Align β-fructofuranosidase (SacA;FF33) (EC 3.2.1.26) (characterized)
to candidate Echvi_2806 Echvi_2806 Beta-fructosidases (levanase/invertase)
Query= CAZy::BAL70276.1 (485 letters) >FitnessBrowser__Cola:Echvi_2806 Length = 498 Score = 469 bits (1208), Expect = e-137 Identities = 235/459 (51%), Positives = 302/459 (65%), Gaps = 18/459 (3%) Query: 17 ESGFRPHWRPKRHFTPAKNWMNDPNGMVYLEGVYHLFFQYNPGDSVWGDIHWGHATSTDL 76 + F +RP+ HF+P + WMNDPNGMVYL+G YHLF+Q+ P +VWG +HWGHA S DL Sbjct: 32 QKSFDEQFRPQYHFSPPQQWMNDPNGMVYLDGEYHLFYQHYPDSNVWGPMHWGHAVSEDL 91 Query: 77 LHWQEQPVALASEPDGLGYIFSGGAVVDWENSSGFQSGDQPPLVATFTHHSKEEVQAQSL 136 LHW P+AL PD LGYIFSG AV+D N+SG Q P+VA FT+H E Q+Q + Sbjct: 92 LHWDHLPIALY--PDSLGYIFSGSAVIDHGNTSGLGKNGQDPMVAIFTYHHDENGQSQGI 149 Query: 137 AVSTDGGLSWDKYPHNPVIPNPGIKDFRDPKVIWH---RDSGHWVMVLAVGDQVHFYRSR 193 A S D G SW KY +NPV+ +PGI DFRDPKV W+ SG W+M LAV D++ FY S Sbjct: 150 AFSNDKGRSWTKYRNNPVLESPGIPDFRDPKVSWYDRGNGSGKWIMTLAVKDKISFYSSP 209 Query: 194 DLKDWVFTSGFGRTSGAHGGVWECPDLFPLRDADGEERWCLLVSINPGGPNGGSATQYFI 253 +L DW S F A+GGVWECPDLFPL+ G E+W LLVSINPGGPNGGSATQYFI Sbjct: 210 NLIDWTHESDFNPEWAAYGGVWECPDLFPLKTNSGNEKWMLLVSINPGGPNGGSATQYFI 269 Query: 254 GGFDGEAFVPEHEDIRWLDYGTDNYAGVTWDGLQRVDDRRLFIGWMSNWQYANKVPTSLW 313 G FDG+ + E E I+WLDYGTDNYAGVTW + D RRLFIGWMSNWQYAN VPT+ W Sbjct: 270 GNFDGQNYTAEGESIKWLDYGTDNYAGVTWSNIPPEDGRRLFIGWMSNWQYANIVPTTEW 329 Query: 314 RGAMTIPRELSLYRDKGALRLANAPAREVDEARRRVVSMPLQPGNSIALPGN-SALDLVL 372 R A TIPREL+L D G R+A+ P +E+++ R+ + + G++ AL L+L Sbjct: 330 RSANTIPRELALITDHGVERVASRPIKELEQLRQ---TTEIIQGSTHALKDPLFELELEK 386 Query: 373 KIGGAPELELEFSAGENGGRLLLALSAERGALLLDRRESGWV--EEGFGREISAPLAHAL 430 + G + + L+ GE + ++ E L+ DR ESG + EEGFG+ I+AP+ Sbjct: 387 ESGESARITLKNELGEK-----VMITFEDNQLIFDRTESGKISFEEGFGKRITAPITDIT 441 Query: 431 HGESELRILIDGSSVEVFIDDGRTAVTALFFSSAPLSHM 469 +R+ D SS+E+FI+DG +T + F +AP S + Sbjct: 442 --IETIRMYADRSSLEIFINDGALVMTEIIFPNAPYSQL 478 Lambda K H 0.319 0.138 0.449 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: 949 Number of extensions: 45 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: 485 Length of database: 498 Length adjustment: 34 Effective length of query: 451 Effective length of database: 464 Effective search space: 209264 Effective search space used: 209264 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 (21.7 bits) S2: 52 (24.6 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