Align sucrose hydrolase (XAC3490) (EC 3.2.1.-) (characterized)
to candidate 3608427 Dshi_1824 alpha amylase catalytic region (RefSeq)
Query= CAZy::AAM38333.1 (644 letters) >FitnessBrowser__Dino:3608427 Length = 587 Score = 162 bits (410), Expect = 4e-44 Identities = 164/558 (29%), Positives = 240/558 (43%), Gaps = 77/558 (13%) Query: 105 LQGVAERVPYLQELGVRYL-------HLLPFLRARAGDNDGGFAVSDYGQVEPSLGSNDD 157 + GV + + L + V YL H+LPF + D GFAV+DY V P+LG D Sbjct: 76 MDGVHKPLDLLHDFLVEYLKGVVNGVHILPFFPFTSDD---GFAVTDYRAVNPTLGDWPD 132 Query: 158 LVALTSRLREAGISLCADFVLNHTADDHAWAQAARAGDARYLDYYHHFADRTLPDRYEAT 217 + + L +D VLNH + AW A R G A Y ++ + E Sbjct: 133 INRIADEFL-----LMSDLVLNHVSSQGAWFNAYRQGHAPYDRFFFEASP-------EDD 180 Query: 218 LGQVF-PHTAPGNFTWVDDTA---QWMWTTFYPYQWDLNWSNPAVFGDMALAMLRLANLG 273 L V P T P +TA + +W TF Q DL++ NP V + M + G Sbjct: 181 LSDVVRPRTTP--LLQQVETANGPRHVWCTFSHDQIDLDFRNPEVLLEFLRIMRLHIDNG 238 Query: 274 VETFRLDSTAYLWKRIGTDCMNQPEAHTLLVALRAVTDIVAPAVVMKAEAIVPMTQLPPY 333 V RLD+ A++WK IGT ++ P+ H ++ +R + D V++ E VP + Y Sbjct: 239 VRIIRLDAVAFIWKVIGTPSIHLPQTHAIVRLMRLLCDFAQEPVILLTETNVPNAENLSY 298 Query: 334 FGSGVDEGHECHLAYHSTLMAAGWSALALQRGDILHNVIAHSPPLPRHCAWLSYVRCHDD 393 FG+ +E H Y+ TL A+ L+ PP CA+L++ HD Sbjct: 299 FGN----RNEAHAVYNFTLPPLVLHAMMSGTATYLNRWSTGMPPAQLGCAYLNFTASHDG 354 Query: 394 IGW----NVLQHEACGNAAQPPFSLRDVARFYA-NAVPGSYARGESFQSSGDGVHGTNGM 448 IG VL + A+ ++RD+ + A+PG GES + M Sbjct: 355 IGMRPAEGVLPED---EKARVIDTVRDLGGLVSMRALPGG---GESPYEL--NITFFEAM 406 Query: 449 AAALAGIQAAQEAGDAAALAVAVDRLVLLYAIALAMPGVPLIYMGDELAMVNDPGYRHDP 508 A G Q V R + I +++ G+P Y+ LA ND HD Sbjct: 407 GATYKGRDDYQ-----------VARFLCSQTIVMSLEGIPAFYIHSMLATPND----HDQ 451 Query: 509 -HRQHEGRWLHRPAMDW-QLAAQRHDANSLSGTVYRRLRGLIRQRAALGALAADQALASI 566 R+ R ++R D+ L A HD +++ V L +R RA A + ++ Sbjct: 452 VTRRGMNRAINRHNWDYPHLKALLHDPDTVQAQVLGALSDRLRLRARQSAFHPNATQFTL 511 Query: 567 ALNDPRVF-----VLTRGDSFIALHNFSDQPLDVELAAIGI---DGWTLLAIDDAIGGAA 618 L DPR+F L R S ALHN SD+ + V AAI + +GW D + G A Sbjct: 512 QL-DPRIFGVWRQSLDRHQSIFALHNVSDETVVVSPAAINLIEGEGW-----HDLLSGEA 565 Query: 619 ARGDGS-IVLPPYGVRWL 635 R G+ IVL PY RW+ Sbjct: 566 IRNGGAEIVLAPYQCRWI 583 Lambda K H 0.322 0.136 0.433 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: 899 Number of extensions: 36 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 644 Length of database: 587 Length adjustment: 37 Effective length of query: 607 Effective length of database: 550 Effective search space: 333850 Effective search space used: 333850 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 (21.9 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