Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate H281DRAFT_03422 H281DRAFT_03422 dihydroxyacid dehydratase (EC 4.2.1.9)
Query= curated2:P31961 (608 letters) >FitnessBrowser__Burk376:H281DRAFT_03422 Length = 592 Score = 197 bits (500), Expect = 1e-54 Identities = 161/517 (31%), Positives = 248/517 (47%), Gaps = 43/517 (8%) Query: 63 MNQANVAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGM 122 M + +A+V+ ++++ S H F++ +K+ + + AGG P +T EP Sbjct: 41 MGKPVIAVVNTWSEINSCHTHFKQRVEEVKRGIWQ-------AGGFPVEMPVMTLAEPFQ 93 Query: 123 E-LSLASRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPM 181 + ++ R+ +AM T L FD + +G CDK PGLL+G++ +LP++F+PAGPM Sbjct: 94 KPTTMLYRNFLAMETEEILKSYPFDGCVLMGGCDKTTPGLLMGAISM-NLPSIFLPAGPM 152 Query: 182 PTGISNKEKAA----VRQLFAE---GKATREELLASEMASYHAPGTCTFYGTANTNQLLV 234 G N + +AE GK T +E E +PG C GTA+T Sbjct: 153 LRGNWNGRTLGSGSDTWKYWAELRAGKITEDEWKGIESGIARSPGHCMTMGTASTMTSAA 212 Query: 235 EVMGLHLPGASFVNPNTPLRDELTRE-AARQASRLTPENGNYVPMAEIVDEKAIVNSVVA 293 E +GL LPG S + P D + A+ R+ V ++I+ K+ N+V Sbjct: 213 EALGLTLPGFSSI----PAVDSRHAQFASLTGQRIVEMVWTDVKPSDILTAKSFDNAVTT 268 Query: 294 LLATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQADINHFQAAGGM 353 +LA GSTN +HL+A+A+ AGI LT ELS + P + + P+GQ + F AGG+ Sbjct: 269 VLAMSGSTNAIVHLVAVARRAGIDLTTARFDELSRITPVIGNLRPSGQYLMEDFFYAGGL 328 Query: 354 SFLIRQLLDGGLLHEDVQTVAGPGLRRYTREPFLEDGRLVWREGPERSLDEAILRPLDKP 413 L+ +L G L+ TV G L G E D+ ++R P Sbjct: 329 RALLLEL--GDLIDGSQMTVNGSTLGENI-------------AGAEIFNDD-VIRKRGNP 372 Query: 414 FSAEGGLRLMEGNLGRGVMKVSAVAPEHQVVEAPVR--IFHDQASLAAAFKAGELE--RD 469 A GL ++ GNL + A E ++ R +F D A +AA +L+ D Sbjct: 373 VVASDGLAVLTGNLAPDGAVIKPAAMEAHLLNHRGRAVVFKDYADMAARIDMEDLDITAD 432 Query: 470 LVAVVRFQGP-RANGMPELHKLTPFLGVLQDRGFKVALVTDGRMSGASGKVPAAIHVSPE 528 V V++ GP A GMPE +L +L+ + ++D RMSG S +HV+PE Sbjct: 433 SVIVLQHAGPVGAPGMPEWGQLPIPQKLLKQGVRDMVRISDARMSGTSYGA-CVLHVAPE 491 Query: 529 AIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEWQAR 565 + GGPLA ++DGD +++D L + V D E AR Sbjct: 492 SFVGGPLALVKDGDMIQLDVAARRLHLEVSDEELSAR 528 Lambda K H 0.319 0.135 0.397 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: 821 Number of extensions: 51 Number of successful extensions: 7 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: 608 Length of database: 592 Length adjustment: 37 Effective length of query: 571 Effective length of database: 555 Effective search space: 316905 Effective search space used: 316905 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 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