Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate CCNA_03139 CCNA_03139 dihydroxy-acid dehydratase
Query= reanno::ANA3:7024896 (586 letters) >FitnessBrowser__Caulo:CCNA_03139 Length = 617 Score = 220 bits (561), Expect = 1e-61 Identities = 178/562 (31%), Positives = 275/562 (48%), Gaps = 71/562 (12%) Query: 35 RSWMKNQGIPEHHFQNKPVIGICNTWSELTPCNGHLRELAQRVKNGIREAGGIPVEFPVF 94 R + G+ + F KP+I + N++++ P + HL++L Q V I AGG+ EF Sbjct: 19 RGLWRATGMKDEDF-GKPIIAVANSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTI 77 Query: 95 SNGES-NLRPSAML----TRNLAAMDTEEAIRGNPIDGVVLLVGCDKTTPALLMGAASCD 149 + + + ML +R+L A E + + D +V + CDK TP +LM A + Sbjct: 78 AVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCISNCDKITPGMLMAAMRLN 137 Query: 150 LPTIVVTGGPM------LNGKHKGKDVGSGTLVWELHQEYKAGNISLAAFMNAEADMSRS 203 +P + V+GGPM + GK + D+ +V Y + E + Sbjct: 138 IPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVV-AADDSYSDEEVEA-----IEKAACPT 191 Query: 204 TGTCNTMGTASTMACMVETLGVSLPHNATIPAVDSRRQVLAHMSGMRIVDMV-----KED 258 G+C+ M TA++M C+ E LG+SLP N ++ A + R+ L +G +VD+ +ED Sbjct: 192 CGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVVDLCQRWYEQED 251 Query: 259 LTL--SKILSRDAFINAIKVNAAIGGSTNAVIHLKAIAGRIGVELSLDDW-RHGYTVPTI 315 T I +R AF NA+ ++ A+GGSTN V+HL A A G++ S+ D R VP + Sbjct: 252 ATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMADIDRLSRHVPCL 311 Query: 316 VNLKPS-GQYLMEDFYYAGGLPAVLRQLFEHDLLSKNTLTVNAASL------WD------ 362 + P+ MED + AGG+ A+L +L L+ + TV+A ++ WD Sbjct: 312 SKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEALARWDIGRTNS 371 Query: 363 -----NVKEAP-------CYNQE-------------VIMSLENPLVENGGIRVLRGNLAP 397 K AP ++Q VI S+E+P ++GG+ VL GNLAP Sbjct: 372 QIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDGGLAVLFGNLAP 431 Query: 398 RGAVIKPSAASAHLMQHRGKAVVFESFDDYNARIGDPELDIDENSIMVLKNCGPKGYPGM 457 G ++K + ++ RG A VFES D + I ++ E ++V++ GPKG PGM Sbjct: 432 EGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGE--VVVIRYEGPKGGPGM 489 Query: 458 AEVGNMGLPPKLLK-KGI-KDMVRISDARMSGTAFGTVVLHVAPEAQALGPLAAVQNGDM 515 E M P LK KG+ ++D R SG G + HV+PEA G +A V+ GD Sbjct: 490 QE---MLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIALVETGDP 546 Query: 516 IALDTYAGTLQLEISDQELQAR 537 I +D + LE+SD L AR Sbjct: 547 ILIDIPTRGITLEVSDAVLAAR 568 Lambda K H 0.318 0.135 0.403 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: 866 Number of extensions: 42 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 586 Length of database: 617 Length adjustment: 37 Effective length of query: 549 Effective length of database: 580 Effective search space: 318420 Effective search space used: 318420 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 Sep 17 2021. The underlying query database was built on Sep 17 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