Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011159013.1 TX73_RS17715 dihydroxy-acid dehydratase
Query= curated2:B8FU95 (563 letters) >NCBI__GCF_000195775.1:WP_011159013.1 Length = 602 Score = 282 bits (722), Expect = 2e-80 Identities = 198/546 (36%), Positives = 280/546 (51%), Gaps = 29/546 (5%) Query: 23 GLTDRELS--KPFIGVVNSFTELVPGHMHLRQVTEAVKAGIRENGGTPFEFSTIAVCDGI 80 GLT EL KP IG+ + +L P + H + V+ GIR GG EF + + Sbjct: 39 GLTRAELQSGKPIIGIAQTGNDLSPCNRHHLDLAHRVREGIRAAGGIAMEFPVHPIQETG 98 Query: 81 AMGHEGMHYSLASREIVADAIEVMAKGHQLDALVLIPSCDKVVPGMLMAAMRLNIPAIVV 140 + +LA +V EV+ G+ LD +VL CDK P LMAA +NIPAIV+ Sbjct: 99 KRPTAALDRNLAYLGLV----EVLF-GYPLDGVVLTTGCDKTTPACLMAAATVNIPAIVL 153 Query: 141 SGGPMLPGRFEGNPVTLSTV-FEGVGQVHAGKKDEAWLHELEAKACPTCGSCAGMFTANS 199 SGGPML G G TV ++ ++ AG+ D E+ A + P+ G C M TA++ Sbjct: 154 SGGPMLNGWHNGERTGSGTVVWKSRERLAAGEIDYEQFMEIVASSAPSVGHCNTMGTAST 213 Query: 200 MNCLTEALGMALPGNGTIPAVYSERLVLAKETGYQVMELYRQDLKPRDIVTQSTLKNGVA 259 MN L EALGM+LPG IPA Y ER +A ETG + +E+ +DLKP DI+T+ +N + Sbjct: 214 MNSLAEALGMSLPGCAAIPAPYRERGQIAYETGVRAVEMVWEDLKPSDILTRKAFENAIV 273 Query: 260 VDMALGCSTNTILHLPAIANEGDIDWDLGKVNEVSEKTPQICKLAPASETPLAALHEAGG 319 V+ A+G STN +HL A+A ++ + V P + L PA H AGG Sbjct: 274 VNSAIGGSTNAPIHLNALARHVGVELSIDDWQSVGHAIPLLVNLQPAGLYLGEEYHRAGG 333 Query: 320 VSAVLKQLLDAGLIDGSTMTVSGVTMAERLKDAKVVDTEIIRPQSNPFSQRGGLRILFGN 379 V V+ +L+ G I +TV+G TM E A D ++I P G +L GN Sbjct: 334 VPTVVGELMRHGKIHQDALTVNGKTMGENCASAPAPDGDVIHRYDTPLVHDAGFLVLRGN 393 Query: 380 LAPEGAVIKQGALS-----------SQDFVFEGSAKVFNGEVPAAEAIRN--LEIKAGDV 426 L + A++K +S FEG A VF G I + L+I + Sbjct: 394 LF-DSAIMKTSVISLEFRERYLSNPKDPNAFEGRAIVFEGPEDYHHRIDDPALDIDEHCI 452 Query: 427 VVIRYEGPKGGPGMREMLG--PTATLAGMGLDSDVALLTDGRFSGASRGLSIGHVSPEAA 484 + +R GP G PG E++ P A L G+ S + + DGR SG S SI + +PEAA Sbjct: 453 LFVRGTGPIGYPGGAEVVNMQPPAALIKRGIHS-LPCIGDGRQSGTSGSPSILNATPEAA 511 Query: 485 LGGDIALLKDGDKIRIDIGKGRLEWIVSEEEREQRRQEFAAMA--VKPDHLKP--ELRQG 540 G +ALLK GD++RID+ KG + ++S+EE +QRR + AA P H P EL + Sbjct: 512 ANGGLALLKTGDRVRIDLNKGSADILISDEELKQRRADLAAHGGFAYPKHQTPWQELYRS 571 Query: 541 YLGRYA 546 +G++A Sbjct: 572 TVGQHA 577 Lambda K H 0.317 0.135 0.390 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: 799 Number of extensions: 47 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 563 Length of database: 602 Length adjustment: 36 Effective length of query: 527 Effective length of database: 566 Effective search space: 298282 Effective search space used: 298282 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