Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_034632534.1 G496_RS0105830 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000429985.1:WP_034632534.1 Length = 573 Score = 372 bits (954), Expect = e-107 Identities = 229/563 (40%), Positives = 321/563 (57%), Gaps = 39/563 (6%) Query: 17 SLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEGVNAAGGVAFEFNTMAI 76 +L+ T DD EKP I + + + D PG HL L+ G+ AGG +F+ I Sbjct: 18 ALMMGMNWTRDDVEKPQILVDDVHGDSHPGSYHLDVLSNEASTGIYEAGGRPAQFHVTDI 77 Query: 77 CDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKIVPGMLMAAARLDIP 136 CDG A H+GM + L SR I+AD VE A DG++LL CDK P LMAAAR+DIP Sbjct: 78 CDGWAQGHEGMNFILCSRGIIADMVEIHASVIPWDGMILLSGCDKSTPAHLMAAARMDIP 137 Query: 137 AIVVTGGPML--PGEFKGRKVDLINVYEGVGTVSAGEMSEDELEELERCACPGPRSCAGL 194 I + GG M PG ++ + G V EM + +L CP +C + Sbjct: 138 TIHIPGGAMRSGPGNSTSGLAGPLSARKKKGLVEPAEMRDYKL-----TGCPSCGACQFM 192 Query: 195 FTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQENLKPTMIMSQEAF 254 TA+TM C++EALGM+LPG A A + +++AR +GK+I+ + ++ + I+++ F Sbjct: 193 GTASTMQCMSEALGMALPGTALMPATMNDIKRMARAAGKQIMYLAEKGITARKILTKANF 252 Query: 255 ENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHIASISPAGEHMMLD 314 NA+ V A+GGSTN +H+PAIA E+ G+ I+ FD + + I ++ ++ P+G++ Sbjct: 253 MNAMKVHAAIGGSTNAYIHMPAIAHEL-GIKIDPKEFDAIGQEIKYLTNVQPSGKYTAEL 311 Query: 315 LDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIE----------------NVKVGHRDV 358 AGGIP V L D ++ + +T TGRT+ +++E + + ++ Sbjct: 312 FWFAGGIPMVQHMLRDQLDLDVMTVTGRTLGDSLEILEQDGFFNRCHGHLKSYNIPRNEI 371 Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418 IR + S G +A+L GN+AP+GSVVK AV DM H GPA VFNSED+ AI G Sbjct: 372 IRTTEESTKS-GSIAVLDGNIAPKGSVVKYAAVKPDMHKHVGPAAVFNSEDDAQAAIIAG 430 Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIA--GMGLERVALITDGRFSGGTRGPCVGH 476 +I+ G V+VIRYEGPKG GM EM T AI VAL+TDGRFSG T GPC+GH Sbjct: 431 QINPGSVVVIRYEGPKGS-GMPEMFMTTDAIVYDEKLNGTVALVTDGRFSGATSGPCIGH 489 Query: 477 VSPEAMEDGPLAAVNDGDIIRIDIPSRKLEV------DLSPREIE----ERLQSAVKPRR 526 VSPEA++ GP+A + D DII IDIPSR L+V + +P+E+E ER ++ P R Sbjct: 490 VSPEAVDGGPIALLEDDDIISIDIPSRSLQVIGVKGEEKTPKEMEAILAERRKNWTLPER 549 Query: 527 -SVKGWLARYRKLAGSADTGAVL 548 KG L RY A SA GA + Sbjct: 550 PQKKGVLKRYSDSAVSAMEGAYM 572 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: 896 Number of extensions: 56 Number of successful extensions: 6 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: 573 Length adjustment: 36 Effective length of query: 513 Effective length of database: 537 Effective search space: 275481 Effective search space used: 275481 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