Align β-galactosidase (Mbgl) (EC 3.2.1.23) (characterized)
to candidate CA265_RS16425 CA265_RS16425 beta-glucosidase
Query= CAZy::AEQ38581.1 (447 letters) >FitnessBrowser__Pedo557:CA265_RS16425 Length = 445 Score = 392 bits (1008), Expect = e-114 Identities = 204/440 (46%), Positives = 275/440 (62%), Gaps = 6/440 (1%) Query: 9 FGPGGLWGVASAAYQIEGAVNEDGRSPSIWDTFSHTPGNLKTGENGDVACDFYHRYHDDI 68 FG LWGVA+AA QIEG + G+ PSIWDTF+ G +K D ACDFYHRY +D+ Sbjct: 7 FGQNFLWGVATAAAQIEGTATQYGKGPSIWDTFTAKNGKIKKNHKLDPACDFYHRYAEDL 66 Query: 69 AFIREMNMQVHRFSLAWPRILPGGTGPVNQKGLDFYHRVIDRTLELGLQPWVTLIHWDLP 128 A ++ + +V RFS+AW RILP G G +NQ+G+ FYH +ID L G+ P+VTL HWDLP Sbjct: 67 ALVKLLGFKVFRFSIAWSRILPAGRGEINQEGIRFYHNLIDECLTQGITPYVTLYHWDLP 126 Query: 129 QCWRQGAAGTNRDICGLVSQLRGKVCSMSFGGLDQATWNVASR--CPTVLGYMQGTHAPG 186 Q T+ I + +C++ +G W V + T LGYM G HAPG Sbjct: 127 QALEDEGGWTSFSINAAFNAF-VSICAIEYGD-KVKNWIVLNEPFGYTSLGYMLGVHAPG 184 Query: 187 RRGFGNFLPAVHHAALAQAEGGRVLRAHVPDAQIGTTFSASYVQPAGPTWLSRMAAANYD 246 + G GNF AV H ALAQA+GG++LRA + A IGTTFS S + P+ + + A D Sbjct: 185 KTGLGNFFSAVLHTALAQADGGKILRAEISKANIGTTFSCSEIIPSTQSDSDVLVARRVD 244 Query: 247 VIANRLFLEPALGLGYPWKTTPFLLALQ-RYIRPGDMERLAFNFDFIGLQTYFRQLVRFD 305 + NRLF+EP G+G+P L Q Y ER+ F+FDFIGLQ YF +V+++ Sbjct: 245 CLMNRLFVEPTQGMGFPTANWDALEKFQIEYGTWRLHERMKFDFDFIGLQNYFPLVVKYN 304 Query: 306 LLNPGTWGREVPHAERGSKELTEMGWEVWPENIYRLLKQFAAYKGVKRIIITENGAAFPD 365 P EV A+ K T MGWEV ++ Y ++KQFAAY +K I+ITENGAA+ D Sbjct: 305 AFIPVIQAWEV-KAKSRKKPHTAMGWEVNADSFYNIVKQFAAYPNIKNILITENGAAYHD 363 Query: 366 KLEGEQVHDPQRIQFVQDHLAQVLRAKQEGVPVEGYFYWSLLDNFEWAEGYRPRFGLVYV 425 KL +V DP+RI++ + +L +L+ K+EG+ V GY W+L+DNFEWAEG+ RFGL+Y Sbjct: 364 KLINGKVEDPERIEYFKLYLKALLKLKKEGINVTGYMAWTLMDNFEWAEGFTARFGLIYN 423 Query: 426 DYPTQKRVLKDSGKWFRAFL 445 D+ TQ+R +KDSG W++ FL Sbjct: 424 DFKTQERSIKDSGYWWQNFL 443 Lambda K H 0.323 0.140 0.460 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: 682 Number of extensions: 30 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: 447 Length of database: 445 Length adjustment: 32 Effective length of query: 415 Effective length of database: 413 Effective search space: 171395 Effective search space used: 171395 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 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