Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_078430190.1 BK574_RS22725 dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >NCBI__GCF_002019605.1:WP_078430190.1 Length = 555 Score = 249 bits (637), Expect = 2e-70 Identities = 173/563 (30%), Positives = 290/563 (51%), Gaps = 52/563 (9%) Query: 26 MVRAAASKGPHRGTLPCGNLAHGVAACGESDKQTLRLMNQANVAIVSAYNDMLSAHQPFE 85 M++ + PHR L A E D M++ + + ++Y D++ H Sbjct: 5 MIKKGIDRAPHRSLLRA-------AGVKEED------MDKPFIGVCNSYIDIIPGHMHLN 51 Query: 86 RFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLASRDVIAMSTAIALSHNMF 145 +F + K+A+ E G + F + DG+ G GM SL SR++I + ++ + F Sbjct: 52 KFAEVAKEAIREAGGI-PFEFNTIGVDDGIAMGHIGMRYSLPSREIICDAAETVINAHWF 110 Query: 146 DAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGISNKEK----AAVRQ---LFA 198 D + CDKI PG+L+ S+R ++P+VFV GPM G + K A+V + FA Sbjct: 111 DGVFYIPNCDKITPGMLMASVRT-NVPSVFVSGGPMEAGRTKDGKSLSLASVFEGVGAFA 169 Query: 199 EGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLHLPGASFVNPNTPLRDELT 258 G +REELL E ++ G+C+ TAN+ L+E++G+ LPG + + R +L Sbjct: 170 SGSMSREELLEIEQSACPTCGSCSGMFTANSMNTLMEMLGVALPGNGTLVATSEGRHQLI 229 Query: 259 REAARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIAQAAGIQL 318 ++AA+ L ++ + +I+ ++AI ++ +A GGSTN LH LAIA A I Sbjct: 230 KDAAKHLMTLIEKD---IRPRDIITKEAIDDAFALDMAMGGSTNTVLHTLAIANEAEIDY 286 Query: 319 TWQDMSELSHVVPTLARIYPNGQADINHFQAAGGMSFLIRQLLD-GGLLHEDVQTVAGPG 377 D+++++ VP L++I P ++ AGG+S ++++L G +H + T++ Sbjct: 287 NISDINKIAERVPYLSKISPASDYSMDDVHKAGGVSAIMKELCQIEGAIHPERITIS--- 343 Query: 378 LRRYTREPFLEDGRLVWREGPERSL-DEAILRPLDKPFSAEGGLRLMEGNLG--RGVMKV 434 G+ +W + + ++ ++R D P+S+ GGL ++ GNL GV+KV Sbjct: 344 ------------GKTIWETVKDAEITNDEVIRRKDNPYSSVGGLSVLFGNLAPDGGVIKV 391 Query: 435 SAVAPEHQVVEAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPF 493 AV +V E +++ Q G++ V V+R++GP+ GMPE+ L P Sbjct: 392 GAVDASIKVFEGDAIVYNSQEEALEGINNGDVREGHVVVIRYEGPKGGPGMPEM--LAPT 449 Query: 494 LGVL-QDRGFKVALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGE 552 ++ + G KVAL+TDGR SGAS + H+SPEA GGP+A + +GD++ +D N Sbjct: 450 SSIVGRGLGTKVALITDGRFSGASRGISIG-HISPEAAEGGPIAFVENGDKITLDLTNRT 508 Query: 553 LRVLVDDAEWQARS---LEPAPQ 572 + + VDD E R EP P+ Sbjct: 509 ITLNVDDVELANRKEGWKEPEPK 531 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: 823 Number of extensions: 50 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: 608 Length of database: 555 Length adjustment: 36 Effective length of query: 572 Effective length of database: 519 Effective search space: 296868 Effective search space used: 296868 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 Apr 09 2024. 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