Align sucrose hydrolase (Suh) (EC 3.2.1.-) (characterized)
to candidate H281DRAFT_02776 H281DRAFT_02776 maltose alpha-D-glucosyltransferase/ alpha-amylase
Query= CAZy::AAQ93678.1 (644 letters) >FitnessBrowser__Burk376:H281DRAFT_02776 Length = 554 Score = 153 bits (387), Expect = 2e-41 Identities = 152/566 (26%), Positives = 236/566 (41%), Gaps = 81/566 (14%) Query: 103 GTLQGVAERVPYLQELGVRYLHLLPFLRARAGDNDGGFAVSDYGQVEPSLGSNDDLVALT 162 G QG+ R+ YLQ LGV + L+PF + DN G+ +SDY V+P G+ D T Sbjct: 29 GDFQGLLRRLDYLQGLGVTTIWLMPFQPSPGRDN--GYDISDYYNVDPKYGTLGDFSEFT 86 Query: 163 SRLREAGISLCADFVLNHTADDHAWAQAARAG-DARYLDYYHHFADRTVPDRYEATLGQV 221 RE G+ + D V+NHT+D H W + AR+ D++Y D+Y ++D+ P+ A G V Sbjct: 87 HACRERGLRVMIDLVVNHTSDQHPWFREARSDPDSQYRDWY-VWSDKQPPN---AKDGVV 142 Query: 222 FPHTAPGNFTWVDDTAQWMWTTFYPYQWDLNWSNPAVFGDMALAMLRLANLGVEAFRLDS 281 FP +T+ +W + FY +Q DLN +NP V ++ M LGV FR+D+ Sbjct: 143 FPGVQKSTWTFDKQAKRWYFHRFYEFQPDLNTANPYVRAELLKIMGFWIQLGVSGFRMDA 202 Query: 282 TAYLWKRIGTDCMNQSEAHTLLVALRAVTDIVAPAVVMKAEA-IVPMTQLPPYFGSGVDE 340 ++ G E + +L R ++ AEA ++P T L YFG DE Sbjct: 203 VPFVIATKGPKVREPVEQYDMLREFREFLQWRQGDAIILAEANVLPDTDL-EYFG---DE 258 Query: 341 GHECHLAYHSTLMAAGWSALALQRGDILHNVIAHSPPLPRHCAWLSYVRCHDDIGWNVLQ 400 G + ++ L + ALA L + + P P W ++R HD++ L Sbjct: 259 GERLQMMFNFQLNQNTFYALATGDTAPLKKALTATRPRPATAQWGVFLRNHDELDLGRLT 318 Query: 401 HEACGNAAQPPFSLRDVARFYANAVPGSYARGESFQSSGDGVHGTNGMAAALAGIQAAQE 460 E AV ++A Q G+ +A LAG + Sbjct: 319 PE------------------QREAVFAAFAPEPDMQLYERGIR--RRLAPMLAGDRR--- 355 Query: 461 AGDAAALAVAVDRLVLLYAIALAMPGVPLIYMGDELAMVNDPGYRDDPHRQHEGRWLHRP 520 RL L Y++ L +PG P+ GDE+ M +D + + +W P Sbjct: 356 ------------RLELAYSLMLTLPGTPVFRYGDEIGMGDDLRLPERECARTPMQWSTEP 403 Query: 521 AMDW---------------------QLAAQRHDAKSLSGTVYRRLRGLIRQRAALGALA- 558 + +A+QR D S + R +IR R + ++ Sbjct: 404 EGGFTKHAKPPCRVITGGAYGFERVNVASQRRDPNSFLNWMER----MIRMRREVPEISW 459 Query: 559 ADQALASIALNDPRVFALT---RGDSFIALHNFSDQLLDVEL-AAIGVDGWTLL--AIDD 612 D + + +D V AL R +S + LHNF + V+ + G L + D Sbjct: 460 GDFDVLRTSRSD--VLALRFDWRNNSVLCLHNFGAEACTVKFRSGCNEPGQNRLINLLSD 517 Query: 613 AIGGAAARGDGSIVLPPYGVRWLQRG 638 G ++VL PYG RW + G Sbjct: 518 EHSEEQDDGRHAVVLEPYGYRWYRVG 543 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: 968 Number of extensions: 49 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 2 Length of query: 644 Length of database: 554 Length adjustment: 37 Effective length of query: 607 Effective length of database: 517 Effective search space: 313819 Effective search space used: 313819 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