Align Mrub_0288 (EC 3.2.1.21) (characterized)
to candidate CA265_RS16425 CA265_RS16425 beta-glucosidase
Query= CAZy::ADD27066.1 (444 letters) >FitnessBrowser__Pedo557:CA265_RS16425 Length = 445 Score = 366 bits (939), Expect = e-106 Identities = 188/441 (42%), Positives = 260/441 (58%), Gaps = 7/441 (1%) Query: 4 SDFPANFIWGTATSAYQIEGAVSEDGRGPSIWDTFSHTPGKTKGGDHGDVACDHYHRYPE 63 SDF NF+WG AT+A QIEG ++ G+GPSIWDTF+ GK K D ACD YHRY E Sbjct: 5 SDFGQNFLWGVATAAAQIEGTATQYGKGPSIWDTFTAKNGKIKKNHKLDPACDFYHRYAE 64 Query: 64 DIALMKELGVNAYRFSVAWPRILPEGRGRVNPRGLDFYNRLVDALLEQGITPWATLYHWD 123 D+AL+K LG +RFS+AW RILP GRG +N G+ FY+ L+D L QGITP+ TLYHWD Sbjct: 65 DLALVKLLGFKVFRFSIAWSRILPAGRGEINQEGIRFYHNLIDECLTQGITPYVTLYHWD 124 Query: 124 LPQSLEDQGGWPSRETAYAFAEYADLVTRHLGDRVKHWITLNEPWCSAYLGYHAGIHAPG 183 LPQ+LED+GGW S AF + + GD+VK+WI LNEP+ LGY G+HAPG Sbjct: 125 LPQALEDEGGWTSFSINAAFNAFVSICAIEYGDKVKNWIVLNEPFGYTSLGYMLGVHAPG 184 Query: 184 QQNFKHSIWASHHLLLAHGLAVPVIRRNVTGARVGITLNLSPGYPASPDPADVAAARRFD 243 + + A H LA ++R ++ A +G T + S P++ +DV ARR D Sbjct: 185 KTGLGNFFSAVLHTALAQADGGKILRAEISKANIGTTFSCSEIIPSTQSDSDVLVARRVD 244 Query: 244 GFQNRWYLDPLYGLGYPADMLALYGEAPSVQGDDLI--TIAAPTDFLGINYYSRAVVRNS 301 NR +++P G+G+P + G + + DF+G+ Y VV+ + Sbjct: 245 CLMNRLFVEPTQGMGFPTANWDALEKFQIEYGTWRLHERMKFDFDFIGLQNYFPLVVKYN 304 Query: 302 DLEP----YRFQYVRVGEEHTDMDWEVYPEGLYDLLIRLGREYRPKAIYITENGAAYPDA 357 P + + + HT M WEV + Y+++ + K I ITENGAAY D Sbjct: 305 AFIPVIQAWEVKAKSRKKPHTAMGWEVNADSFYNIVKQFAAYPNIKNILITENGAAYHDK 364 Query: 358 VADDGGIHDLERVRYFQRHLALCLEALQHGAPLKGYFAWSLLDNFEWAEGYAKRFGLVYV 417 + +G + D ER+ YF+ +L L+ + G + GY AW+L+DNFEWAEG+ RFGL+Y Sbjct: 365 LI-NGKVEDPERIEYFKLYLKALLKLKKEGINVTGYMAWTLMDNFEWAEGFTARFGLIYN 423 Query: 418 DFPSQRRRIKASGYWFRDFLR 438 DF +Q R IK SGYW+++FL+ Sbjct: 424 DFKTQERSIKDSGYWWQNFLK 444 Lambda K H 0.322 0.140 0.458 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: 659 Number of extensions: 26 Number of successful extensions: 3 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: 444 Length of database: 445 Length adjustment: 32 Effective length of query: 412 Effective length of database: 413 Effective search space: 170156 Effective search space used: 170156 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 (21.9 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