Align 6-phospho-β-glycosidase (GK1856) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate SMc03160 SMc03160 beta-glucosidase
Query= CAZy::BAD76141.1 (470 letters) >FitnessBrowser__Smeli:SMc03160 Length = 458 Score = 289 bits (739), Expect = 2e-82 Identities = 169/463 (36%), Positives = 245/463 (52%), Gaps = 33/463 (7%) Query: 12 RFPAGFWWGSATSATQIEGAANEGGKGKNIWDHWYEQEPHRFFQGVGPEVASDFYHRYKE 71 RFP F +G AT++ QIEGA+ G+ +IWD + P R + +VA D Y+R ++ Sbjct: 11 RFPGDFVFGVATASFQIEGASKADGRKASIWDA-FSNMPGRVYGRHNGDVACDHYNRLEQ 69 Query: 72 DIALMKEIGHNSFRFSISWSRLIPDGVGEVNPEAVRFYNAVIDELLANGIEPFVNLYHFD 131 D+ L+K +G ++RFSI+W R++P+G G +N + + FY+ ++D L A GI+ F LYH+D Sbjct: 70 DLDLIKSLGVEAYRFSIAWPRIVPEGTGPINEKGLDFYDRLVDGLKARGIKAFATLYHWD 129 Query: 132 MPLAMQTIGGWENREVVDAYARYASLCFQLFGDRVKTWFTHNEPIVPVEGGYLYDFHYPN 191 +PLA+ GGW R AY RYA GDR+ T NEP V G+LY H P Sbjct: 130 LPLALMGDGGWTARTTAYAYQRYAKTVIARLGDRLDAVATFNEPWCSVWLGHLYGVHAPG 189 Query: 192 VVDFRRAVQVAYHTMIAHAKAVAAFRRAAIPDGKIGIILNLTPSYPRSQHPADVKAAHIA 251 + A+ + T +AH VAA R+ P+ +GI++N YP S D AA A Sbjct: 190 ERNMDAALAALHFTNLAHGLGVAAI-RSERPELPVGIVINAHSVYPGSNSAEDKAAAERA 248 Query: 252 DLLFNRSFLDPAVKGEYPQDLIELLDEYGFLPVTKANDRELIKENTIDLLGINYYQPRRV 311 N F DP KGEYP+D + L E +P + D I + +D G+NYY P RV Sbjct: 249 FDFHNGVFFDPIFKGEYPEDFLSALGER--MPAIEDGDMATIAQ-PLDWWGLNYYTPMRV 305 Query: 312 KAKENMPNPDAPFLPERFFDY----YAMPGRKMNPYRGWEIYEKGIYDILINIKENYGNI 367 A P + +Y A P + GWE+Y + ++ + Y Sbjct: 306 SAD-----------PAKGAEYPATVNAKPVSNVKTDIGWEVYAPALGSLVETLNARYRLP 354 Query: 368 ECFISENG----MGVEGEERFRDESGMIHDDYRIEFIREHLKWVHRAIEEGVNVKGYHLW 423 +C+I+ENG MGV E+G + D R+++I +HL I +G ++GY W Sbjct: 355 DCYITENGACYNMGV--------ENGTVDDQPRLDYISDHLAVTADLIAKGYPMRGYFAW 406 Query: 424 TFMDNWSWTNAYKNRYGLVAVDLENGLKRTIKKSGYWFKSLAE 466 + MDN+ W Y+ R+G+V VD E + RTIKKSG W+K LAE Sbjct: 407 SLMDNFEWAEGYRMRFGIVHVDYETQV-RTIKKSGRWYKDLAE 448 Lambda K H 0.321 0.140 0.446 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: 712 Number of extensions: 44 Number of successful extensions: 7 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: 470 Length of database: 458 Length adjustment: 33 Effective length of query: 437 Effective length of database: 425 Effective search space: 185725 Effective search space used: 185725 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