Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate SMc03068 SMc03068 phosphogluconate dehydratase
Query= BRENDA::Q8NQZ9 (613 letters) >FitnessBrowser__Smeli:SMc03068 Length = 606 Score = 204 bits (519), Expect = 9e-57 Identities = 170/543 (31%), Positives = 251/543 (46%), Gaps = 49/543 (9%) Query: 35 PIVAIVNSYTQFVPGHVHLKNVGDIVADAVRKAGGVPKEFNTI-AVDDGIAMGHGGMLYS 93 P + I+ SY + H + ++ +A +AGGV + + A+ DG+ G GM S Sbjct: 68 PNLGIITSYNDMLSAHQPFETYPALIREAAHEAGGVAQVAGGVPAMCDGVTQGQPGMELS 127 Query: 94 LPSREIIADSVEYMVNAHTADAMVCISNCDKITPGMLNAAMRL-NIPVVFVSGGPMEAGK 152 L SR++IA + ++ + DA V + CDKI PG+ AA+ ++P VF+ GPM G Sbjct: 128 LFSRDVIAMAAGIGLSHNMFDAAVYLGVCDKIVPGLAIAALTFGHLPAVFIPAGPMTTG- 186 Query: 153 AVVVDGVAHAPTDLITAI-SASASDAVDDAGLAAVEASACPTCGSCSGMFTANSMNCLTE 211 P D + A V L E+ + G+C+ TANS L E Sbjct: 187 ---------LPNDEKAKVRQLFAEGKVGRDELLEAESKSYHGPGTCTFYGTANSNQMLME 237 Query: 212 ALGLSLPGNGSTLATHAARRALFEKAGETVVELCRRYYGEEDESVLPRG-IATKKAFENA 270 +G LPG R AL +A + + + G E P G + +++ N Sbjct: 238 IMGFHLPGASFINPGTPLRDALTREATKRALAITA--LGNE---FTPAGEMIDERSIVNG 292 Query: 271 MALDMAMGGSTNTILHILAAAQEGEVDFDLADIDELSKNVPCLSKVAPNSDYHMEDVHRA 330 + A GGSTN +H++A A+ + DI ELS VP L++V PN + H A Sbjct: 293 VVGLHATGGSTNHTMHLVAMARAAGIVLTWQDISELSDLVPLLARVYPNGLADVNHFHAA 352 Query: 331 GGIPALLGELNRGGLLNKDVHSVHSNDLEGWLDDWDIRSGKTTEVATELFHAAPGGIRTT 390 GG+ L+ +L R GLL+ DV +V+ L + D++ G+ V E AP Sbjct: 353 GGMGFLIAQLLRKGLLHDDVRTVYGQGLSAYA--IDVKLGENGSVKRE---PAP------ 401 Query: 391 EAFSTENRWDELDTDAAKGCIRDVEHAYTADGGLVVLRGNISPDGAVIKSAGIEEELWNF 450 + A + V+ + GGL +L GNI AVIK + ++ E Sbjct: 402 ------------EASADPKVLATVDRPFQHTGGLKMLSGNIGK--AVIKISAVKPESHVI 447 Query: 451 TGPARVVESQEEAVSVILTKTIQAGEVLVVRYEGPSGGPGMQEMLHPTAFLKG--SGLGK 508 PA++ Q E + ++ V VVR++GP GM E LH + G G+ Sbjct: 448 EAPAKIFNDQAELNAAFKAGKLEGDFVAVVRFQGPKAN-GMPE-LHKLTTVLGILQDRGQ 505 Query: 509 KCALITDGRFSGGSSGLSIG-HVSPEAAHGGVIGLIENGDIVSIDVHNRKLEVQVSDEEL 567 K A++TDGR SG S + HV+PEA GG I I+ GDIV ID N K+EV V D L Sbjct: 506 KVAILTDGRMSGASGKVPAAIHVTPEAKEGGPIARIQEGDIVRIDAINGKVEVLVEDIAL 565 Query: 568 QRR 570 + R Sbjct: 566 KTR 568 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: 899 Number of extensions: 51 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: 606 Length adjustment: 37 Effective length of query: 576 Effective length of database: 569 Effective search space: 327744 Effective search space used: 327744 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 09 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