Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate SM_b20510 SM_b20510 galactonate dehydratase
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__Smeli:SM_b20510 Length = 382 Score = 163 bits (413), Expect = 6e-45 Identities = 120/383 (31%), Positives = 185/383 (48%), Gaps = 35/383 (9%) Query: 1 MKITAVRTHLLEHRLDTPFESASMRFDRRAHVLVEIECDDGTVGWGECL--GPARPNAAV 58 MKIT + T+++ R + ++IE D+G VGWGE + G A A Sbjct: 1 MKITKLTTYIVPPRW----------------LFLKIETDEGVVGWGEPVVEGRALTVEAA 44 Query: 59 VQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQRGLSLTALSGIDIALWDIKGKHYGASIS 118 V S +L+G+DP E W VLY +G + ++AL+GID ALWDIKGK G + Sbjct: 45 VHELSDYLVGKDPFLIEDHWNVLYRGGFYRGG-AIHMSALAGIDQALWDIKGKALGQPVH 103 Query: 119 MLLGGRWRESVRAYATGSFKRDNVDRVSDNASEMAERRAEGFHACKIK---------IGF 169 LLGG+ R+ ++ Y+ DR SD A+ E A GF A K+ Sbjct: 104 SLLGGQCRDRIKVYSW-----IGGDRPSDVANNAREVVARGFKAIKLNGCEEMQIVDTNE 158 Query: 170 GVEEDLRVIAAVREAIGPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLD 229 +++ + I +R+AIGP + + +D + A L F + + EEPV+ E + Sbjct: 159 KIDKAVETIGLIRDAIGPHVGIGVDFHGRVHRPMAKVLAKELEPFKLMFIEEPVLSENRE 218 Query: 230 AYARVRAGQPIPVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLATLH 289 A + P+A GE + R+ LS G VDI+QPDL GG +E +KIA +A + Sbjct: 219 ALREIANHCSTPIALGERLYSRWDFKSVLSDGFVDIIQPDLSHAGGITECRKIAAMAEAY 278 Query: 290 GVRIVPHVWGTGVQIAAALQFMAAMTPDPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAV 349 V + PH + +AA LQ A ++ + + ++ ++ +E Sbjct: 279 DVALAPHCPLGPIALAACLQVDAVSYNAFIQEQSLG--IHYNEANDILDYISNKEVFAYE 336 Query: 350 NGVVTIPDGPGLGIEINRDALTE 372 +G V+IP GPGLGIE++ + E Sbjct: 337 DGFVSIPQGPGLGIEVDEAYVME 359 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: 413 Number of extensions: 22 Number of successful extensions: 5 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: 382 Length adjustment: 30 Effective length of query: 348 Effective length of database: 352 Effective search space: 122496 Effective search space used: 122496 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