Align 6-phospho-β-glycosidase (GK1856) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate CA265_RS16425 CA265_RS16425 beta-glucosidase
Query= CAZy::BAD76141.1 (470 letters) >FitnessBrowser__Pedo557:CA265_RS16425 Length = 445 Score = 261 bits (667), Expect = 3e-74 Identities = 159/462 (34%), Positives = 239/462 (51%), Gaps = 30/462 (6%) Query: 13 FPAGFWWGSATSATQIEGAANEGGKGKNIWDHWYEQEPHRFFQGVGPEVASDFYHRYKED 72 F F WG AT+A QIEG A + GKG +IWD + + + + + A DFYHRY ED Sbjct: 7 FGQNFLWGVATAAAQIEGTATQYGKGPSIWDT-FTAKNGKIKKNHKLDPACDFYHRYAED 65 Query: 73 IALMKEIGHNSFRFSISWSRLIPDGVGEVNPEAVRFYNAVIDELLANGIEPFVNLYHFDM 132 +AL+K +G FRFSI+WSR++P G GE+N E +RFY+ +IDE L GI P+V LYH+D+ Sbjct: 66 LALVKLLGFKVFRFSIAWSRILPAGRGEINQEGIRFYHNLIDECLTQGITPYVTLYHWDL 125 Query: 133 PLAMQTIGGWENREVVDAYARYASLCFQLFGDRVKTWFTHNEPIVPVEGGYLYDFHYPNV 192 P A++ GGW + + A+ + S+C +GD+VK W NEP GY+ H P Sbjct: 126 PQALEDEGGWTSFSINAAFNAFVSICAIEYGDKVKNWIVLNEPFGYTSLGYMLGVHAPGK 185 Query: 193 VDFRRAVQVAYHTMIAHAKAVAAFRRAAIPDGKIGIILNLTPSYPRSQHPADVKAAHIAD 252 HT +A A RA I IG + + P +Q +DV A D Sbjct: 186 TGLGNFFSAVLHTALAQADG-GKILRAEISKANIGTTFSCSEIIPSTQSDSDVLVARRVD 244 Query: 253 LLFNRSFLDPAVKGEYPQDLIELLD----EYGFLPVTKANDRELIKENTIDLLGINYYQP 308 L NR F++P +P + L+ EYG + ++R + D +G+ Y P Sbjct: 245 CLMNRLFVEPTQGMGFPTANWDALEKFQIEYG---TWRLHER---MKFDFDFIGLQNYFP 298 Query: 309 RRVKAKENMPNPDAPFLPERFFDYYAMPGRKMNPYRGWEIYEKGIYDILINIKENYGNIE 368 VK +P A ++ A +K + GWE+ Y+I+ Y NI+ Sbjct: 299 LVVKYNAFIPVIQA-------WEVKAKSRKKPHTAMGWEVNADSFYNIVKQFAA-YPNIK 350 Query: 369 -CFISENGMGVEGEERFRDE--SGMIHDDYRIEFIREHLKWVHRAIEEGVNVKGYHLWTF 425 I+ENG + D+ +G + D RIE+ + +LK + + +EG+NV GY WT Sbjct: 351 NILITENGAA------YHDKLINGKVEDPERIEYFKLYLKALLKLKKEGINVTGYMAWTL 404 Query: 426 MDNWSWTNAYKNRYGLVAVDLENGLKRTIKKSGYWFKSLAEN 467 MDN+ W + R+GL+ D + +R+IK SGYW+++ ++ Sbjct: 405 MDNFEWAEGFTARFGLIYNDFKT-QERSIKDSGYWWQNFLKS 445 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: 673 Number of extensions: 38 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: 445 Length adjustment: 33 Effective length of query: 437 Effective length of database: 412 Effective search space: 180044 Effective search space used: 180044 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 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