Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate Pf1N1B4_4621 L-arabonate dehydratase (EC 4.2.1.25)
Query= curated2:A0Q0E8 (554 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4621 Length = 578 Score = 341 bits (874), Expect = 5e-98 Identities = 211/528 (39%), Positives = 308/528 (58%), Gaps = 17/528 (3%) Query: 31 KPLIGIVNSHNEIIPGHFHLNEIVQAVKLGVASAGGTPIEIPSIGICDGISMNHSGMK-Y 89 KP+IGI N+ +E+ P + H +I + VK GV AGG P+E P S S ++ Sbjct: 41 KPIIGICNTWSELTPCNAHFRQIAEHVKRGVIEAGGFPVEFPVF------SNGESNLRPT 94 Query: 90 PLASRELIADSIEAMTIAHKFDALVLVGNCDKIVPGMLMGAARLNVPAIYVSGGPMLPGK 149 + +R L + +E + D +VL+ CDK P +LMGAA +VPAI V+GGPML GK Sbjct: 95 AMLTRNLASMDVEEAIRGNPIDGVVLLTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGK 154 Query: 150 LKGKKIDLVHGAFEAVGSYAEGILSDDDLNKIEQHSCPTCGSCAGLFTANSMNSLAEALG 209 KG+ I ++ G ++ DD E + G+C + TA++M +AEALG Sbjct: 155 HKGQDIGSGTVVWQLSEQVKAGTITLDDFLAAEGGMSRSAGTCNTMGTASTMACMAEALG 214 Query: 210 VALPGNGTIPAPYGRRKQLAKYAGVKIMELVKKKIKLRDILTKEAFKNAIALDMAIGGSS 269 +LP N IPA RR LA +G++ +E+V++ +KL ILTKEAF+NAI ++ AIGGS+ Sbjct: 215 TSLPHNAAIPAVDARRYVLAHMSGMRAVEMVREDLKLSKILTKEAFENAIRVNAAIGGST 274 Query: 270 NTTLHLMAIAHEAKVYLTLEDFDEISRRIPHITKLSPAGTHHMVDLDEAGGISAVLKELM 329 N +HL AIA V L L+D+ I R +P I L P+G M + AGG+ AVL+ L Sbjct: 275 NAVIHLKAIAGRIGVELDLDDWSRIGRGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRRLG 334 Query: 330 DANLI-FKDQLTVTGKTLEENIKNSLVL-NDSVIRPLNNPYSNEGGIAILRGNLAPDGAV 387 +ANLI + LTV GKT+ EN K++ + D VIR L+NP +GGI +LRGNLAP GAV Sbjct: 335 EANLIPNPNALTVNGKTIGENTKDAPIYGQDEVIRTLDNPIRADGGICVLRGNLAPLGAV 394 Query: 388 VKQSAVEPEMLYHKGVARVFDGEELAFDAIMNK---KIHPGDVVVIRYEGPKGCPGMREM 444 +K SA E++ H+G A VF+ ++ + A +N + ++V++ GPKG PGM E+ Sbjct: 395 LKPSAASAELMQHRGRAVVFENFDM-YKARINDPELDVDANSILVMKNCGPKGYPGMAEV 453 Query: 445 --LSPTAAIIGLGLEKSTALITDGRFSGGTRGPCIGHISPEASEGGPIALIEEGDLIEID 502 + A ++ G+ I+D R SG G + H++PEA+ GGP+A ++EGD IE+D Sbjct: 454 GNMGLPAKLLAQGV-TDMVRISDARMSGTAYGTVVLHVAPEAAAGGPLATVKEGDWIELD 512 Query: 503 ISNRRISLLVSPEELSKRKENWIQPPCKAPDGTYLKRYSKLVTSASTG 550 +N R+ L + EL+ R + +QPP + G Y + Y V A G Sbjct: 513 CANGRLHLDIPDAELAARMAD-LQPPQQLIVGGYRQLYIDHVLQADQG 559 Lambda K H 0.317 0.136 0.392 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: 795 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: 554 Length of database: 578 Length adjustment: 36 Effective length of query: 518 Effective length of database: 542 Effective search space: 280756 Effective search space used: 280756 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 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