Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate 3607836 Dshi_1244 Dihydroxy-acid dehydratase (RefSeq)
Query= curated2:P31961 (608 letters) >FitnessBrowser__Dino:3607836 Length = 569 Score = 172 bits (436), Expect = 3e-47 Identities = 148/511 (28%), Positives = 236/511 (46%), Gaps = 43/511 (8%) Query: 68 VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLA 127 + I + ++++ + +K+ + E G F P M G TQ +P ++ Sbjct: 41 IGICNTWSELTPCNHGLRTLAEGVKRGVWEAGG---FPVEFPVMSLGETQMKP---TAML 94 Query: 128 SRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGI-- 185 R+++AM ++ D + LG CDK PG L+G+ LP++ V AGPM G Sbjct: 95 FRNLLAMDVEESIRAYGMDGVVLLGGCDKTTPGQLMGAASVD-LPSIVVSAGPMLNGKYR 153 Query: 186 -----SNKEKAAVRQLFAEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLH 240 S + + G+ T + + +E + G C GTA+T LVE MG+ Sbjct: 154 GQDIGSGTDVWKFSEAVRAGEMTLADFMNAEAGMSRSAGVCMTMGTASTMASLVEAMGMS 213 Query: 241 LPGASFVNPNTPLRDELTREAARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGGS 300 LP + + R L ++ + E+ + + I+ + A N+++A A GGS Sbjct: 214 LPLNAALPAVDARRMALAHLTGKRIVEMVEED---LRPSAILTKPAFENAILANAAVGGS 270 Query: 301 TNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQADINHFQAAGGMSFLIRQL 360 TN +HLLA+A AG+ LT +D E+ +P L P+G+ + F AGGM ++ +L Sbjct: 271 TNAVMHLLALAGRAGVDLTLKDF-EIGGEIPLLVNCMPSGKYLMEDFAYAGGMPVVLSEL 329 Query: 361 LDGGLLHEDVQTVAGPGLRRYTREPFLEDGRLVWREGPERSLDEAILRPLDKPFSAEGGL 420 D TV G + YT EG E + ++ D P GL Sbjct: 330 RDH---LRPATTVLGKDIAAYT-------------EGAE-CFNRDVIHAYDAPVKPAAGL 372 Query: 421 RLMEGNLGR--GVMKVSAVAPEHQVVEAPVRIFHDQASLAAAFKAGELE--RDLVAVVRF 476 R++ G+L ++K SA E P +F + + A +L D + V++ Sbjct: 373 RVLRGSLAPDGAIVKPSAATDALLEHEGPAFVFENIEDMKANIDRDDLPITPDTILVLKG 432 Query: 477 QGPRAN-GMPELHKLTPFLGVLQDRGFKVALVTDGRMSG-ASGKVPAAIHVSPEAIAGGP 534 GP+ GMPE+ + ++++ + V+D RMSG A G V +HV+PEA AGGP Sbjct: 433 CGPKGYPGMPEVGNMPIPAKLVREGVRDMIRVSDARMSGTAYGTV--ILHVAPEAQAGGP 490 Query: 535 LARLRDGDRVRVDGVNGELRVLVDDAEWQAR 565 LA ++ GDR+RV G L +LVD E AR Sbjct: 491 LALVKTGDRIRVSAREGVLDLLVDATELAAR 521 Lambda K H 0.319 0.135 0.397 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: 790 Number of extensions: 56 Number of successful extensions: 8 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: 569 Length adjustment: 37 Effective length of query: 571 Effective length of database: 532 Effective search space: 303772 Effective search space used: 303772 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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