Align 6-P-β-glucosidase A (BglA;b2901) (EC 3.2.1.86) (characterized)
to candidate BWI76_RS23855 BWI76_RS23855 6-phospho-beta-glucosidase
Query= CAZy::AAC75939.1 (479 letters) >FitnessBrowser__Koxy:BWI76_RS23855 Length = 477 Score = 960 bits (2482), Expect = 0.0 Identities = 446/477 (93%), Positives = 465/477 (97%) Query: 3 VKKLTLPKDFLWGGAVAAHQVEGGWNKGGKGPSICDVLTGGAHGVPREITKEVLPGKYYP 62 +KK+ LPKDFLWGGAVAAHQVEGGWNK GKGPSICDVLTGGAHGVPREIT++V PGKYYP Sbjct: 1 MKKIPLPKDFLWGGAVAAHQVEGGWNKDGKGPSICDVLTGGAHGVPREITQQVEPGKYYP 60 Query: 63 NHEAVDFYGHYKEDIKLFAEMGFKCFRTSIAWTRIFPKGDEAQPNEEGLKFYDDMFDELL 122 NHEA+DF+G YKEDIKLFAEMGFKCFRTSIAWTRIFP GDE+QPNEEGLKFYDDMFDELL Sbjct: 61 NHEAIDFHGRYKEDIKLFAEMGFKCFRTSIAWTRIFPLGDESQPNEEGLKFYDDMFDELL 120 Query: 123 KYNIEPVITLSHFEMPLHLVQQYGSWTNRKVVDFFVRFAEVVFERYKHKVKYWMTFNEIN 182 KYNIEPVITLSHFEMPLHLVQQYG WTNRKVVDFFVRFAEVVFERYKHKVKYWMTFNEIN Sbjct: 121 KYNIEPVITLSHFEMPLHLVQQYGGWTNRKVVDFFVRFAEVVFERYKHKVKYWMTFNEIN 180 Query: 183 NQRNWRAPLFGYCCSGVVYTEHENPEETMYQVLHHQFVASALAVKAARRINPEMKVGCML 242 NQRNWRAPLFGYCCSGVVYTEHENPEETMYQVLHHQFVASALAVKAAR+INP+M+VGCML Sbjct: 181 NQRNWRAPLFGYCCSGVVYTEHENPEETMYQVLHHQFVASALAVKAARQINPQMQVGCML 240 Query: 243 AMVPLYPYSCNPDDVMFAQESMRERYVFTDVQLRGYYPSYVLNEWERRGFNIKMEDGDLD 302 AMVPLYPYSC P+DVMFAQESMRERYVFTDVQLRGYYPSYVLNEWERRGF+IKMEDGD Sbjct: 241 AMVPLYPYSCKPEDVMFAQESMRERYVFTDVQLRGYYPSYVLNEWERRGFSIKMEDGDAQ 300 Query: 303 VLREGTCDYLGFSYYMTNAVKAEGGTGDAISGFEGSVPNPYVKASDWGWQIDPVGLRYAL 362 +LREGTC YLGFSYYMTNAVKAEGG+GDAISGFEGSVPNP+VKASDWGWQID VGLRYAL Sbjct: 301 ILREGTCAYLGFSYYMTNAVKAEGGSGDAISGFEGSVPNPHVKASDWGWQIDSVGLRYAL 360 Query: 363 CELYERYQRPLFIVENGFGAYDKVEEDGSINDDYRIDYLRAHIEEMKKAVTYDGVDLMGY 422 CELYERYQ+PLFIVENGFGAYDKVEEDGSINDDYRIDYLRAH+EEM KAVTYDGV+LMGY Sbjct: 361 CELYERYQKPLFIVENGFGAYDKVEEDGSINDDYRIDYLRAHVEEMIKAVTYDGVELMGY 420 Query: 423 TPWGCIDCVSFTTGQYSKRYGFIYVNKHDDGTGDMSRSRKKSFNWYKEVIASNGEKL 479 TPWGCIDCVSFTTGQYSKRYGFIYVNKHDDGTGDMSRSRKKSFNWYK+VIASNGEKL Sbjct: 421 TPWGCIDCVSFTTGQYSKRYGFIYVNKHDDGTGDMSRSRKKSFNWYKDVIASNGEKL 477 Lambda K H 0.321 0.140 0.447 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: 1073 Number of extensions: 26 Number of successful extensions: 1 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: 479 Length of database: 477 Length adjustment: 34 Effective length of query: 445 Effective length of database: 443 Effective search space: 197135 Effective search space used: 197135 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