Align Beta-N-acetylglucosaminidase/beta-glucosidase; 3-beta-N-acetyl-D-glucosaminidase/beta-D-glucosidase; Nag3; EC 3.2.1.21; EC 3.2.1.52 (characterized)
to candidate WP_011653854.1 RL_RS23135 glycoside hydrolase family 3
Query= SwissProt::Q7WUL3 (564 letters) >NCBI__GCF_000009265.1:WP_011653854.1 Length = 559 Score = 355 bits (911), Expect = e-102 Identities = 218/568 (38%), Positives = 320/568 (56%), Gaps = 26/568 (4%) Query: 3 DLTAAPFSLDDDGIAWVRTTLAEMGEDEKLGQLFCLITYTSDPEYLGYLTRGLHVGGVML 62 +L APF+LDD I+WVR A + D+K+GQLF LI +D E + L GGV Sbjct: 6 ELRKAPFNLDDAAISWVRDVYASLDLDDKIGQLFTLIMIGTDEEDFKRIA-SLRPGGVT- 63 Query: 63 RTMTA--ADAAATVTTLQSTATVPLLISANLEGGASQTVQEATHVGSNMALAATGSTDHV 120 R TA ++ L + + VP +ISA+LEG + + T V + LAA Sbjct: 64 RFFTADLEFERRVISDLVAKSKVPPIISADLEG-SRHSFAFGTPVLGQLGLAAVDDVQAT 122 Query: 121 RRAATVIGREARALGINWAFTPVVDIDLNFRNPITNTRTFGADAATVAAMGAEYVEAIQA 180 +++ ++ RE RA+G+ W+FTPV+DI+ FR+PI TR++G+D + + +V +Q Sbjct: 123 EKSSEILAREGRAMGVRWSFTPVIDINAAFRSPIVGTRSYGSDVSKIERHAVAHVHGLQR 182 Query: 181 QGLAASAKHFPGDGVDERDQHLLASVNTMSVEEWDDSFGVVYRAAIAAGVKTVMVGHIML 240 G+AA+AKH+PG+G D+RDQHL+ + N +S++EW ++FG +YR I GV +M GHI L Sbjct: 183 NGVAATAKHWPGEGYDDRDQHLVTTTNPLSMDEWKETFGRLYRTLITEGVLAIMSGHISL 242 Query: 241 PAYSRALRPGVADRDILPGVVAEELLNDLLRDRLGFNGLVVSDSTTMAGLASVLPRSQAV 300 PAY R+ P P V+ L DLLRD LGFNG++VSD+T M GL++ + Sbjct: 243 PAYIRSKMPDAGLEAFRPASVSRLLNVDLLRDELGFNGIIVSDATPMGGLSAWGHHLDTL 302 Query: 301 PRVIAAGCDMFLFTKNLDEDFGYMRAGIRDGVITPERLDEAVTRILALKASLGLHRGTN- 359 P +IA GCDM LF+ +ED ++A + DG IT ERL+EAV R+LALKA L L + ++ Sbjct: 303 PDIIANGCDMILFSDAPEEDMAAVKAAVEDGRITQERLEEAVLRVLALKAHLKLFQPSDV 362 Query: 360 LPAQG-AAGVLADPDHSATAREVAASSITLVKEEPGVLPITRERYPRVLVYDLQNGGSPI 418 LP + +LA PD A +RE S TLVK+ G+ P+ + RVL+ D GG I Sbjct: 363 LPDEAEVRHLLAHPDSVAASREYIGRSPTLVKDVNGIFPLDPAKTKRVLLVD---GG--I 417 Query: 419 GQGARAGAVEQFVDALV-EAGHDVTRFEPGGGWEGMAAPTTDVTERHDLVLYLANLSTRS 477 +E + AL+ + G +VT P PT D DLVLY + Sbjct: 418 IHPLMPQPLEFLLPALLRKEGFEVTIDRPD------IVPTPD---DFDLVLYTLGDESLL 468 Query: 478 NQTVVRIEWAEPMGANVPAYVH----SVPTVFVSFENPYHLFDVPRVRTLINTYGSSPVV 533 + + ++W G + ++ ++P+ +SF +PYHL+D PRV IN Y + V Sbjct: 469 VRGRIFVDWHRMGGGGLFKAMYRPWTNIPSAMISFGHPYHLYDAPRVPAYINAYSTMDSV 528 Query: 534 LETLLAALQGKAPFAGSSPVDAFCGQWD 561 E ++ + G+ PF G++PVD FCG D Sbjct: 529 QEAVVDCMLGRKPFLGTNPVDPFCGLED 556 Lambda K H 0.318 0.134 0.391 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: 771 Number of extensions: 28 Number of successful extensions: 5 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: 564 Length of database: 559 Length adjustment: 36 Effective length of query: 528 Effective length of database: 523 Effective search space: 276144 Effective search space used: 276144 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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