Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate WP_085634854.1 MGEO_RS01140 dihydroxy-acid dehydratase
Query= SwissProt::P21909 (607 letters) >NCBI__GCF_002115805.1:WP_085634854.1 Length = 587 Score = 184 bits (468), Expect = 7e-51 Identities = 151/515 (29%), Positives = 236/515 (45%), Gaps = 43/515 (8%) Query: 70 IGVVTSYNDMLSAHEPYYRYPEQMKVFAREVGATVQVAGGVPAMCDGVTQGQPGMEESLF 129 +GV T +N+ + R + +K+ ++ T + + + DG+ G GM SL Sbjct: 44 VGVATCWNEAAPCNIALNRQAQAVKMGVKQAFGTPREFTTI-TVTDGIAMGHEGMRSSLA 102 Query: 130 SRDVIALATSVSLSHGMFEGAALLGICDKIVPGLLMGALRFGHLPTILVPSG-------P 182 SR+ IA +++ ++ L CDK +PG++M +R ++P++ + G P Sbjct: 103 SREAIADTVELTMRGHCYDAVVGLAGCDKSLPGMMMAMVRL-NVPSVFIYGGSILPGKAP 161 Query: 183 MTTGIPNKEKIRIRQLYAQ------GKIGQKELLD-----MEAACYHAEGTCTFYGTANT 231 IP E R R L Q G+ EL D +E + G C TANT Sbjct: 162 QVAEIP--EDFRTRDLTVQDMFEAVGRHQNNELSDKALDMLERVACPSAGACGGQFTANT 219 Query: 232 NQMVMEVLGLHMPGSAFVTPGTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVN 291 V E +GL + S+ + R A A+ V +L + R I+ +++ N Sbjct: 220 MACVSEAIGLALFNSSGMPAPYESRDAYGEASGRAVMDLIEQNIKARD---IVTREALEN 276 Query: 292 AIVGLLATGGSTNHTMHIPAIARAAGVIVNWNDFHDLSEVVPLIARIYPNGPRDINEFQN 351 A + TGGSTN +H+PAIA AG+ D D+ + P + P G + + Sbjct: 277 AARVVACTGGSTNAGLHLPAIAHEAGIEFYLEDVCDIFKDTPYFVDLKPGGTYVAKDLYD 336 Query: 352 AGGMAYVIKELLSANLLNRDVTTIAKGGIEEYAKAPALNDAGELVWKPAGEPGDDTILRP 411 AGG+ V+KEL A L++ D T A + + + + + A D ++ Sbjct: 337 AGGIPVVMKELRKAGLIHEDCVT---------ASTRTIGEELDRIEREA----DGKVIYS 383 Query: 412 VSNPFAKDGGLRLLEGNLG--RAMYKASAVDPKFWTIEAPVRVFSDQDDVQKAFKAGELN 469 + P K GG+ L+GNL A+ K + + + P RVF ++D A KA + Sbjct: 384 IETPITKTGGVVGLKGNLAPEGAIVKVAGIKAEDQIFTGPARVFECEEDAFAAVKARDYK 443 Query: 470 KDVIVVVRFQGPRAN-GMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVS 528 + ++V+R +GP GM E+ T AL Q G KVAL+TDGR SGAT V HV Sbjct: 444 EGEVIVIRNEGPAGGPGMREMLATTAALSG-QGMGKKVALITDGRFSGATRGFCVG-HVG 501 Query: 529 PEALGGGAIGKLRDGDIVRISVEEGKLEALVPADE 563 PEA GG I L++GD++ I G L + +E Sbjct: 502 PEAALGGPIALLKNGDMITIDAVNGSLSVDLSDEE 536 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: 957 Number of extensions: 50 Number of successful extensions: 7 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: 607 Length of database: 587 Length adjustment: 37 Effective length of query: 570 Effective length of database: 550 Effective search space: 313500 Effective search space used: 313500 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