Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_106711690.1 CU102_RS13880 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >NCBI__GCF_003010955.1:WP_106711690.1 Length = 557 Score = 224 bits (572), Expect = 6e-63 Identities = 158/468 (33%), Positives = 240/468 (51%), Gaps = 28/468 (5%) Query: 107 GTPAMCDGVTQGEAGMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGAL 166 GTP + DG+ G GM+ SL SREVIA ++ D L++G CDK +PG M+ Sbjct: 76 GTPTISDGMAMGTEGMKYSLISREVIADCIETCVNGQWMDGVLVIGGCDKNMPGGMIAIA 135 Query: 167 RFGHLPTIFVPGGPMPSG------ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGT 220 R ++P I+V GG + G +S + + GK + E+ E + S G+ Sbjct: 136 RT-NVPAIYVYGGTIKPGKWKGKDLSIVSSFEAVGSFMAGKMSEEDFEGIERHACPSTGS 194 Query: 221 CTFYGTANTNQLLMEVMGLHLPGAS-FVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIG 279 C TANT E +G+ L +S NP D+ T E+A+ + ++ N P Sbjct: 195 CGGMYTANTMSSAFEALGMSLMSSSTMANPDAEKVDS-TAESARVLVEAVRR--NIRP-R 250 Query: 280 EIVDERSLVNSIVALHATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN 339 +I+ +S+ N++ + ATGGSTN LH AIA AA ++ T D + VP L ++ P+ Sbjct: 251 DIITRKSIENAVALIMATGGSTNGVLHFLAIAHAAEVEWTLDDFERVRRKVPVLCNLRPS 310 Query: 340 GKADINHFQAAGGMAFLIRELLEAGLLHEDVNTVAGRGLS-RYTQEPFLDNGKLVWRDGP 398 G+ GG+ +++ LL AGLLH D T+ GR L+ P D P Sbjct: 311 GQYMAVDLHKVGGIPQVLKILLNAGLLHGDCLTITGRTLADELAHIP----------DSP 360 Query: 399 IESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLA 458 D+NI+RP+ +A EG L +++GNL G L++ +++ PA VF D+Q Sbjct: 361 --PADQNIIRPIDKALYKEGHLAILKGNLATGGAVAKITGLKNPVIKGPARVFDDEQSAM 418 Query: 459 DAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASG 517 DA + ++ V V+R+ GP+ GMPE+ T + + + G V L+TDGR SG + Sbjct: 419 DAILSDKIRPGDVLVLRYLGPKGGPGMPEMLAPTSAI-IGRGLGESVGLITDGRFSGGTW 477 Query: 518 KIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAR 565 + HV+PEA GG +A VR+GD+I +D + L+L VD E R Sbjct: 478 GMVVG-HVTPEAFEGGTIALVREGDMITIDAHQQLLQLDVDEAELEKR 524 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: 886 Number of extensions: 56 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 24 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