Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate 5207771 Shew_0292 dihydroxy-acid dehydratase (RefSeq)
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__PV4:5207771 Length = 616 Score = 208 bits (529), Expect = 6e-58 Identities = 182/584 (31%), Positives = 268/584 (45%), Gaps = 49/584 (8%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 VAI +S+ + H + + A+ E G + + T A+ DG+ G GM SLP Sbjct: 37 VAIANSFTQFVPGHVHLKDMGSLVAGAIEEAGGIAK-EFNTIAVDDGIAMGHGGMLYSLP 95 Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG--- 184 SRE+IA S ++ + DA + + CDKI PG++M ALR ++P +FV GGPM +G Sbjct: 96 SRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRL-NIPVVFVSGGPMEAGKTK 154 Query: 185 ISNK----EKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 +S+K + D A+ + + E+ + E + + G+C+ TAN+ L E +GL Sbjct: 155 LSDKLIKLDLVDAMVAAADDRVSDEDSEKIERSACPTCGSCSGMFTANSMNCLTEALGLS 214 Query: 241 LPGASFVNPYTPLRDALTHEAAQQV----TRLTKQSGNFTPIGEIVDERSLVNSIVALHA 296 LPG + R L EA ++V R + I ++ N++ A Sbjct: 215 LPGNGSLLATHSDRRELFLEAGRRVMALANRYYRDDDESALPRNIASFKAFENAMALDIA 274 Query: 297 TGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGGMAF 355 GGS+N LH+ A AQ A + T D+ LS VP L V P+ K + AGG+ Sbjct: 275 MGGSSNTVLHLLAAAQEAKVDFTMADIDRLSRQVPHLCKVAPSTPKYHMEDVHRAGGVMG 334 Query: 356 LIRELLEAGLLHEDVNTVAGRGLS----RYTQEPFLDNG-KLVWRDGPI----------- 399 ++ EL AGLLH DV+ VAG L +Y D + + GP Sbjct: 335 ILGELDRAGLLHTDVSHVAGENLKAVLVQYDLVQTQDEAVQQFYAAGPAGIPTTKAFSQS 394 Query: 400 ---ESLD----ENILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQIVEAPAVV 450 SLD E +R AFS EGGL V+ GN+ ++K + V + A V Sbjct: 395 CRWPSLDVDRQEGCIRTREFAFSQEGGLAVLSGNIAADGCIVKTAGVDEANHTFVGHARV 454 Query: 451 FQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTD 509 ++ Q D GE+ V V+R++GP+ GM E+ T +L + G AL+TD Sbjct: 455 YESQDDAVAGILGGEVVAGDVVVIRYEGPKGGPGMQEMLYPTSYL-KSKGLGTSCALITD 513 Query: 510 GRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAREPAK 569 GR SG + + HVSPEA GG +A V GD I +D ++ L V + R A Sbjct: 514 GRFSGGTSGLSIG-HVSPEAAAGGTIALVETGDRIEIDIPARSITLAVSDEVLETRRQAM 572 Query: 570 GLLG-------NNVGSGRELFGFMRMAFSSAEQGASAFTSALEN 606 G N S M +SA++GA S LE+ Sbjct: 573 QARGKQAWKPVNRERSVSLALKAYAMLATSADKGAVRDVSKLED 616 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: 894 Number of extensions: 54 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 608 Length of database: 616 Length adjustment: 37 Effective length of query: 571 Effective length of database: 579 Effective search space: 330609 Effective search space used: 330609 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