Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF233 Psest_0234 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__psRCH2:GFF233 Length = 612 Score = 214 bits (545), Expect = 9e-60 Identities = 166/534 (31%), Positives = 262/534 (49%), Gaps = 40/534 (7%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 +AI +S+ + H + + + + + + G V + T A+ DG+ G GM SLP Sbjct: 37 IAIANSFTQFVPGHVHLKDLGQLVAREIEKHGGVAK-EFNTIAVDDGIAMGHDGMLYSLP 95 Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGIS- 186 SRE+IA S ++ + DA + + CDKI PG++M ALR ++P +FV GGPM +G + Sbjct: 96 SREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMAALRL-NIPVVFVSGGPMEAGKTK 154 Query: 187 ----NKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLP 242 + D A+ A+ E++ E E + + G+C+ TAN+ L E +GL LP Sbjct: 155 LASHGLDLVDAMVIAADESASDEKVAEYERSACPTCGSCSGMFTANSMNCLAEALGLALP 214 Query: 243 GASFVNPYTPLRDALTHEAAQQVTRLTKQ---SGNFTPI-GEIVDERSLVNSIVALHATG 298 G R+ L A + V L K+ G+ + + I R+ N++ A G Sbjct: 215 GNGSTLATHSDREQLFLRAGRTVVELCKRYYGEGDESVLPRNIASRRAFENAMTLDIAMG 274 Query: 299 GSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGGMAFLI 357 GSTN LH+ A AQ A + + + LS VP L V PN K + AGG+ ++ Sbjct: 275 GSTNTILHLLAAAQEAEVDFDLRAIDALSRKVPQLCKVAPNIQKYHMEDVHRAGGIFSIL 334 Query: 358 RELLEAGLLHEDVNTVAGR----GLSRYTQEPFLDNG-KLVWRDGPI------------- 399 EL GLLH DV TV R G++++ D ++ GP Sbjct: 335 GELARGGLLHTDVPTVHSRTLAEGIAQWDITQTQDEAVHTFFKAGPAGIPTQTAFSQSTR 394 Query: 400 -ESLDEN----ILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQIVEAPAVVFQ 452 +SLD++ +R V A+S EGGL V+ GN+ V+K + V + E A +++ Sbjct: 395 WDSLDDDRENGCIRSVEHAYSQEGGLAVLYGNIALDGCVVKTAGVDESIHVFEGTAKIYE 454 Query: 453 DQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGR 511 Q A E++ + ++R++GP+ GM E+ T +L + G AL+TDGR Sbjct: 455 SQDSAVKGILADEVKAGDIVIIRYEGPKGGPGMQEMLYPTSYL-KSKGLGKDCALLTDGR 513 Query: 512 MSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAR 565 SG + + H SPEA GGA+ VRDGD + +D +++L+V +E + R Sbjct: 514 FSGGTSGLSIG-HASPEAAAGGAIGLVRDGDKVLIDIPNRSIQLQVSDEELSHR 566 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: 871 Number of extensions: 58 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: 612 Length adjustment: 37 Effective length of query: 571 Effective length of database: 575 Effective search space: 328325 Effective search space used: 328325 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 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