Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_012385795.1 BIND_RS14500 dihydroxy-acid dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000019845.1:WP_012385795.1 Length = 599 Score = 298 bits (763), Expect = 4e-85 Identities = 197/549 (35%), Positives = 307/549 (55%), Gaps = 41/549 (7%) Query: 23 GLIDEELR--RPLIGVANSWNEIVP-GHVHLDKVAEAVKAGIRMAGGTPLEFGTIAVCDG 79 GL +EL+ +P+IG+A + +++ P HL+ +A+ V+ GIR AGG +EF + + Sbjct: 36 GLTAKELQSGKPIIGIAQTGSDLSPCNRPHLE-LAKRVREGIREAGGIAIEFPVHPIQE- 93 Query: 80 IAMGHEGMR--YSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLEVPV 137 G R +L VEI+ + LD VV+ T CDK TP L+AAA +++P Sbjct: 94 -----TGKRPTAALDRNLAYLGLVEILY-GYPLDGVVLTTGCDKTTPACLMAAATVDLPA 147 Query: 138 ILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTEELRKLE--ESALPGPGSCAGLFT 195 I++ GGPM+ G + ER ++ + L+ +G + + +E S+ P G C + T Sbjct: 148 IVLTGGPMLNGWFNGERTGSGTIIWKARELLAKGEIDYQKFIELVASSAPSAGYCNTMGT 207 Query: 196 ANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRKALEN 255 A TMN L+EA+G+ LPG + +PA R A TG RIV MV E L P I+TR+ALEN Sbjct: 208 ATTMNSLAEALGMSLPGCAAIPAPYRERGQIAYETGKRIVDMVFEDLKPSDIITRQALEN 267 Query: 256 AIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDR 315 I V+ A+GGSTN+ +H+ A+A +G+ L ++ ++ + +VP I ++ P+G + D R Sbjct: 268 VIIVNSAIGGSTNAPIHINAIARHVGVPLEVDDWERVGGQVPLIVNLQPAGTYLGEDFHR 327 Query: 316 AGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLAIL 375 AGG+PAV+ EL GLIH++ALTV G+T+ +N + A LD +VIR + P G ++ Sbjct: 328 AGGVPAVVHELMRHGLIHENALTVNGRTMGDNCHERAALDADVIRTFETALVPAAGFKVV 387 Query: 376 KGSLAPNGAVVKASAVKRELW-----------KFKGVARVFDREEDAVKAIRGG--EIEP 422 +G+L + A++K + E F+G A VFD ED + I I+ Sbjct: 388 RGNLF-DSAIMKTCVISDEFRTRYLSNPQDPDAFEGRAVVFDGPEDYHQRIDDPSLNIDE 446 Query: 423 GTVIVIRYEGPRGGPGMREMLTATAAVMALGLG-DKVALVTDGRFSGATRGPAIGHVSPE 481 ++ IR G G PG E++ A L + + DGR SG + P+I + SPE Sbjct: 447 HCLLFIRGTGAIGFPGSAEVVNMRAPSYLLQRNITSLPCIGDGRQSGTSGSPSILNASPE 506 Query: 482 AAAGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEERRA--------RWKPKVKP---LR 530 AAAGG +AL++ GD + ID+ K R D+L+ ++EL +RRA ++ P P ++ Sbjct: 507 AAAGGGLALLRTGDRVRIDLLKGRADILISDEELAQRRADFQAHGGYKYPPSQTPWQEIQ 566 Query: 531 RGILRRYAK 539 RGI+ + A+ Sbjct: 567 RGIVDQLAQ 575 Lambda K H 0.319 0.138 0.401 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: 827 Number of extensions: 36 Number of successful extensions: 4 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: 552 Length of database: 599 Length adjustment: 36 Effective length of query: 516 Effective length of database: 563 Effective search space: 290508 Effective search space used: 290508 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 (21.7 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