Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF723 PGA1_c07380 dihydroxy-acid dehydratase IlvD
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__Phaeo:GFF723 Length = 571 Score = 191 bits (486), Expect = 6e-53 Identities = 154/515 (29%), Positives = 250/515 (48%), Gaps = 43/515 (8%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGME-LSL 126 + I ++++++ + E +K+ + E AGG P ++ GE M+ ++ Sbjct: 41 IGICNTWSELTPCNSGLRDLAEGVKRGVWE-------AGGFPVEFPVMSLGETQMKPTAM 93 Query: 127 PSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGI- 185 R ++A+ ++ D ++LG CDK PG +MGA LP I V GPM +G Sbjct: 94 LFRNLLAMDVEESIRAYGIDGVVLLGGCDKTTPGQLMGAASVD-LPAIVVSSGPMLNGKW 152 Query: 186 ------SNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGL 239 S + + G+ T ++ + +E S G C GTA+T L+E MG+ Sbjct: 153 QGKDIGSGTDVWKFSEAVRAGEMTLQDFMAAESGMSRSKGVCMTMGTASTMASLVEAMGM 212 Query: 240 HLPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGG 299 LP + + R AL H +++ + ++ + P +++ + VN+I+A A GG Sbjct: 213 SLPTNAALPAVDARRMALAHLTGKRIVEMVEE--DIKP-SDVLTREAFVNAIMANAAVGG 269 Query: 300 STNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRE 359 STN +H+ A+A G +L+ D DL +P L + P+GK + F AGGM ++++ Sbjct: 270 STNAVVHLLALAGRVGAELSLDDF-DLGSDIPLLVNCMPSGKYLMEDFCYAGGMPVVLKQ 328 Query: 360 LLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGG 419 L + G L + TV G + Y + G + D I+S DE + P G Sbjct: 329 LADNGHLRSNT-TVLGGDILAYAE------GAECFNDDVIKSFDEPV--------KPAAG 373 Query: 420 LRVMEGNLG-RGVMKVSAVALQHQIV-EAPAVVFQDQQDLADAFKAGELE--KDFVAVMR 475 LRV+ GNL G + + A H + E A VF+ +D+ +L KD + V++ Sbjct: 374 LRVLRGNLAPNGAIVKPSAATDHLLEHEGVAHVFETIEDMKANIDRDDLPVTKDSILVLK 433 Query: 476 FQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSG-ASGKIPAAIHVSPEAQVGG 533 GP+ GMPE+ M ++++ + ++DGRMSG A G + +HVSPE+Q GG Sbjct: 434 GVGPKGYPGMPEVGNMPIPRKLVREGVRDMIRISDGRMSGTAFGTV--ILHVSPESQAGG 491 Query: 534 ALARVRDGDIIRVDGVKGTLELKVDADEFAAREPA 568 L V+ GD IRV GTL+L V +E AR A Sbjct: 492 PLGLVQTGDRIRVSAKNGTLDLLVSEEELTARREA 526 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: 840 Number of extensions: 46 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: 571 Length adjustment: 37 Effective length of query: 571 Effective length of database: 534 Effective search space: 304914 Effective search space used: 304914 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