Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_068169507.1 HTA01S_RS08935 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_001592305.1:WP_068169507.1 Length = 593 Score = 273 bits (699), Expect = 1e-77 Identities = 185/549 (33%), Positives = 290/549 (52%), Gaps = 31/549 (5%) Query: 23 GLTDDDFE--KPFIGIANSYTDIVP-GHIHLRELAEAVKEGVNAAGGVAFEFNTMAICDG 79 GLT ++ +P IGIA + +D+ P IHL +LA V++G+ AGG+ EF I + Sbjct: 35 GLTPEELRSGRPIIGIAQTGSDLSPCNRIHL-DLAHRVRDGIRDAGGIPMEFPVHPIFEN 93 Query: 80 IAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKIVPGMLMAAARLDIPAIV 139 + +LA +V + + +D +VL CDK P +MAA+ +DIPAIV Sbjct: 94 CRRPTAALDRNLAYLGLV-----EILYGYPIDAVVLTTGCDKTTPAGIMAASTVDIPAIV 148 Query: 140 VTGGPMLPGEFKGRKVDLINV-YEGVGTVSAGEMSEDELEELERCACPGPRSCAGLFTAN 198 ++GGPML G G V V + ++AGE+ E+E + + P C + TA+ Sbjct: 149 LSGGPMLDGWHDGELVGSGTVIWRSRRQLAAGEIDEEEFLQRACSSAPSAGHCNTMGTAS 208 Query: 199 TMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQENLKPTMIMSQEAFENAV 258 TM + EALG+SLPGCA A + Q+A +G+RIVEM E+L+P+ I+++E+F NA+ Sbjct: 209 TMNAVAEALGLSLPGCADIPAPYRERGQMAYETGRRIVEMAYEDLRPSRILTRESFLNAL 268 Query: 259 MVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHIASISPAGEHMMLDLDRA 318 V GGS+N +HI A+A G+ + + E + +P + ++ PAG+ + RA Sbjct: 269 SVVSVAGGSSNAQVHIMAMARHA-GVVLEAQDWTEHAYDLPLLLNMQPAGKFLGERFFRA 327 Query: 319 GGIPAVLKTLED--HINRECVTCTGRTVQENIENVKVGHRDVIRPLDSPVHSEGGLAILR 376 GG+PA++ L+ ++ +C + TG+T+ EN++ R+VIRP + P+ + G +L Sbjct: 328 GGVPALMWELQQAGRLHNDCASVTGKTIGENLQGRDARDREVIRPFNEPLMEKAGFMVLS 387 Query: 377 GNLAPRGSVVKQGAVAEDMMVH-----------EGPAKVFNSEDECMEAIFGG--RIDEG 423 GNL G ++K ++E H E A VF D+ I IDEG Sbjct: 388 GNLFDFG-IMKTSVISEAFRAHYLSRSGQEGIFEARAVVFEGADDYHARINDPALNIDEG 446 Query: 424 DVIVIRYEGPKGGPGMREMLN--PTSAIAGMGLERVALITDGRFSGGTRGPCVGHVSPEA 481 ++V+R GP G PG E++N P A+ G+ + + DGR SG P + + SPE+ Sbjct: 447 CILVMRGAGPIGWPGSAEVVNMQPPDALIRRGINTLPTLGDGRQSGTADSPSILNASPES 506 Query: 482 MEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKP--RRSVKGWLARYRKLA 539 G L+ + GD IRID+ + + + ++P EI R + P +S W A YR+ Sbjct: 507 AVGGGLSWLMSGDTIRIDLNTGRCDALVAPEEIARRQRELPAPPIPQSHSPWEALYREKT 566 Query: 540 GSADTGAVL 548 G GA L Sbjct: 567 GQLADGATL 575 Lambda K H 0.319 0.136 0.397 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: 804 Number of extensions: 49 Number of successful extensions: 7 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: 549 Length of database: 593 Length adjustment: 36 Effective length of query: 513 Effective length of database: 557 Effective search space: 285741 Effective search space used: 285741 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