Align Extracellular sucrase; Beta-fructofuranosidase; Invertase; Protein B46; Saccharase; EC 3.2.1.26 (characterized)
to candidate AO356_15155 AO356_15155 sucrase
Query= SwissProt::F8DT27 (413 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_15155 Length = 424 Score = 377 bits (968), Expect = e-109 Identities = 189/409 (46%), Positives = 259/409 (63%), Gaps = 25/409 (6%) Query: 7 SRWTRAQAMKVNKFDLTTSMPEIGTDFPIMRDDLWLWDTWPLRDINGNPVSFKGWNVIFS 66 S WTRA A+KV D TT+ P + DFP++ +D+++WDT PLRD++GN S GW+VIF+ Sbjct: 16 SLWTRADALKVRADDPTTTQPLVSADFPVLNNDVFIWDTMPLRDLDGNVTSVDGWSVIFT 75 Query: 67 LVADR--NIP--------------WNDRHSHARIGYFYSKDGKSWVYGGHLLQESANTRT 110 L ADR N P WNDRH A++ Y++S+ GK+W +GG ++ E + Sbjct: 76 LTADRHPNDPQYLDEDGNYDILRDWNDRHGRAKMYYWFSRTGKNWEFGGRVMAEGVSPTA 135 Query: 111 AEWSGGTIMAPGSRNQVETFFTSTLFDKNGVREAVAAVTKGRIYADSEGVWFKGFDQSTD 170 EW+G I+ R +V+ ++T+ A +GR+ GV GF++ Sbjct: 136 REWAGTPILL-NDRGEVDLYYTAV------TPGATIVKVRGRVVTTEHGVSMVGFEKVKP 188 Query: 171 LFQADGLFYQNYAENNLWNFRDPHVFINPEDGETYALFEANVATVRGEDDIGEDEIGPVP 230 LF+ADG YQ A+N W FRDP F +P DG+ Y LFE NVA RG +GE EIG VP Sbjct: 189 LFEADGKMYQTEAQNAFWGFRDPWPFRDPNDGKLYMLFEGNVAGERGSHKVGEAEIGDVP 248 Query: 231 ANTVVPKDANLCSASIGIARCLSPDRTEWELLPPLLTAFGVNDQMERPHVIFQNGLTYLF 290 ++ +A +GIA D +WE+LPPLLTA GVNDQ ERPH +FQ+G YLF Sbjct: 249 PGYEDVGNSRYQTACVGIAVARDADGDDWEMLPPLLTAVGVNDQTERPHFVFQDGKYYLF 308 Query: 291 TISHDSTYADGLTGSDGLYGFVSENGIFGPYEPLNGSGLVLGGPASQPTEAYAHYIMNNG 350 TISH TY DG+TG DG+YGFV+++ +FGPY PLNGSGLVLG P+SQP + Y+HY+M NG Sbjct: 309 TISHTFTYGDGVTGPDGVYGFVADS-LFGPYVPLNGSGLVLGNPSSQPFQTYSHYVMPNG 367 Query: 351 LVESFINEIIDPKSG-KVIAGGSLAPTVRVELQGHETFATEVFDYGYIP 398 LV SFI+ + ++G ++ GG+ APTV ++++G +TF +DYGYIP Sbjct: 368 LVTSFIDSVPTDETGTQIRVGGTEAPTVGMKIKGQQTFVVAEYDYGYIP 416 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: 652 Number of extensions: 50 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: 424 Length adjustment: 32 Effective length of query: 381 Effective length of database: 392 Effective search space: 149352 Effective search space used: 149352 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