Align 6-P-β-glucosidase (YckE;BglC;BSU03410) (EC 3.2.1.86) (characterized)
to candidate AZOBR_RS26075 AZOBR_RS26075 beta-glucosidase
Query= CAZy::CAB12135.1 (477 letters) >FitnessBrowser__azobra:AZOBR_RS26075 Length = 444 Score = 313 bits (803), Expect = 6e-90 Identities = 181/469 (38%), Positives = 248/469 (52%), Gaps = 33/469 (7%) Query: 4 QHPESFPKHFLWGSASAAYQIEGAWNEDGKGPSVWDVFTKIPGKTFKGTNGEIAVDHYHR 63 +H FP+ FLWG++++A+Q+EGA EDG+ PS+WD F ++ G+ G G++A DHYHR Sbjct: 2 EHKAVFPEGFLWGTSTSAFQVEGAATEDGRAPSIWDSFCRLKGRVDNGDTGDVACDHYHR 61 Query: 64 FKEDVALMAEMGLKAYRFSVSWPRVFPKGKGEINEAGLAFYDSLIDELLSHHIEPVLTLY 123 + EDVALM +G+ AYRFSV+WPRV P+G+G NEAGL FYD LID +L IEP L +Y Sbjct: 62 YAEDVALMRGLGVDAYRFSVAWPRVLPRGRGMANEAGLDFYDRLIDTVLEAGIEPWLCVY 121 Query: 124 HWDLPQALMDEYGGFESRNIIEDFNHYCITLYKRFGDRVKYWVTLNEQNYNFNHGFITAM 183 HWDLPQAL D GG+ +R+ + Y L +R+GDRVK W+T NE + G+ Sbjct: 122 HWDLPQALQD-LGGWANRDSAGWYADYTTLLARRYGDRVKRWITFNEFSVFTLFGYAIPW 180 Query: 184 HPPGVKDRKRFYEANHIAFLANAKAIESFREYVPEGKIGPSFAYSPAYPLSSHPEDILAF 243 PG+ DR + A H LA+ +++ R VP IG P PE+ A Sbjct: 181 AAPGITDRGQHLRAIHHVNLAHGAGVDAVRALVPGASIGAVHNRQRVLPEGGKPENAEAA 240 Query: 244 ENAEEFTNNWWLDMYCWGTYPQIPFRCLEKQGWAPTIEAGDMDLLAKGKPDFVGVNYYQT 303 +E N + D G YP R +E P ++AGDM + + D+ G+N+Y Sbjct: 241 ALLDEHWNLAFCDPQLLGHYPPRVARAIE-----PCVKAGDMARICR-PMDWFGLNHYGP 294 Query: 304 ITYERNPLDGVSEGKMNTTGQKGTNQETGIPGVFKTKKNPHLTTSNWDWTIDPIGLRIGL 363 I NP TT G P T W + P R L Sbjct: 295 IFARVNP---------ETTWGYGWGDAP-----------PDSPTHGVGWAVFPDAFRDEL 334 Query: 364 RRITSRYQLPVFITENGLGEFDKV-EDGTVQDDYRIDYLRSHLEQCRQAISDGVDLIGYC 422 IT RY++P+ ITENG G D E G + D +RI+YL+ + +AI G D+ GY Sbjct: 335 LEITRRYRMPIVITENGCGGSDSPDESGDIVDQHRINYLQLYNASMHEAIRGGADVRGYF 394 Query: 423 SWSFTDLLSWLNGYQKRYGFVYVNRDEESTSDLKRLKKKSFYWYQDVIK 471 WS D W +GY R+G V+V+ + + KR K S WY D+IK Sbjct: 395 VWSLLDNFEWGSGYGNRFGIVHVDFESQ-----KRTPKASARWYADLIK 438 Lambda K H 0.319 0.138 0.445 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: 757 Number of extensions: 31 Number of successful extensions: 5 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: 477 Length of database: 444 Length adjustment: 33 Effective length of query: 444 Effective length of database: 411 Effective search space: 182484 Effective search space used: 182484 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 (21.7 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