Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011842504.1 RSPH17029_RS18285 dihydroxy-acid dehydratase
Query= curated2:A0Q0E8 (554 letters) >NCBI__GCF_000015985.1:WP_011842504.1 Length = 599 Score = 280 bits (716), Expect = 1e-79 Identities = 192/536 (35%), Positives = 283/536 (52%), Gaps = 37/536 (6%) Query: 23 GYTPEDLK--KPLIGIVNSHNEIIPGHFHLNEIVQAVKLGVASAGGTPIEIPSIGICDGI 80 G T +L+ KP+IGI + +++ P + H E+ + V+ G+ +AGG P+EIP I Sbjct: 38 GLTRAELQGGKPIIGIAQTGSDLSPCNRHHIELAKRVRDGITAAGGIPMEIPVHPI---- 93 Query: 81 SMNHSGMKYPLAS--RELIADSIEAMTIAHKFDALVLVGNCDKIVPGMLMGAARLNVPAI 138 +G K P AS R L + + D +VL CDK P +LM AA +N+PAI Sbjct: 94 --QETG-KRPTASLDRNLAYLGLVEALHGYPIDGVVLTIGCDKTTPALLMAAATVNIPAI 150 Query: 139 YVSGGPMLPGKLKGKKIDLVHGAFEAVGSYAEGILSDDDLNKIEQHSCPTCGSCAGLFTA 198 S GPML G +G++ + A A G + ++ ++ S P+ G C + TA Sbjct: 151 AYSVGPMLNGWHRGERAGSGTAVWRARELLARGEIDEEGFYELVASSAPSVGYCNTMGTA 210 Query: 199 NSMNSLAEALGVALPGNGTIPAPYGRRKQLAKYAGVKIMELVKKKIKLRDILTKEAFKNA 258 ++MNSLAE LG+ LPG+ IPAPY R Q+ G +I+E+V + ++ DILT+EAF+NA Sbjct: 211 STMNSLAEVLGMQLPGSAAIPAPYRERGQMGHATGRRIVEMVWEDLRPSDILTREAFENA 270 Query: 259 IALDMAIGGSSNTTLHLMAIAHEAKVYLTLEDFDEISRRIPHITKLSPAGTHHMVDLDEA 318 I A+GGS+N +HL A+A A V L +D+ + +P + L PAGT+ D A Sbjct: 271 IVACSALGGSTNAPIHLNAVARHAGVALDNDDWQRLGHAVPLLVNLQPAGTYLGEDFYRA 330 Query: 319 GGISAVLKELMDANLI-FKDQLTVTGKTLEENIKNSLVLNDSVIRPLNNPYSNEGGIAIL 377 GG+ AVL EL+ A+L+ + TV G L S L VIRP+ P E G L Sbjct: 331 GGVPAVLGELLAADLLPHPEAPTVFGTPLSAGAMRS--LETDVIRPVVEPLKGEAGFINL 388 Query: 378 RGNLAPDGAVVKQSAVEPEMLYH-----------KGVARVFDGEELAFDAIMNKKIHPGD 426 GNL D A++K S + P+ +G VFDG E I + + G+ Sbjct: 389 SGNLF-DSAIMKTSVISPDFRARYLSDPADPEAFEGTVFVFDGPEHFHAVIDDPALGMGE 447 Query: 427 --VVVIRYEGPKGCPGMREMLS--PTAAIIGLGLEKSTALITDGRFSGGTRGPCIGHISP 482 V+V+R GP G PG E+++ P A ++ G+ + I DGR SG + P I + SP Sbjct: 448 DAVLVMRGAGPLGYPGAAEVVNMRPPAYLLKRGI-PAVPCIGDGRQSGTSGSPSILNASP 506 Query: 483 EASEGGPIALIEEGDLIEIDISNRRISLLVSPEELSKRKE------NWIQPPCKAP 532 EA+ GG +AL+ GD I +D+ R+ +L+ EEL R+ + PP + P Sbjct: 507 EAAAGGGLALLRNGDRIRVDLRRGRVDVLLPDEELEARRTALAEAGGYAMPPSQTP 562 Lambda K H 0.317 0.136 0.392 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: 848 Number of extensions: 40 Number of successful extensions: 5 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: 554 Length of database: 599 Length adjustment: 36 Effective length of query: 518 Effective length of database: 563 Effective search space: 291634 Effective search space used: 291634 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 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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