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:B9MPM8 (552 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4621 Length = 578 Score = 370 bits (949), Expect = e-106 Identities = 218/544 (40%), Positives = 322/544 (59%), Gaps = 20/544 (3%) Query: 16 RSLFKAMGYTDEEIR-RPLIAVVNSWNEVVPGHIHLDRIAEAVKAGIRLAGATPMEFNVI 74 RS K G D + +P+I + N+W+E+ P + H +IAE VK G+ AG P+EF V Sbjct: 25 RSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIAEHVKRGVIEAGGFPVEFPVF 84 Query: 75 GVCDGIAMGHIGMK-YSLITRELIADSIEAMVMAHQFDGMVLIPNCDKIVPGMLIAAARV 133 + G ++ +++TR L + +E + + DG+VL+ CDK P +L+ AA Sbjct: 85 ------SNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVLLTGCDKTTPALLMGAASC 138 Query: 134 NIPAILISGGPMLAGKI-GDKVCDLNSVFEGVGAYSAGKISEEDLYALEENACPGCGSCS 192 ++PAI+++GGPML GK G + V++ AG I+ +D A E G+C+ Sbjct: 139 DVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITLDDFLAAEGGMSRSAGTCN 198 Query: 193 GMFTANTMNCLSEVLGLALPGNGTIPAVMAARIRLAKMAGMKIVELVEKDIKPSDILTVE 252 M TA+TM C++E LG +LP N IPAV A R LA M+GM+ VE+V +D+K S ILT E Sbjct: 199 TMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMRAVEMVREDLKLSKILTKE 258 Query: 253 AFENALAVDMALGGSTNTILHLPAIANEVGIKLNLDIINAISDRTPNLCKLSPAGQHHIE 312 AFENA+ V+ A+GGSTN ++HL AIA +G++L+LD + I P + L P+G+ +E Sbjct: 259 AFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWSRIGRGMPTIVDLQPSGRFLME 318 Query: 313 DLYFAGGVQAVMNELSKKGLL-HLNLMTVTGKTVGENIKDANVKNYN-VIRPIDNPYSET 370 + Y+AGG+ AV+ L + L+ + N +TV GKT+GEN KDA + + VIR +DNP Sbjct: 319 EFYYAGGLPAVLRRLGEANLIPNPNALTVNGKTIGENTKDAPIYGQDEVIRTLDNPIRAD 378 Query: 371 GGLVIVRGNLAPDGAVVKKSAVPPKLMKHRGPARVFESGEEVFEAILKG---KIQKGDVI 427 GG+ ++RGNLAP GAV+K SA +LM+HRG A VFE+ ++++A + + ++ Sbjct: 379 GGICVLRGNLAPLGAVLKPSAASAELMQHRGRAVVFEN-FDMYKARINDPELDVDANSIL 437 Query: 428 VIRYEGPKGGPGMRE---MLSPTSALAGVGLIEDVALITDGRFSGATRGACFGHVSPEAA 484 V++ GPKG PGM E M P LA + D+ I+D R SG G HV+PEAA Sbjct: 438 VMKNCGPKGYPGMAEVGNMGLPAKLLAQG--VTDMVRISDARMSGTAYGTVVLHVAPEAA 495 Query: 485 ERGPIAAVQDGDMISIDIENKTLTLEVPEEEIKRRLEILPPFEPKVKKGYLYRYSKLVRS 544 GP+A V++GD I +D N L L++P+ E+ R+ L P + + GY Y V Sbjct: 496 AGGPLATVKEGDWIELDCANGRLHLDIPDAELAARMADLQPPQQLIVGGYRQLYIDHVLQ 555 Query: 545 ASTG 548 A G Sbjct: 556 ADQG 559 Lambda K H 0.318 0.137 0.394 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: 777 Number of extensions: 42 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: 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 ( 7.3 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