Align Extracellular sucrase; Beta-fructofuranosidase; Invertase; Protein B46; Saccharase; EC 3.2.1.26 (characterized)
to candidate AO353_04255 AO353_04255 sucrase
Query= SwissProt::F8DT27 (413 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04255 Length = 426 Score = 372 bits (955), Expect = e-107 Identities = 189/411 (45%), Positives = 258/411 (62%), Gaps = 27/411 (6%) Query: 7 SRWTRAQAMKVNKFDLTTSMPEIGTDFPIMRDDLWLWDTWPLRDINGNPVSFKGWNVIFS 66 S WTRA A+KV+ D TT+ P + DFP++ +++++WDT PLRDI+GN S GW+VIF+ Sbjct: 16 SLWTRADALKVHADDPTTTQPLVSADFPVLSNEVFIWDTMPLRDIDGNVASVDGWSVIFT 75 Query: 67 LVADR--NIP--------------WNDRHSHARIGYFYSKDGKSWVYGGHLLQESANTRT 110 L ADR N P WNDRH A++ Y++S+ GK W +GG ++ + + T Sbjct: 76 LTADRHPNDPEYIDENGNYDIIRDWNDRHGRAKMYYWFSRTGKDWQFGGRVMAQGVSPTT 135 Query: 111 AEWSGGTIMAPGSRNQVETFFTSTLFDKNGVREAVAAVTKGRIYADSEGVWFKGFDQSTD 170 EW+G I+ + V+ ++T+ A +GR+ GV GF + T Sbjct: 136 REWAGSPILL-NDQGDVDLYYTAV------TPGATIVKVRGRVVTTEHGVEMVGFKKVTS 188 Query: 171 LFQADGLFYQNYAENNLWNFRDPHVFINPEDGETYALFEANVATVRGEDDIGEDEIGPVP 230 LF+ADG YQ +N W FRDP F +P+DG+ Y LFE NVA RG +GE EIG VP Sbjct: 189 LFEADGEIYQTETQNPYWGFRDPWPFRDPKDGKLYMLFEGNVAGERGSHKVGEAEIGDVP 248 Query: 231 ANTVVPKDANLCSASIGIARCLSPDRTEWELLPPLLTAFGVNDQMERPHVIFQNGLTYLF 290 ++ +A +GIA D +WE+LPPLLTA GVNDQ ERPH +FQ+G YLF Sbjct: 249 PGYEDVGNSRFQTACVGIAVANDEDGDDWEMLPPLLTAVGVNDQTERPHFLFQDGKYYLF 308 Query: 291 TISHDSTYADGLTGSDGLYGFVSENGIFGPYEPLNGSGLVLGGPASQPTEAYAHYIMNNG 350 TISH TYADG+TG DG+YGFV+++ +FGPY PLNGSGLVLG P+SQP + Y+HY+M NG Sbjct: 309 TISHKFTYADGVTGPDGVYGFVADS-LFGPYVPLNGSGLVLGNPSSQPFQTYSHYVMPNG 367 Query: 351 LVESFINEIIDPKSG---KVIAGGSLAPTVRVELQGHETFATEVFDYGYIP 398 LV SFI+ + +S + GG+ APTV ++++G +TF +DYGYIP Sbjct: 368 LVTSFIDTVPTKESDTGMQYRVGGTEAPTVGIKVKGQQTFVVAEYDYGYIP 418 Lambda K H 0.319 0.137 0.438 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: 658 Number of extensions: 41 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: 413 Length of database: 426 Length adjustment: 32 Effective length of query: 381 Effective length of database: 394 Effective search space: 150114 Effective search space used: 150114 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: 50 (23.9 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