Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_029000136.1 H537_RS0125690 IlvD/Edd family dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000430725.1:WP_029000136.1 Length = 593 Score = 279 bits (713), Expect = 2e-79 Identities = 193/566 (34%), Positives = 298/566 (52%), Gaps = 39/566 (6%) Query: 14 PHRSLLARC--------GLTDDDFE--KPFIGIANSYTDIVP-GHIHLRELAEAVKEGVN 62 PHRS + G+T D+ KP IGIA + +D+ P IHL ELA+ V++G+ Sbjct: 18 PHRSDMTALYLERFMNYGITPDELRCGKPIIGIAQTGSDLSPCNRIHL-ELAKRVRDGIR 76 Query: 63 AAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKI 122 AGG+ EF I + + +LA +V + + +D +VL CDK Sbjct: 77 DAGGIPMEFPVHPIFENCRRPTAALDRNLAYLGLV-----EILYGYPIDAVVLTTGCDKT 131 Query: 123 VPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINV-YEGVGTVSAGEMSEDELEELE 181 P +MAA+ +DIPAIV++GGPML G +G V V + ++AGE+ E+E + Sbjct: 132 TPAGIMAASTVDIPAIVLSGGPMLDGWHEGELVGSGTVIWRSRRKLAAGEIDEEEFLQRA 191 Query: 182 RCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQE 241 + P C + TA+TM + EALG+SLPGCA A ++ Q+A +G+RIVEM E Sbjct: 192 CDSAPSAGHCNTMGTASTMNAVAEALGLSLPGCAAIPAPYRQRGQMAYDTGRRIVEMAYE 251 Query: 242 NLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHI 301 +L+P+ ++++E+F NA+ V GGS+N +H+ A+A D + + + E + +P + Sbjct: 252 DLRPSRLLTRESFLNALSVVSCCGGSSNAQVHLMAMARHAD-VELRPSDWTEHAYDLPLL 310 Query: 302 ASISPAGEHMMLDLDRAGGIPAVLKTLED--HINRECVTCTGRTVQENIENVKVGHRDVI 359 ++ PAG+++ RAGG+PAV+ L+ ++ +C+T TGR++ +N+E + R+VI Sbjct: 311 VNMQPAGKYLGERFYRAGGVPAVMWELQQAGKLHGDCLTVTGRSIAQNLEGREATDREVI 370 Query: 360 RPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMM-----------VHEGPAKVFNSE 408 RP P+ G +L GNL G ++K ++E V E A VF Sbjct: 371 RPFADPLLEAAGFLVLSGNLFDFG-IMKTSVISERFRSRYLSRPGLEGVFEARAIVFEGS 429 Query: 409 DECMEAIFGGR--IDEGDVIVIRYEGPKGGPGMREMLN--PTSAIAGMGLERVALITDGR 464 D+ I IDEG ++V+R GP G PG E++N P A+ G+E + + DGR Sbjct: 430 DDYHARINDPSLDIDEGCILVMRGAGPIGWPGSAEVVNMQPPDALIRRGIETLPTLGDGR 489 Query: 465 FSGGTRGPCVGHVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKP 524 SG P + + SPE+ G LA + GD+I ID+ + ++P EIE R + KP Sbjct: 490 QSGTADSPSILNCSPESAVGGGLAWLRTGDMICIDLNAGTCNAQVAPEEIERRKRELPKP 549 Query: 525 --RRSVKGWLARYRKLAGSADTGAVL 548 S W YR+ G GA L Sbjct: 550 PVPESHSPWEELYRQKTGQLAEGATL 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: 776 Number of extensions: 51 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 Jul 25 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