Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate CA265_RS12250 CA265_RS12250 enolase
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__Pedo557:CA265_RS12250 Length = 388 Score = 191 bits (484), Expect = 4e-53 Identities = 121/394 (30%), Positives = 195/394 (49%), Gaps = 45/394 (11%) Query: 3 ITAVRTHLLEHRLDTPFESASMRFDRRAHVLVEIECDDGTVGWGEC---LGPARPNAAVV 59 I + H+ ++ L T F+ LV I D G G+GE +G A++V Sbjct: 15 IPEAKQHVSDYGLLTSFDMT----------LVVITTDSGLQGFGEAKAAVGSCGICASIV 64 Query: 60 QAYSG----WLIGQDPRQTEKIWAVLYNALRDQ------------GQRGLSLTALSGIDI 103 L+G+ + ++W +YN RD G+RGL+++A+SGID Sbjct: 65 NCIENELKPMLLGKSVKNITRLWEEMYNGTRDHYALSRGRKFPILGRRGLTISAMSGIDT 124 Query: 104 ALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNVDRVSDNASEMAERRAEGFHAC 163 ALWD+KGK ++ LLGG R + AYA+G + + + ++ +GF Sbjct: 125 ALWDLKGKMLNVPVADLLGGACRTKMPAYASGGWADEQ-----NIGEQLMGYVNKGFKGV 179 Query: 164 KIKIGF---GVEEDLRVIAAVREAIGPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFE 220 K+++G V++ + + A R A+GPD++LM+DA+ ++V EA + WFE Sbjct: 180 KMRVGVMDDTVQKSINRVKAARAALGPDIKLMVDAHGTFSVPEAKQFCRGVEDCNVYWFE 239 Query: 221 EPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQ 280 EP+ P+ A VRA IP+A GE+ + + L A+D++QPD GG SE Sbjct: 240 EPISPDNRKGTAEVRAATDIPIAAGESEFTSFDIHDLLQIRAIDVVQPDAAIIGGISEAM 299 Query: 281 KIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTPDPVRVNPIEPIMEFDRTHNPFRQA 340 +++ LA++H V + PH WG +A FMA +T + I+EF NP Sbjct: 300 RVSHLASVHQVELAPHCWG------SAFSFMAGLT--VAFASASATIIEFSLGGNPMMYD 351 Query: 341 VLREPLEAVNGVVTIPDGPGLGIEINRDALTEFR 374 ++ E + VNG ++ P PGLG+ N D + +F+ Sbjct: 352 LVNEQIAVVNGEISAPTAPGLGLTPNWDFVKQFK 385 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: 388 Number of extensions: 17 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: 388 Length adjustment: 30 Effective length of query: 348 Effective length of database: 358 Effective search space: 124584 Effective search space used: 124584 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