Align β-galactosidase; β-D-fucosidase (GalF) (EC 3.2.1.23|3.2.1.38) (characterized)
to candidate N515DRAFT_0922 N515DRAFT_0922 beta-galactosidase
Query= CAZy::CAZ44333.1 (583 letters) >FitnessBrowser__Dyella79:N515DRAFT_0922 Length = 623 Score = 383 bits (983), Expect = e-110 Identities = 226/581 (38%), Positives = 325/581 (55%), Gaps = 44/581 (7%) Query: 11 FKMGDRPIQLISGAIHYFRIVPAYWEDRLRKIKAMGCNCIETYVAWNVHEPREGEFHFER 70 F + R QL SG +H R+ YW R+R +KAMG N + Y+ WN E G F FE Sbjct: 50 FLLDGREFQLRSGEMHPIRVPAEYWTQRIRMVKAMGLNTVAIYLMWNALEKEPGVFDFES 109 Query: 71 -MADVAEFVRLAGELGLYVIVRPSPYICAEWEFGGLPAWLLKD-DMRLRC-NDPRFLEKV 127 D F++L + G++V +RP PY+CAEW+FGGLP +LL++ DMR+R +D R+++ V Sbjct: 110 GNRDFVRFIKLCQQEGMWVYLRPGPYVCAEWDFGGLPPYLLREPDMRVRHKDDARYMKAV 169 Query: 128 SAYYDALLPQLTPLLATKGGPIIAVQIENEYGSYGNDQAYLQAQRAMLIERGVDVLLFTS 187 + Y DA+ P++ PL+A +GGPI+ VQ+ENEY S+G D AYL+ +AM ERG+ S Sbjct: 170 TRYMDAIAPRIAPLMAERGGPILMVQVENEYASFGGDLAYLEQIQAMWRERGIHGPFSIS 229 Query: 188 DG----PQDDMLQGGMAEGVLATVNFGSRPKEAFDKLKEYQPDGPLMCMEYWNGWFDHWF 243 DG + G A G+ +F + A + P+ E + GW HW Sbjct: 230 DGLATIQKQQTYLPGTALGLDGDTDFAAAQAIAGEM--------PVWVGEGYPGWLTHWG 281 Query: 244 EPHHTRDAKDAARVLDDMLGMGASVNFYMVHGGTNFGFGSGANHS---DKYEPTVTSYDY 300 + R D A L ++ G S N Y+ HGGTNFGFG+GAN K+EPT+TSYDY Sbjct: 282 DQEFQRG--DYAATLKKLMAEGRSFNLYVAHGGTNFGFGAGANADADYGKFEPTITSYDY 339 Query: 301 DAAISEAGDLTPKYHAFREVIGKYVSLPEGELPANTPKADYGSVPVTRRVKLFDTLEPMT 360 A I E G+ T Y FRE+IG+++S P E+PA P + + + L+D L P Sbjct: 340 GAPIDERGEATADYRQFREIIGEHLSRPLSEVPAAPPAMRFAKIELKPYASLWDNLTPAP 399 Query: 361 E-VKDSICPEPMEKYGQNNGFIVY-STRISGPRPESRLTIQDVRDRALVFLDRKLIGVVE 418 + V+D + Q++G ++Y + + G RL+I+ VRD A VF + +G + Sbjct: 400 KSVEDGPVANEL-LLAQDHGMVLYRAMSLKG----GRLSIEGVRDYATVFGAGRYLGYIS 454 Query: 419 RWNPQSLP----VTVP----EDGAQLDILVENMGRVNYGPQLYDRKGITHGVRLNGQFLF 470 R L V VP +DG ++ILV++ G V YG + DRKGI +RLNG+ Sbjct: 455 RVRKPGLSEATEVEVPAPHAQDGEAIEILVDSFGHVGYGQAMADRKGIVGAIRLNGELQR 514 Query: 471 HWEVRSLELET--LAGLSFDTAGARAWEEEQPG-FYEAKLVIEDEPKDTFLRLEGWKKGV 527 W V L+ LAGL A E+P F++ L +E + DT+L ++ W KG Sbjct: 515 RWSVHGFPLDAAYLAGLR-----PLAQAPERPAVFFKGTLTLE-KTADTYLGMDAWDKGY 568 Query: 528 VFVNGFNLGRYWEVGPQQALYVPAPVLRQGENEIVVFELHR 568 V+VNG LGRYW +GPQQ L+ PA L+ G+NE++VF++HR Sbjct: 569 VWVNGHLLGRYWRIGPQQRLFCPASWLKAGKNEVLVFDMHR 609 Lambda K H 0.320 0.139 0.434 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: 1081 Number of extensions: 56 Number of successful extensions: 8 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: 583 Length of database: 623 Length adjustment: 37 Effective length of query: 546 Effective length of database: 586 Effective search space: 319956 Effective search space used: 319956 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: 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