Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate Dsui_1122 Dsui_1122 dihydroxy-acid dehydratase
Query= SwissProt::Q1JUQ1 (583 letters) >FitnessBrowser__PS:Dsui_1122 Length = 619 Score = 237 bits (605), Expect = 9e-67 Identities = 183/576 (31%), Positives = 286/576 (49%), Gaps = 73/576 (12%) Query: 16 TNDKNGFMYRSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHFRKLAEHVKRGISEAG 75 T+ +N R+ + G+ D +F G+PII + N++++ P + H + L + V R I AG Sbjct: 10 THGRNMAGARALWRATGMKDGDF-GKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAG 68 Query: 76 GFPVEFPVFSNGES-NLRPSAML----TRNLASMDVEEAIRGNPIDAVVLLAGCDKTTPA 130 G EF + + + ML +R+L + VE + + DA+V ++ CDK TP Sbjct: 69 GIAKEFNTIAIDDGIAMGHDGMLYSLPSRDLIADSVEYMVNAHCADAMVCISNCDKITPG 128 Query: 131 LLMGAASCDVPAIVVSGGPMLNGKL--EGKNIGSGTAVWQLHEALKAG-----EIDVHHF 183 +LM A ++P I VSGGPM GK+ EGK I AV + +KAG + +V F Sbjct: 129 MLMAAMRVNIPTIFVSGGPMEAGKVKWEGKTI----AVDLIDAMIKAGDSNCSDAEVEEF 184 Query: 184 LSAEAGMSRSAGTCNTMGTASTMACMAEALGVALPHNAAIPAVDSRRYVLAHMSGIRIVE 243 E + G+C+ M TA++M C+ EALG++LP N + A + R L +G RIV Sbjct: 185 ---ERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTLVATHADRKGLFLEAGRRIVR 241 Query: 244 MALE-------GLVLSKILTRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDW 296 +A ++ I + AFENA + A+GGSTN V+HL A A GV + D Sbjct: 242 LAQRWYEENDASVLPRSIANQKAFENAFALDVAMGGSTNTVLHLLATAQEAGVTFTMADI 301 Query: 297 MRIGRDTPTIVDLMPSGR-FPMEEFYYAGGLPAVLRRLGEGGLLPNPDALTVNGKSLWDN 355 I R P + + P+ + + +E+ + AGG+ A+L L GGL+ + D TV+ +L + Sbjct: 302 DAISRKVPCLCKVAPATQDYHIEDVHRAGGIMAILGELSRGGLI-HRDTPTVHCHTLGEA 360 Query: 356 V-----------------REAP-------------NYDE-------EVIRPLDRPLIADG 378 + R AP Y E IR + +G Sbjct: 361 IDTYDVQRAGSQRTLEFFRAAPGGIPTQTAFSQDRRYTELDQDRSNGCIRNVAHAYSKEG 420 Query: 379 GIRILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLDHYKATINDEALDIDASSVMVL 438 G+ +L GN+A G ++K + + K G+A V+E+ D I ++ A V+V+ Sbjct: 421 GLAVLHGNIALDGCIVKTAGVDESIWKFTGKAKVYESQDSAVTAILGG--EVVAGDVVVI 478 Query: 439 KNCGPRGYPGMAEVGNMGLPPKLLR-QGV-KDMVRISDARMSGTAYGTVVLHVAPEAAAG 496 + GP+G PGM E M P L+ +G+ K+ ++D R SG G + H +PEAA G Sbjct: 479 RYEGPKGGPGMQE---MLYPTSYLKSRGLGKECALLTDGRFSGGTSGLSIGHASPEAAEG 535 Query: 497 GPLAAVRNGDWIELDCEAGTLHLDITDDELHRRLSD 532 G + VR GD IE+D +HL ++D EL +R ++ Sbjct: 536 GAIGLVRTGDTIEIDIPGRRIHLAVSDAELEKRRAE 571 Lambda K H 0.319 0.136 0.412 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: 904 Number of extensions: 51 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: 583 Length of database: 619 Length adjustment: 37 Effective length of query: 546 Effective length of database: 582 Effective search space: 317772 Effective search space used: 317772 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