Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate Synpcc7942_0626 Synpcc7942_0626 dihydroxy-acid dehydratase
Query= reanno::ANA3:7024896 (586 letters) >FitnessBrowser__SynE:Synpcc7942_0626 Length = 619 Score = 219 bits (558), Expect = 3e-61 Identities = 178/572 (31%), Positives = 277/572 (48%), Gaps = 82/572 (14%) Query: 35 RSWMKNQGIPEHHFQNKPVIGICNTWSELTPCNGHLRELAQRVKNGIREAGGIPVEFPVF 94 R+ + G+ + F+ KP+I + N++++ P + HL++L Q V I AGG+ EF Sbjct: 19 RALWRATGMKDEDFE-KPIIAVANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTI 77 Query: 95 SNGES-NLRPSAML----TRNLAAMDTEEAIRGNPIDGVVLLVGCDKTTPALLMGAASCD 149 + + + ML +R+L A E + + D +V + CDK TP +LM A + Sbjct: 78 AVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLN 137 Query: 150 LPTIVVTGGPM------LNGKHKGKDVGSGTLVWELHQEYKAGNISLAAFMNAEADMSRS 203 +P + V+GGPM LNG+ + D+ +V +E S E + Sbjct: 138 IPAVFVSGGPMEAGKVILNGEERHLDLVDAMVVAADDRE------SDEDVATIERSACPT 191 Query: 204 TGTCNTMGTASTMACMVETLGVSLPHNATIPAVDSRRQVLAHMSGMRIVDMVK------- 256 G+C+ M TA++M C+ E LG+SLP N ++ A R+ L +G V + K Sbjct: 192 CGSCSGMFTANSMNCLTEALGLSLPGNGSLLATHGDRKELFLEAGRLAVKLAKQYYEQDD 251 Query: 257 EDLTLSKILSRDAFINAIKVNAAIGGSTNAVIHLKAIAGRIGVELSLDDW-RHGYTVPTI 315 E + I S AF NAI ++ A+GGSTN V+HL A A GV+ ++ D R +P + Sbjct: 252 ESVLPRSIASFKAFENAICLDIAMGGSTNTVLHLLAAAHEAGVDFTMKDIDRLSRKIPNL 311 Query: 316 VNLKPSGQ-YLMEDFYYAGGLPAVLRQLFEHDLLSKNTLTVNAASL------WDNVKE-- 366 + PS Q Y MED + AGG+ A+L +L LL + TV++ SL WD +E Sbjct: 312 CKVAPSTQKYHMEDVHRAGGVIAILGELDRAGLLHREVPTVHSPSLGAALDQWDINRETA 371 Query: 367 ----------AP-------CYNQE-------------VIMSLENPLVENGGIRVLRGNLA 396 AP ++Q I +E+ ++GG+ VL GNLA Sbjct: 372 TEEAKSRYLAAPGGVPTQEAFSQSKRWTALDLDRENGCIRDIEHAYSQDGGLAVLYGNLA 431 Query: 397 PRGAVIKPSAASAHLMQHRGKAVVFESFDD-----YNARIGDPELDIDENSIMVLKNCGP 451 +G ++K + +++ G AVV ES D+ N R + E +++++ GP Sbjct: 432 EQGCIVKTAGVDENILVFSGPAVVCESQDEAVNWILNGR-------VKEGDVVLIRYEGP 484 Query: 452 KGYPGMAEVGNMGLPPKLLK-KGI-KDMVRISDARMSGTAFGTVVLHVAPEAQALGPLAA 509 +G PGM E M P LK KG+ K I+D R SG G + HV+PEA G +A Sbjct: 485 RGGPGMQE---MLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIAL 541 Query: 510 VQNGDMIALDTYAGTLQLEISDQELQARLAKL 541 V+ GD I +D + L +S++EL R A + Sbjct: 542 VEQGDRIEIDIPNRRIHLAVSEEELAHRRAAM 573 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: 838 Number of extensions: 34 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: 586 Length of database: 619 Length adjustment: 37 Effective length of query: 549 Effective length of database: 582 Effective search space: 319518 Effective search space used: 319518 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 Apr 09 2024. 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