Align 6-phospho-β-glycosidase (GK3214) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate 3608250 Dshi_1654 Beta-glucosidase (RefSeq)
Query= CAZy::BAD77499.1 (478 letters) >FitnessBrowser__Dino:3608250 Length = 435 Score = 231 bits (589), Expect = 4e-65 Identities = 156/446 (34%), Positives = 221/446 (49%), Gaps = 42/446 (9%) Query: 9 FPPGFLWGAASAAYQVEGAWNEDGKGLSVWDVFAKQPGRTFKGTNGDVAVDHYHRYKEDV 68 +P GFL+G A++AYQ+EG + G G + WD F+ PG + +G A H R +ED+ Sbjct: 8 YPDGFLFGVATSAYQIEGH-GQGGAGRTHWDDFSATPGNVARAEHGARACGHLDRLEEDL 66 Query: 69 ALMAEMGLKAYRFSVSWSRVFPDGNGAVNEKGLDFYDRLIEELRTHGIEPIVTLYHWDVP 128 L+A +G+ AYRFS SW+RV P+G GA N +GLDFYDRL++ L GI+P TLYHW++P Sbjct: 67 DLIAGLGVDAYRFSTSWARVLPEGRGAPNMEGLDFYDRLVDGLLARGIKPAATLYHWELP 126 Query: 129 QALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNIFISLGYRLGLHPPGV 188 AL D G W +R I F + T+ R GDRV +NE L + G H PG+ Sbjct: 127 SALAD-LGGWRNRDIASWFGDFTDTIMDRIGDRVWSAAPINEPWCVGWLSHFQGHHAPGL 185 Query: 189 KDMKRMYEANHIANLANAKVIQSFRHYVPDGKIGPSFAYSPMYPYDSRPENVLAFENAEE 248 +D++ A H LA+ I R + +G P D P + A E + Sbjct: 186 RDIRATARAMHHILLAHGTAIARMRD-MGMRNLGAVVNMEYAQPLDDSPTAMAAAELYDA 244 Query: 249 FQNHWWMDVYAWGMYPQAAWNYLESQGLEPTVAPGDW--ELLQEAKP-DFMGVNYYQTTT 305 N +++ YP+ GL P + P W + A P D++G+NYY Sbjct: 245 IYNQFFLSGMFHNTYPEPV-----LAGLAPHL-PDRWQDDFDTIATPLDWVGLNYYTRKI 298 Query: 306 VEHNPPDGVSEGVMNTTGKKGTSTSSGIPGLFKTVRNPYVDTTNWDWAIDPVGLRIGLRR 365 + P D S P ++ + P + T W + P GL L Sbjct: 299 I--GPGD------------------SPWPA-YREIDGP-LPKTQMGWEVFPEGLHALLTM 336 Query: 366 IANRYR--LPILITENGLGEFDTLEPDDIVNDDYRIDYLRRHIQEIQRAITDGVDVLGYC 423 + R+ LPI ITENG+ VND R+ YL H+ +++RAI DGV V GY Sbjct: 337 MQARFTGDLPIYITENGMASALP------VNDADRLAYLDAHLAQVRRAIADGVPVDGYF 390 Query: 424 VWSFTDLLSWLNGYQKRYGFVYVNRD 449 +WS D W GY+KR+G V+V+ D Sbjct: 391 IWSLMDNYEWSFGYEKRFGLVHVDFD 416 Lambda K H 0.320 0.139 0.448 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: 746 Number of extensions: 45 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: 478 Length of database: 435 Length adjustment: 33 Effective length of query: 445 Effective length of database: 402 Effective search space: 178890 Effective search space used: 178890 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