Align 6-P-β-galactosidase (Gan1D) (EC 3.2.1.86) (characterized)
to candidate WP_085638906.1 MGEO_RS13930 beta-glucosidase
Query= CAZy::AHL67640.1 (478 letters) >NCBI__GCF_002115805.1:WP_085638906.1 Length = 442 Score = 272 bits (696), Expect = 1e-77 Identities = 173/462 (37%), Positives = 237/462 (51%), Gaps = 42/462 (9%) Query: 9 FPPEFLWGAASAAYQVEGAWNEDGKGLSVWDVFAKQPGRTFKGTNGDVAVDHYHRYQEDV 68 FP +FL+G A+++YQ+EG G G + WD FA PG + NGD+A DHYHR++ED+ Sbjct: 9 FPDDFLFGTATSSYQIEGH-AFGGAGKTHWDTFAATPGNVVRAENGDLACDHYHRFEEDL 67 Query: 69 ALMAEMGLKAYRFSVSWSRVFPDGNGAVNEKGLDFYDRLIEELRNHGIEPIVTLYHWDVP 128 L+ GL AYRFS SW+RV PDG GA N +GLDFYDRL + + G++P TLYHW++P Sbjct: 68 DLVKAAGLDAYRFSTSWARVMPDGRGAPNPEGLDFYDRLTDAMLERGLKPCATLYHWELP 127 Query: 129 QALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNIFISFGYRLGLHPPGV 188 AL D G W + + F +A + R GDR+ +NE + LG H PG+ Sbjct: 128 VALAD-LGGWRNPDLPKWFGDFAEVIMGRIGDRMFSVAPINEPWCVGWLSHFLGHHAPGL 186 Query: 189 KDMKRMYEANHIANLANAKVIQSFRHYVPDGKIGPSFAYSPMYPYDSRPENVLAFENAEE 248 +D++ A H A+ IQ R + G +G F P D E A + Sbjct: 187 RDIRATAHAMHHVLKAHGTAIQVMRG-LGMGNLGGVFNMEWATPADDSAEAQQAAALYDG 245 Query: 249 FQNHWWMDVYAWGMYPQAAWNYLESQGLEPTVAPG---DWELLQAAKPDFMGVNYYQTTT 305 + NH++M G YP N +E GLEP + G D+ ++QA D+ G+NYY Sbjct: 246 YYNHFFMSGVFKGEYPA---NVME--GLEPHMPKGWQEDFGIIQAPL-DWCGINYYTRKI 299 Query: 306 VEHNPPDGVGEGVMNTTGKKGTSTSSGIPGLFKTVRNPHVDTTNWDWAIDPVGLRIGLRR 365 + P DG G + T DW I P GL L R Sbjct: 300 IA--PDDGAWPSHHEVEGP--------------------LPKTFMDWEIYPDGLYNFLTR 337 Query: 366 IANRY--QLPILITENGLGEFDTLEPGDIVNDDYRIDYLRRHVQEIQRAITDGVDVLGYC 423 A Y LP+ +TENG+ D +E G +V+D +RIDYL +HV +QRA+ DG V GY Sbjct: 338 TAREYTGDLPLYVTENGMAAPDVIENG-VVDDPHRIDYLNQHVAAVQRALADGAPVKGYF 396 Query: 424 AWSFTDLLSWLNGYQKRYGFVYVNRDDESEKDLRRIKKKSFY 465 WS D W GY+KR+G V+V+ D L R K S++ Sbjct: 397 IWSLMDNYEWSLGYEKRFGLVHVDFD-----TLDRTPKSSYH 433 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: 805 Number of extensions: 64 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: 478 Length of database: 442 Length adjustment: 33 Effective length of query: 445 Effective length of database: 409 Effective search space: 182005 Effective search space used: 182005 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 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