Align 6-phospho-beta-galactosidase; EC 3.2.1.85; Beta-D-phosphogalactoside galactohydrolase; PGALase; P-beta-Gal; PBG (uncharacterized)
to candidate BPHYT_RS29195 BPHYT_RS29195 beta-glucosidase
Query= curated2:Q97EZ2 (474 letters) >FitnessBrowser__BFirm:BPHYT_RS29195 Length = 470 Score = 286 bits (732), Expect = 1e-81 Identities = 166/464 (35%), Positives = 248/464 (53%), Gaps = 35/464 (7%) Query: 6 EDFIFGGATAAYQAEGATKEDGKGPCIWDEYLKKEGRF----TGDTASDFYHKYKEDLKF 61 + F+ G ATA+YQ EGA EDG+ P IWD + K G+ TG A D YH+++ D+ Sbjct: 34 KSFLLGAATASYQIEGAVNEDGRLPSIWDTFSAKPGKVLAGDTGAVACDHYHRWQADVDL 93 Query: 62 SRKFGVNGIRISIAWSRVIPDGKGEVNPKGLKFYSDLIDECIKNNVEPFVTLHHFDTPLT 121 G+ R+SIAW RV+ D G N KGL FY L+ + + FVTL+H+D P Sbjct: 94 LAGLGLEAYRLSIAWPRVM-DAAGAPNRKGLDFYKRLLARLKEKGITTFVTLYHWDLPQH 152 Query: 122 LFKDGDWLNRNNIDYFVRFAKVCFEALGDRVKKWITFNEAWAVAQNGYIIGNFPPSIKYD 181 L G WLNR+ F +A + L V W+T NE W A GY G+ P + D Sbjct: 153 LEDCGGWLNRDTAYRFADYADLMSRELAGSVDAWMTLNEPWCSAYLGYGNGHHAPGLA-D 211 Query: 182 IPKAAQSMHNMMVAHAKVVELYKSMNLDGEIGIVHTLEGKYPITDSKEDKEAAYLDYMIS 241 A Q+MH++++AH V + ++ + ++GIV + ++S D+ AA+L + Sbjct: 212 ARYATQAMHHLLLAHGLAVPVLRANDPASQVGIVANIGRGTANSESAADQRAAHLFEVQH 271 Query: 242 NKFMLDACFKGEYPKETEKTINEIMSKNGGELKIYDGDLEVLKKASSKIDFLGMNYYSSH 301 N ++LD KG YP++ + E+ G E + DGD++ + ++ +DFLG+NYY Sbjct: 272 NAWILDPLLKGSYPQD----LFELWP--GTEPLVLDGDMQTI---AAPLDFLGINYYF-- 320 Query: 302 FLKAYEGESRIHHNGTGEKGTSIFALKGIGERVNNPEVPTTDWDWPIYPKGLHDMLVRIK 361 R + G G L+G+ ER T W +YP GL D+L K Sbjct: 321 ---------RTNVASDGAHGFRDVPLEGV-ER--------TQMGWEVYPDGLRDLLTGFK 362 Query: 362 NEYPNYKKIYVTENGMGYKDDFKDGKIDDTPRIDYINKHLEAILKAKNEGVVVKGYFVWS 421 Y N IY+TENGM D DG+++D+ RI ++ +HL A+ +A GV ++GYF+WS Sbjct: 363 ATYANLPPIYITENGMASDDKVIDGQVEDSQRISFLKRHLSAVDQAIKAGVEIRGYFLWS 422 Query: 422 LMDVLSWSNGYNKRYGLFYVDFKTQNRYAKKSAYWFKRISYEKK 465 LMD W+ GY +R+G+ +VD+ TQ R K+SA + E+K Sbjct: 423 LMDNFEWAFGYERRFGIVHVDYATQKRTIKRSANLVSKFLKERK 466 Lambda K H 0.318 0.138 0.427 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: 651 Number of extensions: 36 Number of successful extensions: 6 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: 474 Length of database: 470 Length adjustment: 33 Effective length of query: 441 Effective length of database: 437 Effective search space: 192717 Effective search space used: 192717 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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