Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate WP_011842510.1 RSPH17029_RS18320 galactonate dehydratase
Query= BRENDA::A9CEQ8 (378 letters) >NCBI__GCF_000015985.1:WP_011842510.1 Length = 382 Score = 157 bits (398), Expect = 4e-43 Identities = 126/391 (32%), Positives = 183/391 (46%), Gaps = 55/391 (14%) Query: 1 MKITAVRTHLLEHRLDTPFESASMRFDRRAHVLVEIECDDGTVGWGECL--GPARPNAAV 58 MKITA++T ++ R + ++IE D+G VGWGE + G A A Sbjct: 1 MKITALKTFIVPPRW----------------LFLKIETDEGIVGWGEPVVEGKALTVEAA 44 Query: 59 VQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQRGLSLTALSGIDIALWDIKGKHYGASIS 118 V + +LIGQDP + E W VLY +G L ++AL+GID ALWDIKG+ G + Sbjct: 45 VHEMADYLIGQDPLRIEDHWQVLYRGGFYRGGPVL-MSALAGIDQALWDIKGRAAGLPVH 103 Query: 119 MLLGGRWRESVRAYATGSFKRDNVDRVSDNASEMAERRAEGFHACKIKIGFGVEE----- 173 +LGG R+ +R Y+ DR D A E A GF A K+ G EE Sbjct: 104 QMLGGACRDRIRVYSW-----IGGDRPEDVAQGAREAVARGFTAIKLN---GAEELQIVD 155 Query: 174 -------DLRVIAAVREAIGPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPE 226 + I AVR+A+GP + + +D + A L F + + EEPV+ E Sbjct: 156 GHDKIDRIVETIGAVRDAVGPHVGIGVDFHGRVQKPMAKVLIHALDPFRLMFIEEPVLSE 215 Query: 227 QLDAYARVRAGQPIPVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLA 286 L+A + G P+A GE + R+ + VDI+QPDL GG +E +KIA +A Sbjct: 216 NLEALPEITRGTSTPIALGERLYSRWDFKRVFETRCVDIIQPDLSHAGGITECRKIAAMA 275 Query: 287 TLHGVRIVPHVWGTGVQIAAALQFMA----AMTPDP---VRVNPIEPIMEFDRTHNPFRQ 339 + + + H + +AA LQ A A + + N ++++ + FR Sbjct: 276 EAYDIGVAFHCPLGPIALAACLQVDAVSHNAFIQEQSLGIHYNAGSDLLDYLVDPSVFRY 335 Query: 340 AVLREPLEAVNGVVTIPDGPGLGIEINRDAL 370 G V IP GPGLGIEI+ A+ Sbjct: 336 EA---------GAVEIPTGPGLGIEIDEGAV 357 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: 450 Number of extensions: 29 Number of successful extensions: 6 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 Apr 10 2024. 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