Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_012401954.1 BPHY_RS13090 phosphogluconate dehydratase
Query= BRENDA::Q8NQZ9 (613 letters) >NCBI__GCF_000020045.1:WP_012401954.1 Length = 637 Score = 220 bits (561), Expect = 1e-61 Identities = 174/548 (31%), Positives = 266/548 (48%), Gaps = 48/548 (8%) Query: 34 KPIVAIVNSYTQFVPGHVHLKNVGDIVADAVRKAGGVPKEFNTI-AVDDGIAMGHGGMLY 92 +P + IV+SY + + H K+ DI+ A R+ GGV + + A+ DG+ G+ GM Sbjct: 68 QPNIGIVSSYNEMLSAHAPYKDFPDIIKAAARENGGVAQFAGGVPAMCDGVTQGNAGMEL 127 Query: 93 SLPSREIIADSVEYMVNAHTADAMVCISNCDKITPGMLNAAMRL-NIPVVFVSGGPMEAG 151 SL SRE+IA S + + DA +C+ CDKI PG+L A++ ++P +FV GPM +G Sbjct: 128 SLFSREVIAMSTAVALTHNMFDAALCLGVCDKIVPGLLIGALQFGHLPTIFVPAGPMTSG 187 Query: 152 KAVVVDGVAHAPTDLITAISASASDAVDDAGLAAVEASACPTCGSCSGMFTANSMNCLTE 211 + A A A DA+ ++ EA+A G+C+ TANS L E Sbjct: 188 ----ISNDAKAKVRQEFATGQCGRDALLES-----EAAAYHGHGTCTFYGTANSNQMLME 238 Query: 212 ALGLSLPGNGSTLATHAARRALFEKAGETVVELCRRYYGEEDESVLPRG-IATKKAFENA 270 +GL LPG+ R AL +A V++L E + +P G + +KA N Sbjct: 239 IMGLHLPGSAFVHPHTPLRDALTAQAARRVLDLT-----VERGNYMPIGHVIDEKAIVNG 293 Query: 271 MALDMAMGGSTNTILHILAAAQEGEVDFDLADIDELSKNVPCLSKVAPNSDYHMEDVHRA 330 + +A GGSTN LH++A A+ + D D D LS +VP L+KV PN + H A Sbjct: 294 IVGLLATGGSTNHTLHLVAIARAAGIIIDWDDFDTLSASVPLLAKVYPNGKADVNHFHAA 353 Query: 331 GGIPALLGELNRGGLLNKDVHSVHSNDLEGWLDDWDIRSGKTTEVATELFHAAPGGIRTT 390 GG+ L L GGLL+ DV++V L + ++ + GK T V PG + Sbjct: 354 GGMAFLTRNLLEGGLLHDDVNTVAGKGLSHYTEEPKLLDGKLTWV--------PGVSESQ 405 Query: 391 EAFSTENRWDELDTDAAKGCIRDVEHAYTADGGLVVLRGNISPDGAVIKSAGIEEELWNF 450 ++ +R ++ + DGGL +++G + VIK + + ++ Sbjct: 406 DS----------------AVLRRIDEPFQPDGGLRLMQGKLG--RGVIKISAVAKQHRTV 447 Query: 451 TGPARVVESQEEAVSVILTKTIQAGEVLVVRYEGPSGGPGMQEMLHPTAFLKG--SGLGK 508 PA V +SQE ++ + VVR++G GM E LH L G G Sbjct: 448 KAPAIVFDSQEAVQEAFDNGELKRDFIAVVRFQGARAN-GMPE-LHRLTPLLGVLQDQGF 505 Query: 509 KCALITDGRFSGGSSGL-SIGHVSPEAAHGGVIGLIENGDIVSIDVHNRKLEVQVSDEEL 567 AL+TDGR SG S + ++ HVSPEA G +G + GD++ ID L+V++ E Sbjct: 506 HVALVTDGRMSGASGKVPAVIHVSPEALLQGPLGKVRTGDMLVIDAEAGLLDVEMDAAEW 565 Query: 568 QRRRDAMN 575 R A++ Sbjct: 566 AARPIAVS 573 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: 905 Number of extensions: 42 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: 613 Length of database: 637 Length adjustment: 37 Effective length of query: 576 Effective length of database: 600 Effective search space: 345600 Effective search space used: 345600 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: 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