Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate PfGW456L13_3930 Gluconate dehydratase (EC 4.2.1.39)
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3930 Length = 394 Score = 148 bits (373), Expect = 3e-40 Identities = 109/342 (31%), Positives = 169/342 (49%), Gaps = 24/342 (7%) Query: 32 VLVEIECDDGTVGWGECLGPARPNAAVVQAY-SGWLIGQDPRQTEKIWAVLYNALRDQGQ 90 ++VEIE DGTVG+ G P A +V+ + + +L G EKIW +Y + G+ Sbjct: 59 LVVEIEASDGTVGFAVTTG-GEPAAYIVEKHLARFLEGVRVTDIEKIWDQMYQSTLYYGR 117 Query: 91 RGLSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNVDRVSDNAS 150 +G+ + +SG+D+ALWD+ GK + LLGG R+ ++ YATG+ + D ++ Sbjct: 118 KGIVINTISGVDLALWDLLGKIRQEPVHQLLGGAVRDELQFYATGA-RPDLAQKMGFIGG 176 Query: 151 EMAERR--AEGFHACKIKIGFGVEEDLRVIAAVREAIGPDMRLMIDANHGYTVTEAITLG 208 +M AEG G+ ++L +A +RE +GPD LM+D + A L Sbjct: 177 KMPLHHGPAEGEE--------GLRKNLEELATMRERVGPDFWLMLDCWMSLDLNYATKLA 228 Query: 209 DRAAGFGIDWFEEPVVPEQLDAYARVRAGQP--IPVAGGETWHGRYGMWQALSAGAVDIL 266 A +G+ W EE + P+ YA +R P + V GE R+G L G DI+ Sbjct: 229 VGAHEYGLKWIEEALPPDDYWGYAALRNNVPKGMLVTTGEHEATRWGFRMLLEMGCCDII 288 Query: 267 QPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTPDPVRVNPIEP 326 QPD+ CGG +E+ KI+ LA H ++PH G+ V + F+A P + Sbjct: 289 QPDVGWCGGITELVKISALADAHNALVIPH--GSSVY---SYHFVATRHNSPF-AEFLMM 342 Query: 327 IMEFDRTHNPFRQAVLREPLEAVNGVVTIP--DGPGLGIEIN 366 + D F +L EP+ VNG + + D PG G+ +N Sbjct: 343 APKADEVVPMFHPQLLGEPV-PVNGRMRLSALDQPGFGVTLN 383 Lambda K H 0.321 0.138 0.431 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: 445 Number of extensions: 25 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 378 Length of database: 394 Length adjustment: 30 Effective length of query: 348 Effective length of database: 364 Effective search space: 126672 Effective search space used: 126672 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 (21.9 bits) S2: 50 (23.9 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