Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_011973396.1 MAEO_RS03385 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >NCBI__GCF_000017185.1:WP_011973396.1 Length = 550 Score = 244 bits (623), Expect = 7e-69 Identities = 173/545 (31%), Positives = 278/545 (51%), Gaps = 41/545 (7%) Query: 32 SDGPQRGKLQCANFAHGVAGCGSEDKHSLRMMNAANVAIVSSYNDMLSAHQPYEHFPEQI 91 SD ++G + N + + CG D+ + + IV+S+ +++ H E Sbjct: 3 SDNLKKGVSRAPNRSL-LKACGYTDEE----IEKPFIGIVNSFTEVVPGHIHLNTLAEAA 57 Query: 92 KKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLPSREVIALSTAVALSHNMFDAALML 151 KK + G F T A+CDG+ G GM SLPSRE+IA + + FD +++ Sbjct: 58 KKGVYANGGT-PFEFNTMAVCDGIAMGHEGMRYSLPSREIIADTVESMAKAHGFDGLVLI 116 Query: 152 GICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGISNKEKADVRQ------RYAEGKATRE 205 CDKIVPG++MGALR ++P I + GGPM G + +K D+ Y GK T+E Sbjct: 117 PSCDKIVPGMIMGALRL-NIPFIVITGGPMQPGELHGKKYDLISVFEGVGEYNVGKITKE 175 Query: 206 ELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVNPYTPLRDALTHEAAQQV 265 EL+E E + G+C TAN+ L E +GL LP + + + + + ++ Sbjct: 176 ELMEIETCACPGAGSCAGLFTANSMACLTETLGLSLPMCATTHATDAEKVRIAKRSGMKI 235 Query: 266 TRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIA-QAAGIQLTWQDMA 324 L K+ T +++ + S N+I+ A GGS+N TLH+PA+A + A +T D Sbjct: 236 VDLVKEDIKPT---DLLTKESFENAILVDLALGGSSNTTLHIPALAYEIAPEFITLDDFD 292 Query: 325 DLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLEAGLLHEDVNTVAGRGLSRYTQE 384 L + VP ++ + P G I+ AGG+ +++ +LE + D NTV+G+ + E Sbjct: 293 RLCDEVPHIASLRPGGDHFISDLHRAGGIPAVLK-ILEQKI--RDANTVSGKSIKEIINE 349 Query: 385 PFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQ 442 ++ +D NI+RPV + GLR+++GN+ V+K+SAV + Sbjct: 350 --------------VKYIDYNIIRPVDKPVHETAGLRILKGNIAPDGCVVKISAVNPKMY 395 Query: 443 IVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGF 502 E PA VF +++ DA G++++ V V+R++GP G P + +M + G Sbjct: 396 KHEGPARVFNSEEETIDAILGGDIKEGDVVVIRYEGPA--GGPGMREMLSPTSAICGMGL 453 Query: 503 --KVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDAD 560 VAL+TDGR SG S + P H+SPEA GG +A + +GDII +D + + LK+ + Sbjct: 454 DDSVALITDGRFSGGS-RGPCIGHISPEAMAGGPIAIIEEGDIIAIDMMAKEINLKISEE 512 Query: 561 EFAAR 565 E R Sbjct: 513 EIKER 517 Lambda K H 0.318 0.134 0.386 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: 853 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: 550 Length adjustment: 36 Effective length of query: 572 Effective length of database: 514 Effective search space: 294008 Effective search space used: 294008 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 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