Align Rpal_1936 (EC 3.2.1.21) (characterized)
to candidate WP_050750700.1 AMB_RS11280 beta-glucosidase
Query= CAZy::ACF00459.1 (458 letters) >NCBI__GCF_000009985.1:WP_050750700.1 Length = 449 Score = 501 bits (1290), Expect = e-146 Identities = 240/449 (53%), Positives = 300/449 (66%), Gaps = 11/449 (2%) Query: 14 AGLPVLSHIRKDFIWGVSTASFQIEGAANEDGRGQSIWDVYCR-SGYVANNDTGDVACDH 72 AG ++ +R DF+WGVST++FQ+EGA EDGRG SIWD CR G V DVACDH Sbjct: 3 AGNKNITSLRPDFVWGVSTSAFQVEGATKEDGRGLSIWDTRCRLQGGVWTGANADVACDH 62 Query: 73 YHRYQEDVALMKTLGIQAYRFSIAWPRIFPQGTGAINEPGLAFYDRLIDALEAAGIEPWI 132 YHR+ EDV L+K LG+ AYRFSIAWPR+ P+G G +N+ GL FYDRLID + AGI PW+ Sbjct: 63 YHRWPEDVGLIKDLGVDAYRFSIAWPRLLPKGKGPVNQKGLDFYDRLIDGVLEAGITPWV 122 Query: 133 CLYHWDLPQAMEERGGWMNRDIVGWFADYARVIGERYGKRVKRFATFNEPGIFSLFSRSF 192 CLYHWDLPQA+++ GGW NRD GWFADYA + +RYG RVK FATFNE +F++F + Sbjct: 123 CLYHWDLPQALDDLGGWTNRDCAGWFADYAVLAAKRYGDRVKHFATFNEFSVFTMFGYAI 182 Query: 193 -----GARDRSADEKLHRWIHHVNLAHGAAVDVLRETVADAKIGLVTNYQPVYPSSDKPE 247 G DR+A K IHHVNLAHG VDVLR+ V D IG + N Q V P E Sbjct: 183 DWAAPGVTDRAAHMKA---IHHVNLAHGMGVDVLRDHVKDVSIGAIHNRQIVRPEGGLAE 239 Query: 248 DVAEAKLISDYWNRAFADPQYRGEYPGLIRDAVKPYIQPGDMERIHRPLDWFGLNHYSPV 307 + A A L+ +WN F DPQ+ G YP ++ V+PY+Q GD+ RI RP DW GLNHY P+ Sbjct: 240 NQAAADLLDAHWNGVFCDPQHLGHYPEIMARDVEPYVQAGDLARICRPTDWMGLNHYGPI 299 Query: 308 YINSDPNAIVGLGWGPKPEGIPRSPIDWTIEPDAFRDTLIEISRRYGKPVYVTENGY--G 365 Y +DP G GWG PE + W I P+ F+D L+ ++RRYG PVYVTENG G Sbjct: 300 YAKADPATTWGYGWGAPPESANHPEVGWPIFPEVFKDELLTLTRRYGLPVYVTENGCGGG 359 Query: 366 SNIEKPDANGEVVDPGRIGFLRDYITALDQAVAAGADVRGYMVWSLLDNFEWESGYSVRF 425 + + PD NG V D R+ + R+Y A+ AVA GADVRGY VW+LLDNFEW SGY RF Sbjct: 360 AGSDTPDENGVVDDTHRLAYFREYQQAMLDAVAEGADVRGYFVWALLDNFEWGSGYGPRF 419 Query: 426 GLIYIDYATLRRIPKASFKWFADVIRHAR 454 GL ++D+ + +R K S KW+ D+I+ R Sbjct: 420 GLYHVDFDSQKRTLKNSGKWYRDMIKGQR 448 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: 831 Number of extensions: 43 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: 449 Length adjustment: 33 Effective length of query: 425 Effective length of database: 416 Effective search space: 176800 Effective search space used: 176800 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