Align sucrose hydrolase (SuxB;XCC3359) (EC 3.2.1.-) (characterized)
to candidate H281DRAFT_06049 H281DRAFT_06049 trehalose synthase
Query= CAZy::AAM42629.1 (637 letters) >FitnessBrowser__Burk376:H281DRAFT_06049 Length = 1153 Score = 163 bits (412), Expect = 5e-44 Identities = 124/447 (27%), Positives = 204/447 (45%), Gaps = 59/447 (13%) Query: 69 QARPAALRHLDDSRAPGWFGQQDMLGYSAYVDRF-------AGTLRGVAERVPYLQELGV 121 + +PA L DD P W+ +D + Y ++ F G G+ ++ Y+ ELGV Sbjct: 30 RGKPATLS--DD---PLWY--KDAIIYQVHIKSFFDANNDGVGDFPGLIAKLDYIAELGV 82 Query: 122 RYLHLLPFLRARAGDNDGGFAVSDYGQVEPALGSNDDLVALTARLRAANISLCADFVLNH 181 + LLPF + D+ G+ ++DY V P G D+ A I + + V+NH Sbjct: 83 NAIWLLPFYPSPRRDD--GYDIADYRNVHPDYGQLSDVKRFIQEAHARGIRVITELVINH 140 Query: 182 TADDHAWAQAARAGDTRYLDYYHHFADRNAPDQYDTTLVQVFPQTAPGNFTWVDETRQWM 241 T+D H W Q AR ++ + + + +Y T + +F + P N+T + Sbjct: 141 TSDQHPWFQRARRAKPGS-NHRNFYVWSDTDQKYQETRI-IFIDSEPSNWTHDPVAGAYY 198 Query: 242 WTTFYPYQWDLNWSNPAVFGEMALAMLELANLGVEAFRLDSTAYLWKRPGTNCMNQPEAH 301 W FY +Q DLN+ NPAV E+ M ++G++ RLD+ YL +R GTN N PE H Sbjct: 199 WHRFYSHQPDLNFDNPAVLREVLQIMRFWLDMGIDGLRLDAVPYLVEREGTNNENLPETH 258 Query: 302 TILVALRAVADIVAPSVVMKAEAIVPMAELPPYFGSGVQRGHECHLAYHSTLMAAGWSAL 361 IL +RA D P+ ++ AEA ++ YFG ECH+A+H LM + ++ Sbjct: 259 AILKKIRATIDAEYPNRMLLAEANQWPEDVKEYFGD----EDECHMAFHFPLMPRIYMSI 314 Query: 362 ALQRGDILQDVIAHSPPLPPNCAWLSYVRCHDDIGWNVLQHEAAGTAAQPPFSLREVAQF 421 A + + D++ +P L W ++R HD++ +L V Sbjct: 315 ASEDRFPITDIMRQTPDLAETNQWAIFLRNHDEL------------------TLEMVTDS 356 Query: 422 YANAVPGSYARGESFQSSGDGVHGTNGMSAALVGVQAAHEHADAAAAARAVDRLVLLYAV 481 + + +YA ++ + +G++ A R R+ L+ ++ Sbjct: 357 ERDYLWNTYA--------------SDRRARLNLGIR----RRLAPLMERDRRRIELINSL 398 Query: 482 SLAMPGVPLIYMGDELALPNDTAYLDD 508 L+MPG P+IY GDEL + D +L D Sbjct: 399 LLSMPGTPVIYYGDELGM-GDNIHLGD 424 Lambda K H 0.321 0.134 0.422 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: 1772 Number of extensions: 100 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: 637 Length of database: 1153 Length adjustment: 42 Effective length of query: 595 Effective length of database: 1111 Effective search space: 661045 Effective search space used: 661045 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: 56 (26.2 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