Align 6-P-β-glucosidase (BglA) (EC 3.2.1.21|3.2.1.86) (characterized)
to candidate 16981 b2901 6-phospho-beta-glucosidase A (NCBI)
Query= CAZy::AAV37466.1 (480 letters) >FitnessBrowser__Keio:16981 Length = 479 Score = 779 bits (2011), Expect = 0.0 Identities = 355/475 (74%), Positives = 412/475 (86%), Gaps = 3/475 (0%) Query: 6 LPKDFLWGGAVAAHQVEGGWDQGGKGVSICDVLSGGAHGVDRVITDGVQPGVSYPNHQAV 65 LPKDFLWGGAVAAHQVEGGW++GGKG SICDVL+GGAHGV R IT V PG YPNH+AV Sbjct: 8 LPKDFLWGGAVAAHQVEGGWNKGGKGPSICDVLTGGAHGVPREITKEVLPGKYYPNHEAV 67 Query: 66 EFYSHYKQDVALFAEMGFKCFRTSIAWTRIFPNGDELEPNEAGLQFYDDLFDELLKYNIE 125 +FY HYK+D+ LFAEMGFKCFRTSIAWTRIFP GDE +PNE GL+FYDD+FDELLKYNIE Sbjct: 68 DFYGHYKEDIKLFAEMGFKCFRTSIAWTRIFPKGDEAQPNEEGLKFYDDMFDELLKYNIE 127 Query: 126 PVITLSHFEMPHHLVKQYGGWLNRKVVDFFVRYSEVVMKRYQSKVKYWMTFNEINNQRNW 185 PVITLSHFEMP HLV+QYG W NRKVVDFFVR++EVV +RY+ KVKYWMTFNEINNQRNW Sbjct: 128 PVITLSHFEMPLHLVQQYGSWTNRKVVDFFVRFAEVVFERYKHKVKYWMTFNEINNQRNW 187 Query: 186 QYPVFGYCCSGVIFTDHDKPEQAMYQTLHHQFVASAKVVKLGHEINPNFKIGCMLALVPI 245 + P+FGYCCSGV++T+H+ PE+ MYQ LHHQFVASA VK INP K+GCMLA+VP+ Sbjct: 188 RAPLFGYCCSGVVYTEHENPEETMYQVLHHQFVASALAVKAARRINPEMKVGCMLAMVPL 247 Query: 246 YPWSCHPDDVMFAQEAMRERHLFGDVQLRGYYPSYILKEWARKGYQIDMQPEDEQTLRDG 305 YP+SC+PDDVMFAQE+MRER++F DVQLRGYYPSY+L EW R+G+ I M+ D LR+G Sbjct: 248 YPYSCNPDDVMFAQESMRERYVFTDVQLRGYYPSYVLNEWERRGFNIKMEDGDLDVLREG 307 Query: 306 CTDYLGFSYYMSSAVQLAAKGQKKEDSITGFDGGVKNPHVKASEWGWQIDPVGLRYTLNS 365 DYLGFSYYM++AV+ A+G D+I+GF+G V NP+VKAS+WGWQIDPVGLRY L Sbjct: 308 TCDYLGFSYYMTNAVK--AEG-GTGDAISGFEGSVPNPYVKASDWGWQIDPVGLRYALCE 364 Query: 366 FYERYQKPMFIVENGFGAVDKVEADGSINDDYRIEYLKAHIDQMKKTVVEDGVELMGYTP 425 YERYQ+P+FIVENGFGA DKVE DGSINDDYRI+YL+AHI++MKK V DGV+LMGYTP Sbjct: 365 LYERYQRPLFIVENGFGAYDKVEEDGSINDDYRIDYLRAHIEEMKKAVTYDGVDLMGYTP 424 Query: 426 WGCIDCVSFTTGQYSKRYGFIYVDKHDDGTGTFKRSKKKSFDWYKKVISSNGAEL 480 WGCIDCVSFTTGQYSKRYGFIYV+KHDDGTG RS+KKSF+WYK+VI+SNG +L Sbjct: 425 WGCIDCVSFTTGQYSKRYGFIYVNKHDDGTGDMSRSRKKSFNWYKEVIASNGEKL 479 Lambda K H 0.321 0.139 0.445 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: 992 Number of extensions: 32 Number of successful extensions: 2 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: 480 Length of database: 479 Length adjustment: 34 Effective length of query: 446 Effective length of database: 445 Effective search space: 198470 Effective search space used: 198470 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