Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate Echvi_3769 Echvi_3769 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__Cola:Echvi_3769 Length = 386 Score = 142 bits (358), Expect = 2e-38 Identities = 114/359 (31%), Positives = 173/359 (48%), Gaps = 33/359 (9%) Query: 32 VLVEIECDDGTVGWGECL--GPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQG 89 + V+I G VGWGE + G A AA V+ +LIG+ + E IW VLY R Sbjct: 20 LFVKITTKSGLVGWGEPVIEGKADTVAACVREMEQYLIGRGAHEIEDIWQVLY---RGGF 76 Query: 90 QRG--LSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNVDRVSD 147 RG + ++ALSGID ALWDIKGKH + LLGG R+ ++ Y D+ + V + Sbjct: 77 YRGGPILMSALSGIDQALWDIKGKHLNVPVYELLGGAVRQKMKMYCW--IGGDHPEVVLE 134 Query: 148 NASEMAERRAEGFHACKIKIG------FGVEEDLRV---IAAVREAIGPDMRLMIDANHG 198 A E + G+ A K+ V+E +V I +R+ G + + +D + Sbjct: 135 QAQEKVDA---GYTAVKMNATGEMDWVSSVKEVKKVVENIKLIRQHFGDSLDVGLDFHGR 191 Query: 199 YTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGMWQAL 258 L D + F + EEPV+ E DA + IP+A GE R+ + L Sbjct: 192 VHKPMVKRLIDELSPFDPLFIEEPVLAENNDALGHIYRYSAIPIATGERMFSRWDFKEIL 251 Query: 259 SAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAAL--QFMAA--- 313 G VDI+QPDL GG SE+++IAT+A + + I PH + +A+AL F++A Sbjct: 252 HQGVVDIIQPDLSHAGGISEVRRIATMAEAYDITIAPHCPLGPISLASALHVDFVSANAF 311 Query: 314 MTPDPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEINRDALTE 372 + + ++ + D NP E + G + + D PGLG+E++ + L E Sbjct: 312 IQESSLGIHYNQGFDLLDYVKNP-------EVFDLKEGYIDLFDRPGLGVEMDEERLKE 363 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: 392 Number of extensions: 11 Number of successful extensions: 4 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: 386 Length adjustment: 30 Effective length of query: 348 Effective length of database: 356 Effective search space: 123888 Effective search space used: 123888 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