Align 6-phospho-beta-galactosidase; EC 3.2.1.85; Beta-D-phosphogalactoside galactohydrolase; PGALase; P-beta-Gal; PBG (uncharacterized)
to candidate AZOBR_RS26075 AZOBR_RS26075 beta-glucosidase
Query= curated2:Q97EZ2 (474 letters) >FitnessBrowser__azobra:AZOBR_RS26075 Length = 444 Score = 255 bits (652), Expect = 2e-72 Identities = 155/459 (33%), Positives = 230/459 (50%), Gaps = 37/459 (8%) Query: 4 FGEDFIFGGATAAYQAEGATKEDGKGPCIWDEYLKKEGRF----TGDTASDFYHKYKEDL 59 F E F++G +T+A+Q EGA EDG+ P IWD + + +GR TGD A D YH+Y ED+ Sbjct: 7 FPEGFLWGTSTSAFQVEGAATEDGRAPSIWDSFCRLKGRVDNGDTGDVACDHYHRYAEDV 66 Query: 60 KFSRKFGVNGIRISIAWSRVIPDGKGEVNPKGLKFYSDLIDECIKNNVEPFVTLHHFDTP 119 R GV+ R S+AW RV+P G+G N GL FY LID ++ +EP++ ++H+D P Sbjct: 67 ALMRGLGVDAYRFSVAWPRVLPRGRGMANEAGLDFYDRLIDTVLEAGIEPWLCVYHWDLP 126 Query: 120 LTLFKDGDWLNRNNIDYFVRFAKVCFEALGDRVKKWITFNEAWAVAQNGYIIGNFPPSIK 179 L G W NR++ ++ + + GDRVK+WITFNE GY I P I Sbjct: 127 QALQDLGGWANRDSAGWYADYTTLLARRYGDRVKRWITFNEFSVFTLFGYAIPWAAPGIT 186 Query: 180 YDIPKAAQSMHNMMVAHAKVVELYKSMNLDGEIGIVHTLEGKYPITDSKEDKEAAYLDYM 239 D + +++H++ +AH V+ +++ IG VH + P E+ EAA L Sbjct: 187 -DRGQHLRAIHHVNLAHGAGVDAVRALVPGASIGAVHNRQRVLPEGGKPENAEAAALLDE 245 Query: 240 ISNKFMLDACFKGEYPKETEKTINEIMSKNGGELKIYDGDLEVLKKASSKIDFLGMNYYS 299 N D G YP + I E + GD + + +D+ G+N+Y Sbjct: 246 HWNLAFCDPQLLGHYPPRVARAI---------EPCVKAGD---MARICRPMDWFGLNHYG 293 Query: 300 SHFLKAYEGESRIHHNGTGEKGTSIFALKGIGERVNNPEVPTTDWDWPIYPKGLHDMLVR 359 F +R++ T G G P+ PT W ++P D L+ Sbjct: 294 PIF-------ARVNPETTW----------GYGWGDAPPDSPTHGVGWAVFPDAFRDELLE 336 Query: 360 IKNEYPNYKKIYVTENGMGYKDD-FKDGKIDDTPRIDYINKHLEAILKAKNEGVVVKGYF 418 I Y I +TENG G D + G I D RI+Y+ + ++ +A G V+GYF Sbjct: 337 ITRRY--RMPIVITENGCGGSDSPDESGDIVDQHRINYLQLYNASMHEAIRGGADVRGYF 394 Query: 419 VWSLMDVLSWSNGYNKRYGLFYVDFKTQNRYAKKSAYWF 457 VWSL+D W +GY R+G+ +VDF++Q R K SA W+ Sbjct: 395 VWSLLDNFEWGSGYGNRFGIVHVDFESQKRTPKASARWY 433 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: 668 Number of extensions: 36 Number of successful extensions: 4 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: 444 Length adjustment: 33 Effective length of query: 441 Effective length of database: 411 Effective search space: 181251 Effective search space used: 181251 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