Align β-glucosidase / β-xylosidase (BglB;P11-6B) (EC 3.2.1.21|3.2.1.37) (characterized)
to candidate BWI76_RS19550 BWI76_RS19550 phospho-cellobiase
Query= CAZy::ADT62000.1 (464 letters) >FitnessBrowser__Koxy:BWI76_RS19550 Length = 464 Score = 841 bits (2173), Expect = 0.0 Identities = 397/463 (85%), Positives = 428/463 (92%) Query: 1 MKTFPDDFLWGGAVAANQVEGAYLEDGKGLSTSDVQPQGVFGPVVERVAGDSGIKDVAID 60 MKTFP FLWGGA AANQVEGAYLEDGKGL+TSDVQP+GVFG VVERV GDSGIKD+AID Sbjct: 1 MKTFPQAFLWGGATAANQVEGAYLEDGKGLTTSDVQPRGVFGDVVERVPGDSGIKDIAID 60 Query: 61 FYHRYPEDIKLFAEMGFSCLRVSIAWTRIFPNGDEQAPNEAGLAFYDRLFDELAAHDITP 120 FYHRYPEDI LFAEMGF+CLRVSIAW RIFP+GDE PNEAGLAFYD+LFDE+A H+ITP Sbjct: 61 FYHRYPEDISLFAEMGFNCLRVSIAWARIFPHGDEAQPNEAGLAFYDKLFDEMAKHNITP 120 Query: 121 LVTLSHYEMPWGLVKQYGGWGSRQTITFFERYARTVFARYGEKVKLWLTFNEINMSLHAP 180 LVTLSHYEMPW LVK YGGWG+R+ I FFERYARTVF RY KVKLWLTFNEINMSLHAP Sbjct: 121 LVTLSHYEMPWALVKNYGGWGNRKVIGFFERYARTVFERYQAKVKLWLTFNEINMSLHAP 180 Query: 181 MTGVGLPETSSKGEVYQAIHHQLVASALAVKACHEIIPDAKIGNMLLGGLMYPLTCRPED 240 MTGVGLP SSK EVYQAIHHQLVASALA KACH+I+P+ KIGNMLLGGLMYPL+C+P+D Sbjct: 181 MTGVGLPADSSKAEVYQAIHHQLVASALAAKACHDIVPEGKIGNMLLGGLMYPLSCKPDD 240 Query: 241 VLEALQENRAWQFFGDVQCRGAYPGYMLRFFRDSGIQIDITDADRDALKSTVDFISFSYY 300 + E LQ+NR+WQFFGDVQCRGAYPGYMLR+FRD+GI +DITDADR ALK TVDFISFSYY Sbjct: 241 IFETLQQNRSWQFFGDVQCRGAYPGYMLRYFRDNGINLDITDADRAALKETVDFISFSYY 300 Query: 301 MTGCVTTDEELNQQARGNILSMVPNPHLASSEWGWQIDPVGLRTLLNVLWDRYQKPLFIV 360 MTGCVT DEELN++ARGNILSMVPNPHLASSEWGWQIDP+GLRTLLNVLWDRYQKPLFIV Sbjct: 301 MTGCVTADEELNKKARGNILSMVPNPHLASSEWGWQIDPLGLRTLLNVLWDRYQKPLFIV 360 Query: 361 ENGLGAKDKPDADGVVQDDYRISYLNDHLVQVREAIDDGVEVMGYTSWGPIDLVSASKAE 420 ENGLGAKDK +ADG + DDYRISYLNDHLVQVREAI+DGVE+MGYTSWGPIDLVSASKAE Sbjct: 361 ENGLGAKDKVEADGSINDDYRISYLNDHLVQVREAIEDGVELMGYTSWGPIDLVSASKAE 420 Query: 421 LSKRYGFIYVDRDDSGKGTLARSRKKSFYWYKEVIATKGASLK 463 +SKRYGFIYVDRDD G GTLARSRKKSF+WYKEVIAT G SLK Sbjct: 421 MSKRYGFIYVDRDDDGNGTLARSRKKSFWWYKEVIATNGGSLK 463 Lambda K H 0.320 0.138 0.428 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: 857 Number of extensions: 18 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: 464 Length of database: 464 Length adjustment: 33 Effective length of query: 431 Effective length of database: 431 Effective search space: 185761 Effective search space used: 185761 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