Align β-glucosidase (SalB) (EC 3.2.1.21) (characterized)
to candidate Ga0059261_0499 Ga0059261_0499 Beta-glucosidase-related glycosidases
Query= CAZy::AAF21799.1 (649 letters) >FitnessBrowser__Korea:Ga0059261_0499 Length = 622 Score = 615 bits (1587), Expect = e-180 Identities = 313/590 (53%), Positives = 397/590 (67%), Gaps = 5/590 (0%) Query: 41 SFRDLNRDGTLNPYEDWRLSPEVRAADLVARMTLAEKAGAGVHGTAPIQGGPM-ASGPAY 99 ++RDLNR+G ++PYE+ L + R DL+ARMT EKAG +HGT P G + AS Y Sbjct: 14 AYRDLNRNGVMDPYENPALPVDARVDDLLARMTPEEKAGQLLHGTLPGHGSAIGASTSGY 73 Query: 100 DMTAAQAIIRDQHLNSLITRMAIAPADFAAENNRLQGIAAGTRLGIPLTISTDPRNHFQV 159 D+ A+A+I DQH++S ITR+ + PA FA +NN +Q +A TRLGIP TISTDPR+HF Sbjct: 74 DLDKARAMIADQHVSSFITRLVMPPAQFAEQNNAVQKLAEATRLGIPATISTDPRHHFHA 133 Query: 160 LGGASVAASGFSQWPETLGFGALNDPALTRRFADLVRAEYRAVGIQMALSPQADLATEPR 219 GAS GFSQWPETL F A+ DPAL RRF + R EYRAVGI MALSPQAD+ +EPR Sbjct: 134 TAGASTHGGGFSQWPETLAFAAIGDPALVRRFGEAARREYRAVGIHMALSPQADIGSEPR 193 Query: 220 WSRINGTFGEDPARVSAQVKAYVQGMQGADTGLAPGGVATVVKHWVGYGAQIDGYDGHNY 279 W RI TFG DPA VS AYV+G QG +G+ GVATVVKHWVGYGA +G+DGHN+ Sbjct: 194 WPRITATFGSDPATVSRLAGAYVEGFQGGPSGVTRDGVATVVKHWVGYGAAPEGHDGHNF 253 Query: 280 YGRFTDFTKGGFDRHVAAFQGAFEAGATGIMPTYTIQKGLSLEGKPVEPVSGGYNKQMLI 339 YGR T F++HVAAF GAF + G+MPTY I +G L+G +EPV G++KQ+L Sbjct: 254 YGRAVSMTDAEFEKHVAAFDGAFAVRSAGVMPTYVIVRGPRLKGAALEPVGAGFSKQLLN 313 Query: 340 DLLRGTHKFKGLILSDWAITNDCNESCRT--GNPPQQPKDIATPWGVEDLTQPQRFAKGM 397 DLLR + GLI+SDWAIT DC+ +C + PQ P I PWGVE L+ +RFAKG+ Sbjct: 314 DLLRREKGYGGLIISDWAITRDCDAACTAPDASNPQLPGSIGMPWGVEHLSVTERFAKGL 373 Query: 398 LAGIDQFGGVNDGLPLLAAVEQKLLPEARLNEAVATIMTLKFEQGLFENPFVDPAAAATI 457 AG+DQFGGV+D P+LA + + + AR++ +V I+ LKFE GLFENPFVDPA A + Sbjct: 374 EAGLDQFGGVDDPAPILAVMREGKVDAARIDASVRRILRLKFELGLFENPFVDPARAEAV 433 Query: 458 VGRADVVAEGRATQAKSLVMLENRLGPAPLPAGGGKRLFIYGVDAANAKAAGFTIAASLD 517 +G V A+ A Q V+L N+ A LP G RL+++GVDA A+AAGF + + Sbjct: 434 LGDPGVRAQADAAQRAGQVLLRNQ--GALLPLRRGARLWLHGVDADAARAAGFQVVGKPE 491 Query: 518 EADIALIRLKAPFQTLHPGFFFGRMQHEGDLDFKEGDAGLTLVRQAAAKVPVILTIYLDR 577 EAD AL+R PF+TLHP FFG QHEG LDF+ DA + AA VPVI+ + +DR Sbjct: 492 EADAALVRTATPFETLHPHHFFGSRQHEGRLDFRPDDADTKTIAAAARHVPVIVAVEMDR 551 Query: 578 PAILTNIKPHAATLIGEFGITDAALFDALTGKVAPMGKLPFELPATMAAV 627 PAILT + PH+ L+ FG +DAAL D + G P GKLPF+LP +M V Sbjct: 552 PAILTALLPHSRALLVTFGASDAALLDVVQGVAKPRGKLPFDLPRSMEDV 601 Lambda K H 0.319 0.137 0.408 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: 1210 Number of extensions: 71 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: 649 Length of database: 622 Length adjustment: 38 Effective length of query: 611 Effective length of database: 584 Effective search space: 356824 Effective search space used: 356824 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: 54 (25.4 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