Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate BPHYT_RS04815 BPHYT_RS04815 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__BFirm:BPHYT_RS04815 Length = 557 Score = 214 bits (546), Expect = 6e-60 Identities = 150/470 (31%), Positives = 242/470 (51%), Gaps = 26/470 (5%) Query: 107 GTPAMCDGVTQGEAGMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGAL 166 GTP + DG++ G GM+ SL SREVI+ + D +++G CDK +PG M+G L Sbjct: 76 GTPTISDGMSMGTEGMKYSLVSREVISDCIETCVQGQWMDGVVVIGGCDKNMPGGMIGML 135 Query: 167 RFGHLPTIFVPGGPMPSG------ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGT 220 R ++P+I+V GG + G ++ + + G+ ++E+ E + S G+ Sbjct: 136 RT-NVPSIYVYGGTIRPGNWKGTDLTIVSSFEAVGEFTAGRMSQEDFDGIEQNACPSTGS 194 Query: 221 CTFYGTANTNQLLMEVMGLHLPGAS-FVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIG 279 C TANT E +G+ L +S NP D+ A V + K + P Sbjct: 195 CGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVESVKK---DLKP-R 250 Query: 280 EIVDERSLVNSIVALHATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN 339 +IV ++S+ N++ + ATGGSTN LH AIA AA ++ + D + + VP + ++ P+ Sbjct: 251 DIVTKKSIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWSIDDFERMRKKVPVICNLKPS 310 Query: 340 GKADINHFQAAGGMAFLIRELLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPI 399 G+ AGG+ +++ LL+AGLLH D T+ GR ++ ++ GK Sbjct: 311 GQFVATDLHKAGGIPQVMKILLDAGLLHGDCITITGRTIAEELKDV---PGK-------- 359 Query: 400 ESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLAD 459 D+ ++ P+ +A EG L +++GNL L++ ++ PA VF D+Q + Sbjct: 360 PRADQQVIFPIDQALYKEGHLAILKGNLAVDGAVAKITGLKNPVITGPARVFDDEQSALE 419 Query: 460 AFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGK 518 A A ++ V V+R+ GP+ GMPE+ T + + + G V L+TDGR SG + Sbjct: 420 AILADKIVAGDVVVLRYLGPKGGPGMPEMLAPTSAI-IGKGLGESVGLITDGRFSGGTWG 478 Query: 519 IPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAREPA 568 + HV+PEA VGG +A V++GD I +D K L+L +D E R A Sbjct: 479 MVVG-HVAPEAFVGGTIAFVQEGDSITIDAHKLLLQLNIDNAELERRRAA 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: 811 Number of extensions: 53 Number of successful extensions: 6 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: 557 Length adjustment: 36 Effective length of query: 572 Effective length of database: 521 Effective search space: 298012 Effective search space used: 298012 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