Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate Synpcc7942_0626 Synpcc7942_0626 dihydroxy-acid dehydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__SynE:Synpcc7942_0626 Length = 619 Score = 196 bits (499), Expect = 2e-54 Identities = 169/571 (29%), Positives = 264/571 (46%), Gaps = 88/571 (15%) Query: 35 GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94 GM E+ + +PII +A + + P + H +L Q V I AGG+ EF + + Sbjct: 26 GMKDEDFE--KPIIAVANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTIAVDDGI 83 Query: 95 RRPTAAL-----DRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149 + R+L + +++ + D +V + CDK TP LMAA ++PA+ + Sbjct: 84 AMGHGGMLYSLPSRDLIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPAVFV 143 Query: 150 SGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTT---AASPSVGHCNTMGT 206 SGGPM G K L G L ++ A + D E ++ T +A P+ G C+ M T Sbjct: 144 SGGPMEAG--KVILNGEERHLDLVDAMVVAAD-DRESDEDVATIERSACPTCGSCSGMFT 200 Query: 207 ALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICDLVRQ-------DIRPSQIM 259 A SMN L EALG+SLPG S+ A + +R ++ G+ L +Q + P I Sbjct: 201 ANSMNCLTEALGLSLPGNGSLLATHGDRKELFLEAGRLAVKLAKQYYEQDDESVLPRSIA 260 Query: 260 TRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRIGEDVPLLVNCMPA-GK 318 + +AFENAI + A+G S+N HL+A A GV+ +++D R+ +P L P+ K Sbjct: 261 SFKAFENAICLDIAMGGSTNTVLHLLAAAHEAGVDFTMKDIDRLSRKIPNLCKVAPSTQK 320 Query: 319 YLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIG---------------------- 356 Y E HRAGGV +++ EL +AG LH + TV ++G Sbjct: 321 YHMEDVHRAGGVIAILGELDRAGLLHREVPTVHSPSLGAALDQWDINRETATEEAKSRYL 380 Query: 357 ---------EIVSNS-------LTSNTDVIHPFDTPLKHRAGFIVLSGNFFD-SAIMKMS 399 E S S L I + G VL GN + I+K + Sbjct: 381 AAPGGVPTQEAFSQSKRWTALDLDRENGCIRDIEHAYSQDGGLAVLYGNLAEQGCIVKTA 440 Query: 400 VVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALD------IDERCILVIRG 453 V E +VF GP D A++ + E +++IR Sbjct: 441 GVDE------------------NILVFSGPA-VVCESQDEAVNWILNGRVKEGDVVLIRY 481 Query: 454 VGTVGYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGL 512 G G PG E+ + P + L +G+ + + DGR SG ++ SI ++SPEAA GG + Sbjct: 482 EGPRGGPGMQEM--LYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLI 539 Query: 513 ALLKTNDRLKVDLNTRTVNLLIDDAEMAQRR 543 AL++ DR+++D+ R ++L + + E+A RR Sbjct: 540 ALVEQGDRIEIDIPNRRIHLAVSEEELAHRR 570 Lambda K H 0.319 0.135 0.407 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: 924 Number of extensions: 48 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 594 Length of database: 619 Length adjustment: 37 Effective length of query: 557 Effective length of database: 582 Effective search space: 324174 Effective search space used: 324174 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