Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Ac3H11_954 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_954 Length = 567 Score = 226 bits (576), Expect = 2e-63 Identities = 159/510 (31%), Positives = 255/510 (50%), Gaps = 29/510 (5%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 V + + ++ + + + + + E G Q G TP + DG+ G GM+ SL Sbjct: 46 VGVANGHSTITPCNSGLQKLADAAIAGIEEAGGNAQVFG-TPTISDGMAMGTEGMKYSLV 104 Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGISN 187 SREVI+ + D L++G CDK +PG +MG LR ++P I+V GG + G Sbjct: 105 SREVISDCIETCVGGQWMDGVLVVGGCDKNMPGGLMGMLR-ANVPAIYVYGGTILPGHYQ 163 Query: 188 KEKADVRQRY------AEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHL 241 + ++ + A GK + +L E E ++ G+C TANT E +G+ L Sbjct: 164 GKDLNIVSVFEAVGENAAGKLSDFDLKEIEKRAIPGTGSCGGMYTANTMSSAFEALGISL 223 Query: 242 PGAS-FVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300 P +S NP+ ++ A + + K + P +IV ++S+ N++ + ATGGS Sbjct: 224 PYSSTMANPHDEKMNSAKESAKVLIEAIKK---DIKP-RDIVTKKSIENAVAVIMATGGS 279 Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360 TN LH AIA AAG++ + D + P L + P+GK AGG+ +++ L Sbjct: 280 TNAVLHFLAIAHAAGVEWSIDDFERVRVKTPVLCDLKPSGKYLAVDLHRAGGIPQVMKVL 339 Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIE-SLDENILRPVARAFSPEGG 419 L AGLLH D T+ G+ ++ V +D P + D++++RP+ +G Sbjct: 340 LNAGLLHGDCLTIEGKTVAE------------VLKDVPDQPRADQDVIRPINNPMYAQGH 387 Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479 L +++GNL L++ ++ PA VF+D+Q +A AG+++ V V+R+ GP Sbjct: 388 LAILKGNLSPEGAVAKITGLKNPVITGPARVFEDEQSALEAILAGKIKAGDVMVLRYLGP 447 Query: 480 RSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARV 538 + GMPE+ T L + G V L+TDGR SG + + HV+PEA GG +A V Sbjct: 448 KGGPGMPEMLAPTGAL-IGAGLGESVGLITDGRFSGGTWGMVVG-HVAPEAAAGGTIAFV 505 Query: 539 RDGDIIRVDGVKGTLELKVDADEFAAREPA 568 +GD I +D + LEL V +E A R A Sbjct: 506 HEGDSITIDARQLLLELNVSEEEIARRRAA 535 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: 900 Number of extensions: 57 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: 567 Length adjustment: 37 Effective length of query: 571 Effective length of database: 530 Effective search space: 302630 Effective search space used: 302630 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