Align 6-P-β-galactosidase (Gan1D) (EC 3.2.1.86) (characterized)
to candidate AZOBR_RS16895 AZOBR_RS16895 beta-glucosidase
Query= CAZy::AHL67640.1 (478 letters) >FitnessBrowser__azobra:AZOBR_RS16895 Length = 482 Score = 302 bits (773), Expect = 2e-86 Identities = 178/473 (37%), Positives = 240/473 (50%), Gaps = 35/473 (7%) Query: 6 LKPFPPEFLWGAASAAYQVEGAWNEDGKGLSVWDVFAKQPGRTFKGTNGDVAVDHYHRYQ 65 L FP +F+WGA++++YQ+EGA G+G SVWD F+ G+ G GDVA DHY+RY Sbjct: 37 LAAFPDKFVWGASTSSYQIEGAVTAGGRGPSVWDTFSHSFGKVANGDTGDVACDHYNRYA 96 Query: 66 EDVALMAEMGLKAYRFSVSWSRVFPDGNGAVNEKGLDFYDRLIEELRNHGIEPIVTLYHW 125 EDV LMA+ G+ AYRFSV+W RV P G G N +GLDFYDRL + L GI P LYHW Sbjct: 97 EDVDLMAKAGMNAYRFSVAWPRVQPTGTGPANAEGLDFYDRLTDALLAKGIAPWPCLYHW 156 Query: 126 DVPQALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNIFISFGYRLGLHP 185 D+PQAL D G W +R I F YA + R GDR K+W LNE ++ FG+ LG H Sbjct: 157 DLPQALQDR-GGWTNRDIAGWFTDYAQLVAARIGDRAKHWTMLNEPSVHAIFGHGLGGHA 215 Query: 186 PGVKDMKRMYEANHIANLANAKVIQSFRHY--VPDGKIGPSFAYSPMYPYDSRPENVLAF 243 PG+ ++A H NLA +++ R ++G + P++P N A Sbjct: 216 PGMTGKGNYFKAIHHQNLAQGMALKALRAAGGAKGWQLGTVLSLQPVWPVGGLDANYAAS 275 Query: 244 ENAEEFQNHWWMDVYAWGMYPQAAWNYLESQGLEPTVAPGDWELLQAAKPDFMGVNYYQT 303 + N +D G YP+ L G P V GD E ++ DF+G+NYY Sbjct: 276 LMWDAVWNRACLDPLLRGEYPE-----LLRDGFAPLVKAGDLEAIR-QPIDFLGINYYSR 329 Query: 304 TTVEHNPPDGVGEGVMNTTGKKGTSTSSGIPGLFKTVRNPHVDTTNWDWAIDPVGLRIGL 363 H PD G G S G P TT W ++P G+ L Sbjct: 330 M---HQQPDPAG-----LFGTGYGSPPEGTP------------TTGMGWPVEPDGIAEIL 369 Query: 364 RRIANRY-QLPILITENGLGEFDTLEPGDIVNDDYRIDYLRRHVQEIQRAITDGVDVLGY 422 + Y P+ + ENG + P V D+ RI YLRRH+ +A+ +GVD+ G+ Sbjct: 370 IELKQEYGNPPVYVMENGAAYPEQTGPKGFVQDNDRISYLRRHILAGHQALEEGVDLRGW 429 Query: 423 CAWSFTDLLSWLNGYQKRYGFVYVNRDDESEKDLRRIKKKSFYWYQRVIETNG 475 WS D W GYQ+R+G + V+R + L R K S++WY VI G Sbjct: 430 FVWSLLDNFEWAEGYQRRFGLIEVDR-----QTLERRPKASYHWYADVIRKKG 477 Lambda K H 0.320 0.139 0.448 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: 822 Number of extensions: 50 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: 478 Length of database: 482 Length adjustment: 34 Effective length of query: 444 Effective length of database: 448 Effective search space: 198912 Effective search space used: 198912 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 (21.8 bits) S2: 51 (24.3 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