Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Echvi_2055 Echvi_2055 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__Cola:Echvi_2055 Length = 561 Score = 210 bits (535), Expect = 1e-58 Identities = 165/528 (31%), Positives = 247/528 (46%), Gaps = 50/528 (9%) Query: 48 GVAGCGSEDKHSLRMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGG 107 GVA CG E N N+ + S F E IK + + G F Sbjct: 41 GVASCGYES-------NPCNMHLNS--------------FAEDIKASTNQADLSG-FIFN 78 Query: 108 TPAMCDGVTQGEAGMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALR 167 T + DG + G +GM SLPSREVIA S + + FD + + CDK +PG++MG LR Sbjct: 79 TIGISDGQSMGTSGMRYSLPSREVIADSIESFILGHSFDGVVTIPGCDKNMPGVVMGMLR 138 Query: 168 FGHLPTIFVPGGPMPSGISNKEKADVRQRYA------EGKATREELLESEMKSYHSPGTC 221 P I V GG + SG EK ++ + G+ + E+ + + G C Sbjct: 139 VNR-PGIMVFGGTIRSGNYKGEKLNIVSAFEAYGKKINGQISDEDYMGVIKNACPGAGAC 197 Query: 222 TFYGTANTNQLLMEVMGLHLPGASFVNPYTPLRDALTHEAAQQVTRLTKQ--SGNFTPIG 279 TANT +E MGL LP F + Y P E + + + KQ + + P Sbjct: 198 GGMYTANTMSSAIEAMGLSLP---FSSSY-PATSKEKREECKNIGKYIKQLLALDIKP-K 252 Query: 280 EIVDERSLVNSIVALHATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN 339 +I+ ++SL N++ A GGSTN LH+ AIA+ AGI T +D ++ P L P+ Sbjct: 253 DIITKKSLENAVRVTVALGGSTNAALHILAIARTAGIDFTLEDFKRINAETPVLGDFKPS 312 Query: 340 GKADINHFQAAGGMAFLIRELLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPI 399 GK + GG+ ++ L GLLH D TV G+ ++ ++ +D P+ Sbjct: 313 GKFMMEDLYEMGGLPAFLKYFLNEGLLHGDCLTVTGKTMAENLED--ID---------PV 361 Query: 400 ESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLAD 459 + E+++ P+ P G L V+ GNL + + A VF D+ Sbjct: 362 KPSKESVIHPLDNPIKPSGHLCVLHGNLAPEGAVAKISGKEGKSFTGTAKVFDDEPSANA 421 Query: 460 AFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGK 518 A K E++K V V+R+ GP+ GMPE+ K T + + G VAL+TDGR SG + Sbjct: 422 AMKNKEIQKGDVVVIRYVGPKGGPGMPEMLKPTSII-IGAGLGSDVALITDGRFSGGTHG 480 Query: 519 IPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAARE 566 HV+PEA +GG + ++DGD+I +D + + V EFA R+ Sbjct: 481 FVVG-HVTPEAYLGGPIGLLKDGDVITIDAESLEIRVDVSEAEFAERK 527 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: 830 Number of extensions: 52 Number of successful extensions: 7 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: 561 Length adjustment: 36 Effective length of query: 572 Effective length of database: 525 Effective search space: 300300 Effective search space used: 300300 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