Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate BWI76_RS13570 BWI76_RS13570 mandelate racemase/muconate lactonizing protein
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__Koxy:BWI76_RS13570 Length = 398 Score = 149 bits (375), Expect = 2e-40 Identities = 117/380 (30%), Positives = 176/380 (46%), Gaps = 34/380 (8%) Query: 2 KITAVRTHLLEHRLDTPFESASMRFDRR------AHVLVEIECDDGTVGWGECLGPARPN 55 +I V+ L L TP A + R+ A ++ EI DG G G Sbjct: 27 RIEHVKLSLAFLPLATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAGG 86 Query: 56 AAV---VQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQRGLSLTALSGIDIALWDIKGKH 112 + + + L+G+DP +KI+ L A G+ G+++ A+S +DIALWD+K K Sbjct: 87 QGIYAHAKEIADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPLDIALWDMKAKR 146 Query: 113 YGASISMLLGGRWRESVRAYAT-GSFKRDNVDRVSDNASEMAERRAEGFHACKIKIGF-G 170 G ++ LLG R+SV+ Y T G F +D+V N +A R G K+K+G Sbjct: 147 AGLPLAKLLGSH-RDSVQCYNTSGGFLHTPLDQVLKN---VAISRENGIGGIKLKVGQPN 202 Query: 171 VEEDLRVIAAVREAIGPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDA 230 ED+R + AVRE +G D LM+DAN + AI +G + F + W EEP+ ++ Sbjct: 203 TAEDIRRLTAVREVLGDDFPLMVDANQQWDRETAIRMGRKMEPFNLIWIEEPLDAYDVEG 262 Query: 231 YARVRAGQPIPVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLATLHG 290 +A++ A P+A GE Q + A D +QPD GG S KI LA HG Sbjct: 263 HAQLAAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHG 322 Query: 291 VRIVPH-VWGTGVQIAAALQFMAAMTPDPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAV 349 ++ PH + +AAA P+EP +E NP + E LE Sbjct: 323 RKLAPHFAMEVHLHLAAAY--------------PLEPWLEHFEWLNP----LFNEQLELR 364 Query: 350 NGVVTIPDGPGLGIEINRDA 369 +G + + + GLG ++ A Sbjct: 365 DGRMWVSERHGLGFTLSEQA 384 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: 405 Number of extensions: 23 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: 398 Length adjustment: 30 Effective length of query: 348 Effective length of database: 368 Effective search space: 128064 Effective search space used: 128064 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