Align 6-phospho-β-glycosidase (GK1856) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate WP_066329731.1 BLR17_RS09380 family 1 glycosylhydrolase
Query= CAZy::BAD76141.1 (470 letters) >NCBI__GCF_900100165.1:WP_066329731.1 Length = 465 Score = 278 bits (710), Expect = 4e-79 Identities = 167/473 (35%), Positives = 260/473 (54%), Gaps = 24/473 (5%) Query: 6 KQPITYRFPAGFWWGSATSATQIEGAANEGGKGKNIWDHWYEQEPHRFF---QGVGPEVA 62 K+ T + F WG A++A Q+EGA GKG++ WD + F Q VA Sbjct: 4 KEKTTAQEQKPFLWGVASAAYQVEGAYQADGKGESKWDFLTNKVGVTQFIIGQKQTGNVA 63 Query: 63 SDFYHR--YKEDIALMKEIGHNSFRFSISWSRLIPDGVGEVNPEAVRFYNAVIDELLANG 120 + Y R Y +DI LMKE+G NS+RFS+ WSR+IPDG+G VN +A+ Y+ +ID+L A G Sbjct: 64 INMYDRTQYLKDIQLMKELGVNSYRFSLDWSRIIPDGIGAVNEKALAHYDVLIDDLKAAG 123 Query: 121 IEPFVNLYHFDMPLAMQTIGGWENREVVDAYARYASLCFQLFGDRVKTWFTHNEPIVP-V 179 IEP V LYHFD P A+ GGW N E+++ Y YA + F+ +G +VK + T NEP + Sbjct: 124 IEPVVTLYHFDYPFALVQKGGWGNPEMINWYKNYAQIVFKRYGKKVKHFITFNEPYIEFF 183 Query: 180 EGGYLYDFHY---PNVVDFRRAVQVAYHTMIAHAKAVAAFRRAAIPDGKIGIILNLTPSY 236 +L + P V F R + A+ ++A A+ + + + + GKIG+ N +P Sbjct: 184 VAEFLMNMEQSKEPAVTRFARGMMKAHRELVASAEVIKMYHKMNL-GGKIGMTFNFSPCS 242 Query: 237 PRS-QHPADVKAAHIADLLFNRSFLDPAVKGEYPQDLIELLDEYGFLPVTKANDRELIKE 295 P +P DV+A+ + + L N FLD KG YP+++++L +Y A+D +++ Sbjct: 243 PLDPNNPKDVQASALQEKLLNTVFLDGYFKGTYPKEVVDLFTKYDPAFQPAADDMKILAA 302 Query: 296 NTIDLLGINYYQPRRVKAKENMPNPDAPFLPERFFDYYAMPGRKMNPYRGWEIYEKGIYD 355 N D LGIN+Y P VK +P PF + + K+ + G + + +Y Sbjct: 303 NKPDFLGINFYAPALVKY-----DPSEPF----EMKWMDINTDKIKSHNG-PVRPEELYK 352 Query: 356 ILINIKENYGNIECFISENGMGVEGEERFRDESGMIHDDYRIEFIREHLKWVHRAIEEGV 415 L+ IK+ Y N E I+ENG G EGE+ + ++ D R ++I+ H++ V +A +EGV Sbjct: 353 FLVKIKKEYNNPEIMITENGAGFEGED--IKATPIVKDPLRADYIKRHVEAVDKAKKEGV 410 Query: 416 NVKGYHLWTFMDNWSWTNAYKNRYGLVAVDLENGLKRTIKKSGYWFKSLAENN 468 + GY W+ DN+ W Y R+GL+ VD E +R K+S Y ++ + + + Sbjct: 411 KMIGYFPWSGWDNFEWVFGYTKRFGLIYVDFET-QERIPKQSFYEYQKIIKQH 462 Lambda K H 0.321 0.140 0.446 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: 701 Number of extensions: 44 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: 470 Length of database: 465 Length adjustment: 33 Effective length of query: 437 Effective length of database: 432 Effective search space: 188784 Effective search space used: 188784 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: 51 (24.3 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