Align 6-phospho-β-glycosidase (GK1856) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate BWI76_RS23345 BWI76_RS23345 glycoside hydrolase
Query= CAZy::BAD76141.1 (470 letters) >FitnessBrowser__Koxy:BWI76_RS23345 Length = 475 Score = 373 bits (957), Expect = e-108 Identities = 199/457 (43%), Positives = 278/457 (60%), Gaps = 5/457 (1%) Query: 14 PAGFWWGSATSATQIEGAANEGGKGKNIW-DHWYEQEPHRFFQGVGPEVASDFYHRYKED 72 P F G+A SA Q EG + + +G++ W D WY+ + H + G GP VA+DF +R++ED Sbjct: 9 PHDFILGAAASAWQTEGWSGKK-EGQDSWPDLWYKNDRHVWHNGYGPAVATDFINRFRED 67 Query: 73 IALMKEIGHNSFRFSISWSRLIPDGVG-EVNPEAVRFYNAVIDELLANGIEPFVNLYHFD 131 + LMK G +R SI+WSR + D V+ + +Y+ + DELLANGIEP + L H++ Sbjct: 68 VQLMKLAGLTHYRTSINWSRFLTDYENVTVDEDYAAYYDQLFDELLANGIEPMICLEHYE 127 Query: 132 MP-LAMQTIGGWENREVVDAYARYASLCFQLFGDRVKTWFTHNEPIVPVEGGYLYDFHYP 190 +P ++ GGW +++VV+ + +YA F + +V WFT NEPIV YL +P Sbjct: 128 LPGYLLEQYGGWASKKVVELFVQYAEKVFARYHHQVTRWFTFNEPIVVQTRVYLDALRWP 187 Query: 191 NVVDFRRAVQVAYHTMIAHAKAVAAFRRAAIPDGKIGIILNLTPSYPRSQHPADVKAAHI 250 + +Q +H ++A AK V FR G +G ILN +YPRS P DV+AA Sbjct: 188 YEQNTGTWMQWNHHKVLATAKVVRLFREKGYR-GTVGCILNPEVTYPRSNAPHDVRAAER 246 Query: 251 ADLLFNRSFLDPAVKGEYPQDLIELLDEYGFLPVTKANDRELIKENTIDLLGINYYQPRR 310 DL +NR FLDP V G YP +L+ LL+++ A + LI+ENT+D LGIN Y P R Sbjct: 247 YDLFYNRVFLDPLVHGVYPPELLNLLEQHHVSWDYDAQELALIRENTVDELGINLYYPHR 306 Query: 311 VKAKENMPNPDAPFLPERFFDYYAMPGRKMNPYRGWEIYEKGIYDILINIKENYGNIECF 370 VKA +P PF P +++ + +PGR+MN RGWEIY + ++D+ + IK++Y NI F Sbjct: 307 VKAPSRAWHPQTPFHPAYYYEPFELPGRRMNSSRGWEIYPQIVFDMAMRIKQDYRNIPWF 366 Query: 371 ISENGMGVEGEERFRDESGMIHDDYRIEFIREHLKWVHRAIEEGVNVKGYHLWTFMDNWS 430 ++E+GMGVE E +FR+ G I DDYRI FI EHL RA E G N GY LW F DN S Sbjct: 367 VAESGMGVENEGQFRNREGAIADDYRIRFISEHLWQTLRAREAGANCHGYMLWAFTDNVS 426 Query: 431 WTNAYKNRYGLVAVDLENGLKRTIKKSGYWFKSLAEN 467 NA+KNRYGL+ +DL+N R K S WF+ L E+ Sbjct: 427 PMNAFKNRYGLIEIDLQNNRARRPKASASWFRKLGES 463 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: 842 Number of extensions: 54 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: 470 Length of database: 475 Length adjustment: 33 Effective length of query: 437 Effective length of database: 442 Effective search space: 193154 Effective search space used: 193154 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