Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_012170950.1 AZC_RS12545 phosphogluconate dehydratase
Query= BRENDA::Q8NQZ9 (613 letters) >NCBI__GCF_000010525.1:WP_012170950.1 Length = 613 Score = 211 bits (536), Expect = 1e-58 Identities = 177/545 (32%), Positives = 261/545 (47%), Gaps = 57/545 (10%) Query: 37 VAIVNSYTQFVPGHVHLKNVGDIVADAVRKAGGVPKEFNTI-AVDDGIAMGHGGMLYSLP 95 +AIV +Y + H + D++ A R+AGGV + + A+ DGI G GM SL Sbjct: 74 LAIVTAYNDMLSAHQPYERYPDLIRAAAREAGGVAQVAGGVPAMCDGITQGEAGMELSLF 133 Query: 96 SREIIADSVEYMVNAHTADAMVCISNCDKITPGMLNAAMRL-NIPVVFVSGGPMEAGKAV 154 SRE+IA S ++ T D+ V + CDKI PG++ A+ ++P VF+ GPM +G Sbjct: 134 SREVIALSTAVALSHQTYDSAVFLGICDKIVPGLVIGALSFGHLPTVFLPSGPMTSG--- 190 Query: 155 VVDGVAHAPTDLITAI-SASASDAVDDAGLAAVEASACPTCGSCSGMFTANSMNCLTEAL 213 P D T + A V L E+ + G+C+ TAN+ + E + Sbjct: 191 -------LPNDEKTRVRQLFAEGKVGRDALLEAESQSYHGPGTCTFYGTANTNQMMMEIM 243 Query: 214 GLSLPG----NGSTLATHAARRALFEKAGETVVELCRRYYGEEDESVLPRG-IATKKAFE 268 G+ LPG N +T A R ++A + L Y P G I ++AF Sbjct: 244 GVHLPGASFINPNTPLRDAVTREGVKRA-LAITALGNHY--------TPLGRILDERAFV 294 Query: 269 NAMALDMAMGGSTNTILHILAAAQEGEVDFDLADIDELSKNVPCLSKVAPNSDYHMEDVH 328 NA+ A GGSTN LH++A A + D +L++ VP L++V PN + H Sbjct: 295 NAVVGLHATGGSTNHTLHLVAMAAAAGITLTWDDFSDLAEVVPLLARVYPNGKADVNHFH 354 Query: 329 RAGGIPALLGELNRGGLLNKDVHSVHSNDLEGWLDDWDIRSGKTTEVATELFHAAPGGIR 388 AGG+ ++ EL GLL+++V +V L G+ T+E A G + Sbjct: 355 AAGGMGFVIRELLSEGLLHENVETVWGTGLSGY----------TSEPALN----EAGQLT 400 Query: 389 TTEAFSTENRWDELDTDAAKGCIRDVEHAYTADGGLVVLRGNISPDGAVIKSAGIEEELW 448 T+ + DE +R V + GGL VL GN+ AV K++ + E Sbjct: 401 WTDGATATG--DE-------AVLRPVAKPFQPTGGLKVLDGNLGR--AVSKTSAVAPERH 449 Query: 449 NFTGPARVVESQEEAVSVILTKTIQAGEVLVVRYEGP--SGGPGMQEMLHPTAFLKGSGL 506 PARV SQEE + ++ V VVR++GP +G P + +++ P L+ G Sbjct: 450 VIEAPARVFHSQEELQAAFKAGSLTGDFVAVVRFQGPKANGMPELHKLMPPLGVLQDRG- 508 Query: 507 GKKCALITDGRFSGGSSGL-SIGHVSPEAAHGGVIGLIENGDIVSIDVHNRKLEVQVSDE 565 +K AL+TDGR SG S + S HV+PEAA+GG I I++GDIV D N L V V + Sbjct: 509 -QKVALVTDGRMSGASGKVPSAIHVTPEAANGGAIAKIKDGDIVRFDGVNGHLTVLVDEA 567 Query: 566 ELQRR 570 E R Sbjct: 568 EWAAR 572 Lambda K H 0.315 0.132 0.385 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: 928 Number of extensions: 48 Number of successful extensions: 9 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: 613 Length of database: 613 Length adjustment: 37 Effective length of query: 576 Effective length of database: 576 Effective search space: 331776 Effective search space used: 331776 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 (21.6 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