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 Synpcc7942_0354 Synpcc7942_0354 Beta-glucosidase-related glycosidase-like
Query= SwissProt::Q7WUL3 (564 letters) >FitnessBrowser__SynE:Synpcc7942_0354 Length = 542 Score = 148 bits (373), Expect = 6e-40 Identities = 110/346 (31%), Positives = 158/346 (45%), Gaps = 25/346 (7%) Query: 55 LHVGGVMLRTMTAADAAATVTTLQSTATVPLLISANLEGGASQTVQEATHVGSNMALAAT 114 L VGGV+L AA+ A LQ + VPLLI+A++E G Q A +AL+A Sbjct: 54 LGVGGVILLGGNAAEVALRCQQLQEWSRVPLLIAADIEEGVGQRFAGAVQFPPPLALSAI 113 Query: 115 GSTDH------VRRAATVIGREARALGINWAFTPVVDIDLNFRNPITNTRTFGADAATVA 168 + D R + EA A+ +NW P+VDI+ N NP+ N R FG D TV+ Sbjct: 114 AAQDPERAQQLARSFGEITATEAIAIRLNWVLAPIVDINNNPANPVINVRAFGEDPETVS 173 Query: 169 AMGAEYVEAIQAQGLAASAKHFPGDGVDERDQHLLASVNTMSVEEWDDSFGVVYRAAIAA 228 + ++ Q + +AKHFPG G D HL + +R AIAA Sbjct: 174 QLTTAFIAGAQQFPVLTTAKHFPGHGDTATDSHLELPQIPHDRSRLEAVELEPFRRAIAA 233 Query: 229 GVKTVMVGHIMLPAYSRALRPGVADRDILPGVVAEELLNDLLRDRLGFNGLVVSDSTTMA 288 GV VM H+ +PA D D P ++ +L LLR LGF GL+V+D+ M Sbjct: 234 GVDAVMTAHLSIPA---------LDPD-YPATLSPAVLQGLLRRELGFEGLIVTDALVMQ 283 Query: 289 GLASVLPRSQAVPRVIAAGCDMFLFTKNLDEDFGYMRAGIRDGVITPERLDEAVTRILAL 348 +A+ +A AG D+ L + + + IR+G IT +RL++++ RI Sbjct: 284 AIAAHYGPGEAARLAFEAGADILLMPVDPEAAIQEIAKAIREGQITYDRLEQSLARIWRA 343 Query: 349 K--------ASLGLHRGTNLPAQGA-AGVLADPDHSATAREVAASS 385 K AS H PA ++ P H A A E+ +S Sbjct: 344 KQKVCGARPASFLPHAWEQEPAIAIDLEAVSQPKHWAIAAEILTAS 389 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: 649 Number of extensions: 31 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: 564 Length of database: 542 Length adjustment: 36 Effective length of query: 528 Effective length of database: 506 Effective search space: 267168 Effective search space used: 267168 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 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