Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_048082021.1 EJ01_RS03755 dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >NCBI__GCF_000745485.1:WP_048082021.1 Length = 551 Score = 248 bits (634), Expect = 4e-70 Identities = 174/588 (29%), Positives = 293/588 (49%), Gaps = 58/588 (9%) Query: 25 EMVRAAASKGPHRGTLPCGNLAHGVAACGESDKQTLRLMNQANVAIVSAYNDMLSAHQPF 84 + ++ K PHR L ACG +D++ MN+ + + +++ ++ H Sbjct: 4 DAIKKGLQKAPHRSLL---------RACGVTDEE----MNKPFIGVANSFTSIVPGHIHL 50 Query: 85 ERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLASRDVIAMSTAIALSHNM 144 +KQ + E G V F A+CDG++ G GM+ SLASR++IA + + Sbjct: 51 NEVADAVKQGISEAGGV-PFEFNTMAICDGISMGHEGMKYSLASREIIADTVESMAQAHQ 109 Query: 145 FDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTG---------ISNKEKAAVRQ 195 DA + + CDK+VPG+L+ + R +P++ V GPM G IS E Sbjct: 110 MDALVLIPTCDKVVPGMLMAAARL-DIPSIVVTGGPMKPGEFKGKPVDFISVSEGVGA-- 166 Query: 196 LFAEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLHLPGASFVNPNTPLRD 255 + GK T EEL E + G+C TANT + EV+G+ LP + + + Sbjct: 167 -VSSGKMTEEELDELERCACPGAGSCAGLFTANTMACVTEVLGMSLPYCATAHAVDAKKR 225 Query: 256 ELTREAARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIA---Q 312 ++ R++ + L +N + ++I+ ++A N++ A LA GGS+N TLH+ AIA + Sbjct: 226 QIARQSGAKIIELLDKN---ITPSKIMTQEAFENAIAADLALGGSSNTTLHIPAIASELE 282 Query: 313 AAGIQLTWQDMSELSHVVPTLARIYPNGQADINHFQAAGGMSFLIRQLLDGGLLHEDVQT 372 G+ +T E S +P + ++ P+G + AGG+ +++ + D +++D T Sbjct: 283 DKGVNITINSFDEFSKKIPHITKLRPSGVHSLLDLDNAGGIPAVLKVIED--KINQDTLT 340 Query: 373 VAGPGLRRYTREPFLEDGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNLG-RG- 430 G L ++ + DE ++RPL P+S EGGL +++GNL RG Sbjct: 341 CTGKTLGENIKD--------------AKVADEEVIRPLSNPYSKEGGLAILKGNLAPRGS 386 Query: 431 VMKVSAVAPEHQVVEAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRANGMPELHKL 490 V+KV+ V + +V P ++F + + A E++ V V+R++GP+ G P + ++ Sbjct: 387 VVKVAGVNEDMKVHTGPAKVFDGEDACVTAIFNHEIKEGDVVVIRYEGPK--GGPGMREM 444 Query: 491 TPFLGVLQDRGFK-VALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGV 549 + G K VAL+TDGR SG + + P H+SPEA+ GP+A L+DGD +++D Sbjct: 445 LNPTSAISGMGLKTVALITDGRFSGGT-RGPCIGHISPEAMEKGPIAALKDGDIIKIDMN 503 Query: 550 NGELRVLVDDAEWQARSLEPAPQDGNLGCGRELFAFMRNAMSSAEEGA 597 NG L V+D E + R D + + + R SSA++GA Sbjct: 504 NGILEAEVEDKELKKRLENVVMPDKKV---KGWLSRYRKMASSADKGA 548 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: 800 Number of extensions: 55 Number of successful extensions: 9 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: 551 Length adjustment: 36 Effective length of query: 572 Effective length of database: 515 Effective search space: 294580 Effective search space used: 294580 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 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