Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate WP_037450742.1 N825_RS10470 dihydroxy-acid dehydratase
Query= SwissProt::P21909 (607 letters) >NCBI__GCF_000576635.1:WP_037450742.1 Length = 566 Score = 204 bits (519), Expect = 8e-57 Identities = 166/524 (31%), Positives = 259/524 (49%), Gaps = 39/524 (7%) Query: 89 YPEQMKVFAREVGATVQVAGGVPAMCDGVTQGQPGMEE-SLFSRDVIALATSVSLSHGMF 147 +PE ++ R V +AG +P ++ G+ SL R+++A+ T + Sbjct: 63 FPELLEAVKRGV----LMAGALPLEFPTISLGEVFTSPTSLKFRNLMAMDTEEMIRAQPM 118 Query: 148 EGAALLGICDKIVPGLLMGALRFGHLPTILVPSGPMTTGIPNKEKI-------RIRQLYA 200 + L+G CDK VP LMGA+ +P I + +GPM+TG E++ R + Sbjct: 119 DSVVLMGGCDKTVPAQLMGAIS-ADIPAIQLVAGPMSTGRHRGERLGACTDCRRFWAKFR 177 Query: 201 QGKIGQKELLDMEAACYHAEGTCTFYGTANTNQMVMEVLGLHMPGSAFVTPGTPLRQALT 260 G++ +E+ +E GTC GTA+T + E LG+ +PG A + R + Sbjct: 178 AGEVDAEEIETVEGRLATTAGTCAVMGTASTMACLTETLGMSLPGCAAIPAVHSDRLRMA 237 Query: 261 RAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLATGGSTNHTMHIPAIARAAGVIV 320 A R EL G D P +II +I NA+ LLA GSTN +H+ AIAR AG+ V Sbjct: 238 EATGKRAVEL--IGSDLTP-SRIITPAAIRNALRMLLALSGSTNALLHLTAIARRAGIQV 294 Query: 321 NWNDFHDLSEVVPLIARIYPNGPRDINEFQNAGGMAYVIKELLSANLLNRDVTTIAKGGI 380 + ++F+ LS+ P++ + P GP + + AGG+ ++KEL L+ RD T+ Sbjct: 295 DLHEFNRLSDETPVLVNLKPVGPHYMEDLFAAGGVPAILKEL--GGLMERDALTVTG--- 349 Query: 381 EEYAKAPALNDAGELVWKPAGEPGDDTILRPVSNPFAKDGGLRLLEGNLG--RAMYKASA 438 GEL+ P +P D T+++ + P GGL + G+L A+ K +A Sbjct: 350 ---------QTLGELIDAPMIDPVDRTVIKSRAEPVDPQGGLVAVFGSLAPRGAVVKRAA 400 Query: 439 VDPKFWTIEAPVRVFSDQDDVQKAFKAGEL--NKDVIVVVRFQGPRA-NGMPELHKLTPA 495 DP+ E VF D+ + +L + D I++++ GP++ +GMPE L P Sbjct: 401 ADPRLMEHEGRAVVFGSLQDLAERIDDPDLDVSADDILILQNAGPKSDSGMPEAGYL-PI 459 Query: 496 LGVLQDNGYKVAL-VTDGRMSGATGKVPVALHVSPEALGGGAIGKLRDGDIVRISVEEGK 554 L G K L ++D RMSG T + LHV+PEA GG +G R GD VRISV E + Sbjct: 460 PRKLAKAGVKDMLRISDARMSG-TAYGAIVLHVAPEAAVGGPLGLARTGDRVRISVSEHR 518 Query: 555 LEALVPADEWNARPHAEKPAFRPGTGRELFDIFRQNAAKAEDGA 598 L+ LV +E + R A+ A R ++ + +A++GA Sbjct: 519 LDLLVSPEELDRR-RADLMAPDVKRRRGYDRLYNDHVLQADEGA 561 Lambda K H 0.318 0.136 0.403 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: 812 Number of extensions: 49 Number of successful extensions: 6 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: 607 Length of database: 566 Length adjustment: 37 Effective length of query: 570 Effective length of database: 529 Effective search space: 301530 Effective search space used: 301530 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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