Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate 203423 SO4345 dihydroxy-acid dehydratase (NCBI ptt file)
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__MR1:203423 Length = 619 Score = 221 bits (562), Expect = 9e-62 Identities = 191/591 (32%), Positives = 278/591 (47%), Gaps = 60/591 (10%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 +AI +S+ + H + + A+ E G + + T A+ DG+ G GM SLP Sbjct: 37 IAIANSFTQFVPGHVHLKDMGSLVASAIEEAGGIAK-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 LSDKLIKLDLVDAMVAAADSSVSDEDSAKIERSACPTCGSCSGMFTANSMNCLTEALGLS 214 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTK----QSGNFTPIGEIVDERSLVNSIVALHA 296 LPG + R L EA ++V LTK Q I ++ N+ A Sbjct: 215 LPGNGSMLATHSDRRELFLEAGRRVMALTKRYYEQDDTSALPRNIACFKAFENATALDIA 274 Query: 297 TGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGGMAF 355 GGS+N LH+ A AQ A + T D+ +S +VP L V P+ K + AGG+ Sbjct: 275 MGGSSNTVLHLLAAAQEAEVAFTMDDIDRMSRLVPHLCKVAPSTPKYHMEDVHRAGGVMG 334 Query: 356 LIRELLEAGLLHEDVNTVAGRG-------LSRY----TQEPFLDNGKLVWRDGPI----- 399 ++ EL AGLLH DV VA L++Y TQ+ DN K + GP Sbjct: 335 ILGELDRAGLLHTDVPHVAADAGGNLKSVLAKYDVMQTQD---DNVKQFFMAGPAGIPTT 391 Query: 400 ---------ESLD----ENILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQIV 444 SLD E +R AFS EGGL V+ GNL ++K + V + I Sbjct: 392 KAFSQDCRWPSLDDDRREGCIRSREFAFSQEGGLAVLSGNLAENGCIVKTAGVDESNLIF 451 Query: 445 EAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGF-- 502 A V++ Q D GE+ V V+R++GP+ G P + +M L+ RG Sbjct: 452 VGSARVYESQDDAVAGILGGEVVAGDVVVIRYEGPK--GGPGMQEMLYPTSYLKSRGLGK 509 Query: 503 KVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEF 562 AL+TDGR SG + + HVSPEA GG +A + +GD I +D +++L V E Sbjct: 510 ACALITDGRFSGGTSGLSIG-HVSPEAAAGGTIALIENGDRIEIDIPARSIKLAVSDAEL 568 Query: 563 AAREPAKGLLGNNVGS--GRELFGFM-----RMAFSSAEQGASAFTSALEN 606 A R G GRE F M M +SA++GA S LE+ Sbjct: 569 AGRRETMLARGPMAWKPVGRERFVSMALKAYAMLATSADKGAVRDRSKLED 619 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: 931 Number of extensions: 51 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: 619 Length adjustment: 37 Effective length of query: 571 Effective length of database: 582 Effective search space: 332322 Effective search space used: 332322 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