Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 7023120 Shewana3_0358 dihydroxy-acid dehydratase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_609 (578 letters) >FitnessBrowser__ANA3:7023120 Length = 619 Score = 230 bits (586), Expect = 1e-64 Identities = 180/577 (31%), Positives = 280/577 (48%), Gaps = 59/577 (10%) Query: 6 PSLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIAE 65 P LRSA T +N R+ + G+ D+ F GKPII I N++++ P + H + + Sbjct: 2 PKLRSAT--STEGRNMAGARALWRATGVKDNDF-GKPIIAIANSFTQFVPGHVHLKDMGS 58 Query: 66 HVKRGVIEAGGFPVEFPVFSNGES-NLRPTAML----TRNLASMDVEEAIRGNPIDGVVL 120 V + EAGG EF + + + ML +R L + VE + + D +V Sbjct: 59 LVADAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADALVC 118 Query: 121 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITI 180 ++ CDK TP +LM A ++P + V+GGPM GK K D + +++ Sbjct: 119 ISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAAADSSVSD 178 Query: 181 DDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMR 240 +D E + G+C+ M TA++M C+ EALG SLP N ++ A A R L +G R Sbjct: 179 EDSAKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSMLATHADRRELFLEAGRR 238 Query: 241 AVEMVREDLKLS-------KILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVQLDL 293 + + + + I + +AFENA+ ++ A+GGS+N V+HL A A V + Sbjct: 239 VMALTKRYYEQDDASALPRNIASFKAFENAMALDIAMGGSSNTVLHLLAAAQEADVAFTM 298 Query: 294 DDWTRIGRGMPTIVDLQPS-GRFLMEEFYYAGGLPAVLRRLGEANL----IPH------P 342 DD R+ R +P + + PS ++ ME+ + AGG+ +L L A L +PH Sbjct: 299 DDIDRMSRQVPHLCKVAPSTAKYHMEDVHRAGGVMGILGELDRAGLLHTDVPHVAADAGG 358 Query: 343 NALTVSGKSIGENTKDAPI----------------YGQD------------EVIRTLDNP 374 N +V K T+D + + QD IR+ + Sbjct: 359 NLKSVLAKYDVMQTQDDKVKQFFMAGPAGIPTTKAFSQDCRWPSLDDDRREGCIRSREFA 418 Query: 375 IRADGGICVLRGNLAPLGAVLKPSAATAELMQHRGRAVVFENFDEYKARINDPELDVDAS 434 +GG+ VL GNLA G ++K + + G A V+E+ D+ A I E V A Sbjct: 419 FSQEGGLAVLSGNLADNGCIVKTAGVDESNLTFIGSARVYESQDDAVAGILGGE--VVAG 476 Query: 435 SILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGV-TDMVRISDARMSGTAYGTVVLHVAPE 493 ++V++ GPKG PGM E+ + + L ++G+ I+D R SG G + HV+PE Sbjct: 477 DVVVIRYEGPKGGPGMQEM--LYPTSYLKSRGLGKACALITDGRFSGGTSGLSIGHVSPE 534 Query: 494 AAAGGPLAAVKEGDWIELDCTSGRLHLDIPDAELAAR 530 AAAGG +A ++ GD IE+D + L + DAELAAR Sbjct: 535 AAAGGTIALIENGDRIEIDIPKRSIKLAVSDAELAAR 571 Lambda K H 0.319 0.136 0.409 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: 807 Number of extensions: 43 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: 2 Length of query: 578 Length of database: 619 Length adjustment: 37 Effective length of query: 541 Effective length of database: 582 Effective search space: 314862 Effective search space used: 314862 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