Align sucrose phosphorylase (EC 2.4.1.7) (characterized)
to candidate 3608427 Dshi_1824 alpha amylase catalytic region (RefSeq)
Query= CAZy::CAA80424.1 (488 letters) >FitnessBrowser__Dino:3608427 Length = 587 Score = 164 bits (415), Expect = 8e-45 Identities = 137/464 (29%), Positives = 211/464 (45%), Gaps = 62/464 (13%) Query: 7 LITYVDRLSGGGFPELRALLD---GRLQGLFGGVHALPFFNPIDGADAGFDPTDHTIVDP 63 LITY + L G L L D L+G+ GVH LPFF P +D GF TD+ V+P Sbjct: 68 LITYGNSLMDGVHKPLDLLHDFLVEYLKGVVNGVHILPFF-PFT-SDDGFAVTDYRAVNP 125 Query: 64 RLGSWDDVRALAGSVEIMADLIVNHVSAQSSWFQDFIAKGSDSEFADMFMTFGKAFPRGA 123 LG W D+ +A +M+DL++NHVS+Q +WF + + + + F + Sbjct: 126 TLGDWPDINRIADEFLLMSDLVLNHVSSQGAWF---------NAYRQGHAPYDRFFFEAS 176 Query: 124 SEQDLLNIYRPRLGCRFQRPRLQIGSQRMLWTTFTPQQIDIDVHSAHGALYLETILDRFA 183 E DL ++ RPR Q+ G R +W TF+ QID+D + L I+ Sbjct: 177 PEDDLSDVVRPRTTPLLQQVETANG-PRHVWCTFSHDQIDLDFRNPEVLLEFLRIMRLHI 235 Query: 184 EANVTAIRLDAAGYAIKKAGTSCFMIDETYAFLAKLAEKARDRGMEVLV----------E 233 + V IRLDA + K GT + +T+A + +L D E ++ E Sbjct: 236 DNGVRIIRLDAVAFIWKVIGTPSIHLPQTHA-IVRLMRLLCDFAQEPVILLTETNVPNAE 294 Query: 234 IHSYYRDQIEIASKVDRVYDFALPPLILHSLFTGDATALARWLEISPHNA-----ITVLD 288 SY+ ++ ++ VY+F LPPL+LH++ +G AT L RW P + Sbjct: 295 NLSYFGNR----NEAHAVYNFTLPPLVLHAMMSGTATYLNRWSTGMPPAQLGCAYLNFTA 350 Query: 289 THDGIGVIDVGAHSDGRP--GLLEPQAIDHLVEEIHRRSEGQSRLATGAAASNLDLYQVN 346 +HDGIG+ RP G+L +++ + R G Y++N Sbjct: 351 SHDGIGM---------RPAEGVLPEDEKARVIDTV--RDLGGLVSMRALPGGGESPYELN 399 Query: 347 CTYYDALG---RNDDDYLIAR-----AIQFFAPGIPQVYYVGLLGGINDMELLGKTGVGR 398 T+++A+G + DDY +AR I GIP Y +L ND + + + G+ R Sbjct: 400 ITFFEAMGATYKGRDDYQVARFLCSQTIVMSLEGIPAFYIHSMLATPNDHDQVTRRGMNR 459 Query: 399 DINRHFYEDREIDLALESP------LVKRLSDLIRFRNTHPAFN 436 INRH ++ + L P ++ LSD +R R AF+ Sbjct: 460 AINRHNWDYPHLKALLHDPDTVQAQVLGALSDRLRLRARQSAFH 503 Lambda K H 0.322 0.139 0.417 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: 723 Number of extensions: 43 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: 488 Length of database: 587 Length adjustment: 35 Effective length of query: 453 Effective length of database: 552 Effective search space: 250056 Effective search space used: 250056 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: 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