Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_148649357.1 V474_RS08210 dihydroxy-acid dehydratase family protein
Query= curated2:B8FU95 (563 letters) >NCBI__GCF_001046635.1:WP_148649357.1 Length = 597 Score = 308 bits (789), Expect = 4e-88 Identities = 211/569 (37%), Positives = 305/569 (53%), Gaps = 29/569 (5%) Query: 16 RSLLKALGLTDRELSKPFIGVVNSFTELVPGHMHLRQVTEAVKAGIRENGGTPFEFSTIA 75 R L L + + + +P IG+ S ++LVP + H + E VK GIR+ GG P EF T Sbjct: 29 RYLNYGLSIEEMQSDRPIIGIAQSGSDLVPCNRHHLVLAERVKEGIRDAGGIPIEFPTHP 88 Query: 76 VCDGIAMGHEGMHYSLASREIVADAIEVMAKGHQLDALVLIPSCDKVVPGMLMAAMRLNI 135 + + G+ +LA +V EV+ G+ LD +VL CDK P LMAA +NI Sbjct: 89 LQETGKRPTAGLDRNLAYISLV----EVLY-GYPLDGVVLTIGCDKTTPSALMAAATVNI 143 Query: 136 PAIVVSGGPMLPGRFEGNPVTLSTVFEGVGQVHA-GKKDEAWLHELEAKACPTCGSCAGM 194 PAI +S GPML G EG T+ Q+ A G+ D A +L A P+ G C M Sbjct: 144 PAIALSVGPMLNGWHEGERTGAGTIVWKARQMLAKGELDYAGFLKLVASGSPSTGYCNTM 203 Query: 195 FTANSMNCLTEALGMALPGNGTIPAVYSERLVLAKETGYQVMELYRQDLKPRDIVTQSTL 254 TA +MN L EALGM+LPG+ IPA Y +R A ETG ++E+ + D KP DI+T+ Sbjct: 204 GTATTMNSLAEALGMSLPGSAAIPAPYRDRQECAWETGRAIVEMVKADRKPSDILTREAF 263 Query: 255 KNGVAVDMALGCSTNTILHLPAIANEGDIDWDLGKVNEVSEKTPQICKLAPASETPLAAL 314 N + V+ A+G STN +HL AIA ++ L P + L PA E Sbjct: 264 LNAIRVNSAIGGSTNAPIHLNAIARHIGVELTLEDWETTGADVPLLVNLQPAGEYLGEDY 323 Query: 315 HEAGGVSAVLKQLLDAGLIDGSTMTVSGVTMAERLKDAKVVDTEIIRPQSNPFSQRGGLR 374 + AGGV AV+ +L AGLIDG+ +T +G T+AE L ++ D ++IRP P + GL Sbjct: 324 YRAGGVPAVMGELSKAGLIDGAVLTANGRTVAENLVGVRIHDDKVIRPIDRPLKEAAGLT 383 Query: 375 ILFGNLAPEGAVIKQGALSSQ-----------DFVFEGSAKVFNGEVPAAEAI--RNLEI 421 +L GNL EGAV+K +S + FEG+ VF+G I +L I Sbjct: 384 VLSGNLF-EGAVMKLSVISDEFRGRYLSDPANPDAFEGNVVVFDGPEDYHHRIDEPDLGI 442 Query: 422 KAGDVVVIRYEGPKGGPGMREMLG--PTATLAGMGLDSDVALLTDGRFSGASRGLSIGHV 479 ++VIR GP G PG E++ P A L G+ + + + DGR SG S SI + Sbjct: 443 DENSILVIRGAGPVGYPGGAEVVNMRPPAALIRAGVHA-LPCIGDGRQSGTSGSPSILNA 501 Query: 480 SPEAALGGDIALLKDGDKIRIDIGKGRLEWIVSEEEREQRRQEFAAM--AVKPDHLKP-- 535 SPEAA+GG +ALL+ GD++RID+ +V E E ++RR + AA+ + P+ P Sbjct: 502 SPEAAVGGGLALLRTGDRVRIDLKARSANMLVDEAELDRRRADLAAVEDTITPESQTPWQ 561 Query: 536 ELRQGYLGRYA--YFVQSASKGAALRRVK 562 E+++ +G++A ++SA K + ++K Sbjct: 562 EIQRDLVGQFATGAVIESAVKYQRIAQIK 590 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: 797 Number of extensions: 50 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: 563 Length of database: 597 Length adjustment: 36 Effective length of query: 527 Effective length of database: 561 Effective search space: 295647 Effective search space used: 295647 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 Jul 26 2024. The underlying query database was built on Jul 25 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