Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate GFF723 PGA1_c07380 dihydroxy-acid dehydratase IlvD
Query= curated2:A5UY13 (559 letters) >FitnessBrowser__Phaeo:GFF723 Length = 571 Score = 351 bits (900), Expect = e-101 Identities = 214/543 (39%), Positives = 304/543 (55%), Gaps = 17/543 (3%) Query: 22 RAMLKAIGFTDEDL-AKPIIGIANTWIETMPCNINLRALAARVKEGVRAAGGTPMEFNTV 80 R+ +K GF D +PIIGI NTW E PCN LR LA VK GV AGG P+EF + Sbjct: 22 RSWMKNQGFPDHAFDGRPIIGICNTWSELTPCNSGLRDLAEGVKRGVWEAGGFPVEFPVM 81 Query: 81 AIADGVTMGTEGMKASLISRDLIADSIELMGRGYMFDAIIALVACDKTIPGAAMGLTRLN 140 ++ + T+ +++ R+L+A +E R Y D ++ L CDKT PG MG ++ Sbjct: 82 SLGE-----TQMKPTAMLFRNLLAMDVEESIRAYGIDGVVLLGGCDKTTPGQLMGAASVD 136 Query: 141 IPGFLLYGGSIAPGHWRGKEI-TIQHVYEAIGAVAAGKMTDEELKEIEDAACPGPGACGG 199 +P ++ G + G W+GK+I + V++ AV AG+MT ++ E G C Sbjct: 137 LPAIVVSSGPMLNGKWQGKDIGSGTDVWKFSEAVRAGEMTLQDFMAAESGMSRSKGVCMT 196 Query: 200 QYTANTMATVMEIIGLSPMGTAAVPAADPRKDSVGYRAGQLIMDVLRRDLKPRDILTRAA 259 TA+TMA+++E +G+S AA+PA D R+ ++ + G+ I++++ D+KP D+LTR A Sbjct: 197 MGTASTMASLVEAMGMSLPTNAALPAVDARRMALAHLTGKRIVEMVEEDIKPSDVLTREA 256 Query: 260 FENAIASVALTGGSTNAVLHLLALAREAGVPLTLDDFDAISRRTPLCCDLMPSGKYSAIH 319 F NAI + A GGSTNAV+HLLALA G L+LDDFD + PL + MPSGKY Sbjct: 257 FVNAIMANAAVGGSTNAVVHLLALAGRVGAELSLDDFD-LGSDIPLLVNCMPSGKYLMED 315 Query: 320 VDQAGGIQVIARRLVDGGFAHGDAITVTGRTLAEEAADAVETPGQDVIRPLDNPIKPTGG 379 AGG+ V+ ++L D G + + G LA A+ E DVI+ D P+KP G Sbjct: 316 FCYAGGMPVVLKQLADNGHLRSNTTVLGGDILA--YAEGAECFNDDVIKSFDEPVKPAAG 373 Query: 380 LLVLRGNLAPEGSVVKLFGY--ERTYHRGPARVFDGEEAAMAAIVGGE--IRPDDIVIIR 435 L VLRGNLAP G++VK H G A VF+ E A I + + D I++++ Sbjct: 374 LRVLRGNLAPNGAIVKPSAATDHLLEHEGVAHVFETIEDMKANIDRDDLPVTKDSILVLK 433 Query: 436 YEGPRGGPGMREM--LGVTSAIVGAGLGQSVSLITDGRFSGATRGVMIGHVAPEAARGGP 493 GP+G PGM E+ + + +V G+ + I+DGR SG G +I HV+PE+ GGP Sbjct: 434 GVGPKGYPGMPEVGNMPIPRKLVREGVRDMIR-ISDGRMSGTAFGTVILHVSPESQAGGP 492 Query: 494 LAIVQEGDEIEINLDERRVDLLLSEEEIADRLLAWQPPAPRYEWGVMARYGALVSSASEG 553 L +VQ GD I ++ +DLL+SEEE+ R AWQP Y G Y V A +G Sbjct: 493 LGLVQTGDRIRVSAKNGTLDLLVSEEELTARREAWQPEPLHYTRGYAKLYVDSVLQAEKG 552 Query: 554 AVL 556 A L Sbjct: 553 ADL 555 Lambda K H 0.319 0.137 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: 858 Number of extensions: 46 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: 559 Length of database: 571 Length adjustment: 36 Effective length of query: 523 Effective length of database: 535 Effective search space: 279805 Effective search space used: 279805 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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