Align L-arabinose 1-dehydrogenase [NAD(P)+] (EC 1.1.1.376); L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate Ac3H11_3958 UDP-glucose 4-epimerase (EC 5.1.3.2)
Query= BRENDA::D4GP33 (254 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3958 Length = 299 Score = 121 bits (303), Expect = 2e-32 Identities = 90/254 (35%), Positives = 123/254 (48%), Gaps = 35/254 (13%) Query: 3 RIAVTGAAGNVG---RVTVEALASDHDVTPITHREREGLDSVILDVRDEDA--LTEAFEG 57 R+ +TGAAG +G R ++A + ++ I + EG + R EDA + EG Sbjct: 39 RLLLTGAAGGLGQELRTRLKAYCTTLRLSDIANLGDEGAGEELRPARLEDAGAVLGLLEG 98 Query: 58 HDIVVHLAANPNPDAAWDSVYEVNIGGTYNVYEAALAADIDRLVFASTNHVHQMYNIADA 117 D VVHL + + W+ + + NI G YN+YEAA + R+VFAS+NHV Y Sbjct: 99 VDAVVHLGG-VSTEQPWEPILQANIVGVYNLYEAARKQGVKRVVFASSNHVTGFYR---- 153 Query: 118 TRPETLAADAEAVGVSDPPRPDSYYGVSKVFGEALGNYYADRHGLEVLNLRIGWLLTADE 177 E VG+ DP RPD YGVSK FGE L +Y DR+G+E + LRIG Sbjct: 154 --------QDEVVGLRDPARPDGLYGVSKAFGEDLSRFYFDRYGIETVCLRIG------- 198 Query: 178 VREKMDEEESVARYVRAMWLSPGDCEQGMRRAVEASLPDSPLAVNLISANDDRYLSLTET 237 E R + A W+S D E R V ASL + ++I D + + Sbjct: 199 ----SSFPEPRNRRMLATWMSYDDLE----RLVVASLTAPVVGHSIIYGMGDNTTTWWDN 250 Query: 238 --MRAIGYRPRDNS 249 R IGYRP D+S Sbjct: 251 TLARHIGYRPEDSS 264 Lambda K H 0.315 0.132 0.382 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: 210 Number of extensions: 14 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: 254 Length of database: 299 Length adjustment: 25 Effective length of query: 229 Effective length of database: 274 Effective search space: 62746 Effective search space used: 62746 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 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