Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 1937120 b3771 dihydroxy-acid dehydratase (NCBI)
Query= reanno::WCS417:GFF2156 (578 letters) >FitnessBrowser__Keio:1937120 Length = 616 Score = 222 bits (565), Expect = 4e-62 Identities = 175/574 (30%), Positives = 275/574 (47%), Gaps = 56/574 (9%) Query: 6 PGLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIAE 65 P RSA T +N R+ + G+ D F GKPII + N++++ P + H R + + Sbjct: 2 PKYRSATT--THGRNMAGARALWRATGMTDADF-GKPIIAVVNSFTQFVPGHVHLRDLGK 58 Query: 66 HVKRGVIEAGGFPVEFPVFSNGES-NLRPTAML----TRNLASMDVEEAIRGNPIDGVVL 120 V + AGG EF + + + ML +R L + VE + + D +V Sbjct: 59 LVAEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVC 118 Query: 121 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITL 180 ++ CDK TP +LM + ++P I V+GGPM GK K D + Q ++ Sbjct: 119 ISNCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSD 178 Query: 181 DDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMR 240 E + G+C+ M TA++M C+ EALG S P N ++ A A R L +G R Sbjct: 179 SQSDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKR 238 Query: 241 AVEMVR-------EDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDL 293 VE+ + E I +K AFENA+ ++ A+GGSTN V+HL A A ++ + Sbjct: 239 IVELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTM 298 Query: 294 DDWTRIGRGMPTIVDLQPS-GRFLMEEFYYAGGLPAVLRRLGEANLIPHPNALTVNGKSL 352 D ++ R +P + + PS ++ ME+ + AGG+ +L L A L+ + + V G +L Sbjct: 299 SDIDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLL-NRDVKNVLGLTL 357 Query: 353 GEN--------TQDSPI----------------YGQD------------EVIRTLDNPIR 376 + TQD + + QD IR+L++ Sbjct: 358 PQTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYS 417 Query: 377 ADGGICVLRGNLAPLGAVLKPSAASPALMQHRGRAVVFENFDMYKARINDPELDVDANSI 436 DGG+ VL GN A G ++K + ++++ G A V+E+ D I + V A + Sbjct: 418 KDGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGK--VVAGDV 475 Query: 437 LVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSGTAYGTVVLHVAPEAAA 496 +V++ GPKG PGM E+ K + G I+D R SG G + HV+PEAA+ Sbjct: 476 VVIRYEGPKGGPGMQEMLYPTSFLKSMGLGKA-CALITDGRFSGGTSGLSIGHVSPEAAS 534 Query: 497 GGPLATVKEGDWIELDCANGRLHLDIPDAELAAR 530 GG + +++GD I +D N + L + DAELAAR Sbjct: 535 GGSIGLIEDGDLIAIDIPNRGIQLQVSDAELAAR 568 Lambda K H 0.319 0.136 0.413 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: 871 Number of extensions: 41 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: 578 Length of database: 616 Length adjustment: 37 Effective length of query: 541 Effective length of database: 579 Effective search space: 313239 Effective search space used: 313239 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 (21.8 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