Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_012385990.1 BIND_RS15605 dihydroxy-acid dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000019845.1:WP_012385990.1 Length = 578 Score = 386 bits (991), Expect = e-111 Identities = 219/545 (40%), Positives = 323/545 (59%), Gaps = 13/545 (2%) Query: 15 HRALWRASGLIDEELR-RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGT 73 +R+ + SG ++ RP+IG+ N+W+E+ P + H +AE V+ G+ AGG PLEF Sbjct: 26 YRSFLKNSGFPQDQFDGRPVIGICNTWSELTPCNAHFRTIAEHVRYGVLEAGGFPLEFPV 85 Query: 74 IAVCDGIAMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL 133 ++ + + M M + R + + VE + AH LD VV++ CDK TP L+ AA Sbjct: 86 SSLGE-VTMRPTAMLF----RNLASMDVEEAIRAHPLDGVVLLMGCDKTTPALLMGAASA 140 Query: 134 EVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTE--ELRKLEESALPGPGSCA 191 ++P I ++GGP + GVY E I + M+ ++ G E + E + GSC Sbjct: 141 DIPTIGVSGGPQLRGVYRGEIIGSGTNIISMSEQLRAGEITLAEFHEAEAAMNRSAGSCM 200 Query: 192 GLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRK 251 + TA+TM + EA+G+ LP + +PA +ARR A++ G RIV MV E L P ILTR Sbjct: 201 TMGTASTMASMVEALGIGLPENAAIPAADARRNLIARMAGRRIVDMVHEDLKPSDILTRA 260 Query: 252 ALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVV 311 A ENAI A+GGSTN+V+HL A+A +G++L L+ FD++ R + + + PSGR + Sbjct: 261 AFENAIRTLAAIGGSTNAVVHLLAIAGRIGVELTLDDFDQLGRGIHCLVDLMPSGRFLME 320 Query: 312 DLDRAGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFGG 371 D AGG+PAVL+ LGE GL+H+DA TV G+++WENV +A + EVI P D + G Sbjct: 321 DFYYAGGLPAVLRTLGERGLLHRDARTVNGQSIWENVANAPCWNNEVITPFDKAFKADAG 380 Query: 372 LAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGG--EIEPGTVIVIR 429 +AILKG+LAP+GAV+K SA EL G A VF+ E+ A+ +I+ ++V++ Sbjct: 381 IAILKGNLAPDGAVIKPSAASPELMSHTGRAVVFENVEEMHHAVNDETLDIDASCIMVLK 440 Query: 430 YEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAGGP 487 GP+G PGM E+ + A ++ G+ D + ++D R SG G + HV+PEA AGGP Sbjct: 441 NCGPKGYPGMAEVGNMPLPAKLLRQGVRDMIR-ISDARMSGTAYGTVVLHVAPEATAGGP 499 Query: 488 IALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGILRRYAKMALSADKG 547 +ALV++GD I +D+ R L L V ++EL RRA WKP V RG R Y L AD+G Sbjct: 500 LALVRNGDLITLDVPARSLHLHVSQEELAARRAVWKPPVPHADRGYARLYIDHVLQADRG 559 Query: 548 GALEY 552 ++ Sbjct: 560 ADFDF 564 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: 796 Number of extensions: 42 Number of successful extensions: 5 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: 578 Length adjustment: 36 Effective length of query: 516 Effective length of database: 542 Effective search space: 279672 Effective search space used: 279672 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