Align 6-phospho-beta-galactosidase; EC 3.2.1.85; Beta-D-phosphogalactoside galactohydrolase; PGALase; P-beta-Gal; PBG (uncharacterized)
to candidate 6937232 Sama_1402 Beta-glucosidase (RefSeq)
Query= curated2:Q97EZ2 (474 letters) >FitnessBrowser__SB2B:6937232 Length = 452 Score = 254 bits (649), Expect = 4e-72 Identities = 159/454 (35%), Positives = 230/454 (50%), Gaps = 40/454 (8%) Query: 6 EDFIFGGATAAYQAEGATKEDGKGPCIWDEYLKKEGRFT----GDTASDFYHKYKEDLKF 61 +DF+FG ATA++Q EG + + PCIWD + G+ G A D +++D+ Sbjct: 18 KDFLFGVATASFQIEGDAEH--RQPCIWDTFCDTPGKIADGSNGQVACDHVKLWRDDVDL 75 Query: 62 SRKFGVNGIRISIAWSRVI-PDGKGEVNPKGLKFYSDLIDECIKNNVEPFVTLHHFDTPL 120 GV+ R+SI+W RV+ PDG VN +G+ FY +L+DE + + FVTL+H+D P Sbjct: 76 IASLGVDAYRLSISWGRVLHPDGS--VNQRGMDFYINLLDELGRRGINVFVTLYHWDLPQ 133 Query: 121 TLFKDGDWLNRNNIDYFVRFAKVCFEALGDRVKKWITFNEAWAVAQNGYIIGNFPPSIKY 180 L G WLNR+ F +A + ALG+RV + T NE + A GY G P K Sbjct: 134 HLEDKGGWLNRDTAVAFANYAAIVANALGNRVYAYSTLNEPFCSAFLGYEAGIHAPGHK- 192 Query: 181 DIPKAAQSMHNMMVAHAKVVELYKSMNLDGEIGIVHTLEGKYPITDSKEDKEAAYLDYMI 240 + + HN+++AH + + + + GIV YP T S D AA L + Sbjct: 193 SRQQGRTAAHNLLLAHGMAMTEIRREAPEAKAGIVLNFSPAYPYTSSAGDANAARLAHEY 252 Query: 241 SNKFMLDACFKGEYPKETEKTINEIMSKNGGELKIYDGDLEVLKKASSKIDFLGMNYYSS 300 N + L +G YP IN++ ++ GD++++ S+ ID+LG+NYY+ Sbjct: 253 HNTWYLMPLMEGRYPD----IINQLEPHERPVVE--PGDMDII---STPIDYLGINYYTR 303 Query: 301 HFLKAYEGESRIHHNGTGEKGTSIFALKGIGERVNNPEVPTTDWDWPIYPKGLHDMLVRI 360 + +A G G E V VP T DW I P+ D+L + Sbjct: 304 NVYRA-----------GGPLGF---------EEVRIDNVPRTAMDWEICPQAFTDLLTGL 343 Query: 361 KNEYPNYKKIYVTENGMGYKDDFKDGKIDDTPRIDYINKHLEAILKAKNEGVVVKGYFVW 420 E+ N IY+TENG D +G + D R+DY+ HL A+ +A GV +KGYF W Sbjct: 344 AQEF-NLPPIYITENGAAEDDAPFNGTVHDPMRLDYLQSHLLAVHQAIERGVDIKGYFAW 402 Query: 421 SLMDVLSWSNGYNKRYGLFYVDFKTQNRYAKKSA 454 SLMD W+ GY KR+GL YVD+ TQ R K SA Sbjct: 403 SLMDNFEWAEGYRKRFGLVYVDYGTQQRILKSSA 436 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: 632 Number of extensions: 36 Number of successful extensions: 8 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: 452 Length adjustment: 33 Effective length of query: 441 Effective length of database: 419 Effective search space: 184779 Effective search space used: 184779 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