Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate WP_017549877.1 C792_RS0112915 galactonate dehydratase
Query= BRENDA::A9CEQ8 (378 letters) >NCBI__GCF_000330705.1:WP_017549877.1 Length = 382 Score = 151 bits (382), Expect = 3e-41 Identities = 116/355 (32%), Positives = 169/355 (47%), Gaps = 25/355 (7%) Query: 32 VLVEIECDDGTVGWGECL--GPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQG 89 + +++E D G VGWGE + G A A V LIG+DP + E IW LY R Sbjct: 16 LFLKVETDAGLVGWGEPVIEGKAATVKAAVIEMMETLIGRDPLEIEGIWNELY---RSGF 72 Query: 90 QRG--LSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYA-TGSFKRDNVDRVS 146 RG + ++A+SGID ALWDIKGK+YGA + LLGGR R+S++ Y+ G DR + Sbjct: 73 YRGGPILMSAISGIDQALWDIKGKYYGAPVHELLGGRARDSIKVYSWVGG------DRPA 126 Query: 147 DNASEMAERRAEGFHACK---------IKIGFGVEEDLRVIAAVREAIGPDMRLMIDANH 197 D E + +G A K I V+ L + ++R + G D + ID + Sbjct: 127 DVGEASLELKNQGITAVKMNATEELQYIDSYSKVDMVLERVDSIRRSCGTDFGIGIDFHG 186 Query: 198 GYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGMWQA 257 A L F + EEP +PE + + IP+A GE ++ Sbjct: 187 RVHKPMAKVLARELEQFRPMFIEEPALPENNENLRDIAMHTAIPIATGERMFSKWQFKTL 246 Query: 258 LSAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTPD 317 L G DI+QPDL GG +E +KI ++A V PH + +A+ LQ A Sbjct: 247 LQDGYADIIQPDLSHAGGITECKKIMSMAEAFDVAAAPHCPLGPIALASCLQVDATCHNA 306 Query: 318 PVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEINRDALTE 372 ++ + + +++ ++ E +G V IPDGPGLGIEIN D + E Sbjct: 307 IIQEQSLG--IHYNKGNDILDYIKDASVFEYTDGHVKIPDGPGLGIEINEDYVRE 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: 401 Number of extensions: 13 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: 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 24 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