Align Rpal_1936 (EC 3.2.1.21) (characterized)
to candidate AZOBR_RS26075 AZOBR_RS26075 beta-glucosidase
Query= CAZy::ACF00459.1 (458 letters) >FitnessBrowser__azobra:AZOBR_RS26075 Length = 444 Score = 519 bits (1337), Expect = e-152 Identities = 239/435 (54%), Positives = 305/435 (70%), Gaps = 4/435 (0%) Query: 26 FIWGVSTASFQIEGAANEDGRGQSIWDVYCR-SGYVANNDTGDVACDHYHRYQEDVALMK 84 F+WG ST++FQ+EGAA EDGR SIWD +CR G V N DTGDVACDHYHRY EDVALM+ Sbjct: 11 FLWGTSTSAFQVEGAATEDGRAPSIWDSFCRLKGRVDNGDTGDVACDHYHRYAEDVALMR 70 Query: 85 TLGIQAYRFSIAWPRIFPQGTGAINEPGLAFYDRLIDALEAAGIEPWICLYHWDLPQAME 144 LG+ AYRFS+AWPR+ P+G G NE GL FYDRLID + AGIEPW+C+YHWDLPQA++ Sbjct: 71 GLGVDAYRFSVAWPRVLPRGRGMANEAGLDFYDRLIDTVLEAGIEPWLCVYHWDLPQALQ 130 Query: 145 ERGGWMNRDIVGWFADYARVIGERYGKRVKRFATFNEPGIFSLFSRSF-GARDRSADEKL 203 + GGW NRD GW+ADY ++ RYG RVKR+ TFNE +F+LF + A D Sbjct: 131 DLGGWANRDSAGWYADYTTLLARRYGDRVKRWITFNEFSVFTLFGYAIPWAAPGITDRGQ 190 Query: 204 H-RWIHHVNLAHGAAVDVLRETVADAKIGLVTNYQPVYPSSDKPEDVAEAKLISDYWNRA 262 H R IHHVNLAHGA VD +R V A IG V N Q V P KPE+ A L+ ++WN A Sbjct: 191 HLRAIHHVNLAHGAGVDAVRALVPGASIGAVHNRQRVLPEGGKPENAEAAALLDEHWNLA 250 Query: 263 FADPQYRGEYPGLIRDAVKPYIQPGDMERIHRPLDWFGLNHYSPVYINSDPNAIVGLGWG 322 F DPQ G YP + A++P ++ GDM RI RP+DWFGLNHY P++ +P G GWG Sbjct: 251 FCDPQLLGHYPPRVARAIEPCVKAGDMARICRPMDWFGLNHYGPIFARVNPETTWGYGWG 310 Query: 323 PKPEGIPRSPIDWTIEPDAFRDTLIEISRRYGKPVYVTENGYGSNIEKPDANGEVVDPGR 382 P P + W + PDAFRD L+EI+RRY P+ +TENG G + + PD +G++VD R Sbjct: 311 DAPPDSPTHGVGWAVFPDAFRDELLEITRRYRMPIVITENGCGGS-DSPDESGDIVDQHR 369 Query: 383 IGFLRDYITALDQAVAAGADVRGYMVWSLLDNFEWESGYSVRFGLIYIDYATLRRIPKAS 442 I +L+ Y ++ +A+ GADVRGY VWSLLDNFEW SGY RFG++++D+ + +R PKAS Sbjct: 370 INYLQLYNASMHEAIRGGADVRGYFVWSLLDNFEWGSGYGNRFGIVHVDFESQKRTPKAS 429 Query: 443 FKWFADVIRHARGAS 457 +W+AD+I+ AR A+ Sbjct: 430 ARWYADLIKRARSAT 444 Lambda K H 0.321 0.140 0.451 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: 809 Number of extensions: 44 Number of successful extensions: 4 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: 458 Length of database: 444 Length adjustment: 33 Effective length of query: 425 Effective length of database: 411 Effective search space: 174675 Effective search space used: 174675 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