Align 6-P-β-glucosidase (CelF) (EC 3.2.1.86) (characterized)
to candidate 15852 b1734 cryptic phospho-beta-glucosidase, NAD(P)-binding (NCBI)
Query= CAZy::AAC74804.1 (450 letters) >FitnessBrowser__Keio:15852 Length = 450 Score = 908 bits (2347), Expect = 0.0 Identities = 450/450 (100%), Positives = 450/450 (100%) Query: 1 MSQKLKVVTIGGGSSYTPELLEGFIKRYHELPVSELWLVDVEGGKPKLDIIFDLCQRMID 60 MSQKLKVVTIGGGSSYTPELLEGFIKRYHELPVSELWLVDVEGGKPKLDIIFDLCQRMID Sbjct: 1 MSQKLKVVTIGGGSSYTPELLEGFIKRYHELPVSELWLVDVEGGKPKLDIIFDLCQRMID 60 Query: 61 NAGVPMKLYKTLDRREALKDADFVTTQLRVGQLPARELDERIPLSHGYLGQETNGAGGLF 120 NAGVPMKLYKTLDRREALKDADFVTTQLRVGQLPARELDERIPLSHGYLGQETNGAGGLF Sbjct: 61 NAGVPMKLYKTLDRREALKDADFVTTQLRVGQLPARELDERIPLSHGYLGQETNGAGGLF 120 Query: 121 KGLRTIPVIFDIVKDVEELCPNAWVINFTNPAGMVTEAVYRHTGFKRFIGVCNIPIGMKM 180 KGLRTIPVIFDIVKDVEELCPNAWVINFTNPAGMVTEAVYRHTGFKRFIGVCNIPIGMKM Sbjct: 121 KGLRTIPVIFDIVKDVEELCPNAWVINFTNPAGMVTEAVYRHTGFKRFIGVCNIPIGMKM 180 Query: 181 FIRDVLMLKDSDDLSIDLFGLNHMVFIKDVLINGKSRFAELLDGVASGQLKASSVKNIFD 240 FIRDVLMLKDSDDLSIDLFGLNHMVFIKDVLINGKSRFAELLDGVASGQLKASSVKNIFD Sbjct: 181 FIRDVLMLKDSDDLSIDLFGLNHMVFIKDVLINGKSRFAELLDGVASGQLKASSVKNIFD 240 Query: 241 LPFSEGLIRSLNLLPCSYLLYYFKQKEMLAIEMGEYYKGGARAQVVQKVEKQLFELYKNP 300 LPFSEGLIRSLNLLPCSYLLYYFKQKEMLAIEMGEYYKGGARAQVVQKVEKQLFELYKNP Sbjct: 241 LPFSEGLIRSLNLLPCSYLLYYFKQKEMLAIEMGEYYKGGARAQVVQKVEKQLFELYKNP 300 Query: 301 ELKVKPKELEQRGGAYYSDAACEVINAIYNDKQAEHYVNIPHHGQIDNIPADWAVEMTCK 360 ELKVKPKELEQRGGAYYSDAACEVINAIYNDKQAEHYVNIPHHGQIDNIPADWAVEMTCK Sbjct: 301 ELKVKPKELEQRGGAYYSDAACEVINAIYNDKQAEHYVNIPHHGQIDNIPADWAVEMTCK 360 Query: 361 LGRDGATPHPRITHFDDKVMGLIHTIKGFEIAASNAALSGEFNDVLLALNLSPLVHSDRD 420 LGRDGATPHPRITHFDDKVMGLIHTIKGFEIAASNAALSGEFNDVLLALNLSPLVHSDRD Sbjct: 361 LGRDGATPHPRITHFDDKVMGLIHTIKGFEIAASNAALSGEFNDVLLALNLSPLVHSDRD 420 Query: 421 AELLAREMILAHEKWLPNFADCIAELKKAH 450 AELLAREMILAHEKWLPNFADCIAELKKAH Sbjct: 421 AELLAREMILAHEKWLPNFADCIAELKKAH 450 Lambda K H 0.321 0.140 0.417 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: 940 Number of extensions: 29 Number of successful extensions: 1 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: 450 Length of database: 450 Length adjustment: 33 Effective length of query: 417 Effective length of database: 417 Effective search space: 173889 Effective search space used: 173889 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