Align 6-P-β-glucosidase (BglB;SSO_1595) (EC 3.2.1.86) (characterized)
to candidate BWI76_RS20955 BWI76_RS20955 6-phospho-beta-glucosidase
Query= CAZy::AAZ88293.1 (479 letters) >FitnessBrowser__Koxy:BWI76_RS20955 Length = 476 Score = 826 bits (2134), Expect = 0.0 Identities = 377/479 (78%), Positives = 415/479 (86%), Gaps = 3/479 (0%) Query: 1 MSGFKKGFLWGGAVAAHQLEGGWNEGGKGISIADVMTAGAHGVPREVTEGVIDGLNYPNH 60 MSGFK+GFLWGGAVAAHQLEGGW EGGKG+S+ADVMTAGAHGVPRE+T+GV+ G NYPNH Sbjct: 1 MSGFKEGFLWGGAVAAHQLEGGWKEGGKGVSVADVMTAGAHGVPREITDGVLPGKNYPNH 60 Query: 61 EAIDFYHRYKTDIQLFAEMGFKCFRTSIAWTRIFPQGDEQEPNEEGLQFYDDLFDECLKQ 120 EAIDFYHRYK DIQLFAEMGFKCFRTSIAWTRIFP GDEQEPNE GLQFYDDLFDEC K Sbjct: 61 EAIDFYHRYKDDIQLFAEMGFKCFRTSIAWTRIFPLGDEQEPNEAGLQFYDDLFDECRKH 120 Query: 121 GMEPVVTLSHFEMPYHLVTKYGGWRNRKLIDFFIRFASTVFTRYKEKVKYWMTFNEINNQ 180 G+EPV+TLSHFEMPYHLVT+YGGWRNRKLIDFF+RFA VFTRY+ KVKYWMTFNEINNQ Sbjct: 121 GIEPVITLSHFEMPYHLVTEYGGWRNRKLIDFFVRFAQVVFTRYQHKVKYWMTFNEINNQ 180 Query: 181 VNFSESLCPFTNSGILYSPEEDINEREQIMYQAVHYELVASALAVQTGKSINPEFNIGCM 240 NF E PFTNSG+ Y P ED RE +MYQA HYELVASALAV+ + INP +GCM Sbjct: 181 ANFHEDFAPFTNSGLKYLPGED---REPVMYQAAHYELVASALAVKAAREINPSLWVGCM 237 Query: 241 IAMCPIYPLTCAPNDMMMATKAMHRRYWFTDVHARGYYPQHMLNYFARKGFNLDITPEDN 300 IAMCPIYPL+CAPNDMMMA AMHRRYWFTDVH RG YPQH+LNYF R+GF LDIT ED Sbjct: 238 IAMCPIYPLSCAPNDMMMAMNAMHRRYWFTDVHVRGRYPQHLLNYFERRGFALDITEEDR 297 Query: 301 AILASGCVDFIGFSYYMSFTTQFSPDNPQLDYVEPRDLVSNPYIDTSEWGWQIDPAGLRY 360 L GCVD+IGFSYYMSF T+ + DNPQLDY E + LVSNPY+ S+WGWQIDP GLRY Sbjct: 298 VALTQGCVDYIGFSYYMSFATKATDDNPQLDYDESKSLVSNPYVQKSDWGWQIDPVGLRY 357 Query: 361 SLNWFWDHFQLPLFIVENGFGAVDQRQADGTVNDHYRIDYFASHIREMKKAVVEDGVDLI 420 SLNWFWDH+QLPLFIVENGFGA+D R+ADG+V+D YRIDY ++HI EMKKAVVEDGVDL+ Sbjct: 358 SLNWFWDHYQLPLFIVENGFGAIDVREADGSVDDQYRIDYLSAHIAEMKKAVVEDGVDLM 417 Query: 421 GYTPWGCIDLVSAGTGEMKKRYGMIYVDKDNEGKGTLERIRKASFYWYRDLIANNGENI 479 GYTPWGCIDLVSAGTGEMKKRYG IYVDKDNEG GTL R RK SF WY+ +I +NG+ + Sbjct: 418 GYTPWGCIDLVSAGTGEMKKRYGFIYVDKDNEGNGTLARSRKKSFAWYQQVIGSNGDKL 476 Lambda K H 0.322 0.139 0.449 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: 1008 Number of extensions: 37 Number of successful extensions: 2 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: 476 Length adjustment: 34 Effective length of query: 445 Effective length of database: 442 Effective search space: 196690 Effective search space used: 196690 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: 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