ++R++GPR GMPE+ T A+ + G Sbjct: 445 VEAPAVVFDDQDEMMAAFKRGELNHDFVAVLRFQGPRAN-GMPELHKLTPALGLLQDKGY 503 Query: 458 DVALLTDGRFSGASRGI-SVGHISPEAAAGGTIALLEQGDIVCIDVEERLLEVRVSDEEL 516 VALLTDGR SGAS + S H+ PE GG +A + GDI+ ++++ + V V + E Sbjct: 504 KVALLTDGRMSGASGKVPSAIHMYPECINGGPLAKVRNGDIISLNIKTGDVNVLVDETEF 563 Query: 517 DKRKKE---WKRPEPKVKTGWLGRYAQMVTSANTGA 549 + R E K + G + Q T+A TGA Sbjct: 564 NGRLPEENSAKNHHFGMGREMFGGFRQGATTAETGA 599 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: 827 Number of extensions: 54 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: 606 Length adjustment: 36 Effective length of query: 521 Effective length of database: 570 Effective search space: 296970 Effective search space used: 296970 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 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