Align Trehalase; Alpha,alpha-trehalase; Alpha,alpha-trehalose glucohydrolase; EC 3.2.1.28 (characterized)
to candidate BPHYT_RS10000 BPHYT_RS10000 glucoamylase
Query= SwissProt::P71741 (680 letters) >FitnessBrowser__BFirm:BPHYT_RS10000 Length = 623 Score = 337 bits (865), Expect = 8e-97 Identities = 218/617 (35%), Positives = 320/617 (51%), Gaps = 18/617 (2%) Query: 50 PFPPIADYAFLSDWETTCLISPAGSVEWLCVPRPDSPSVFGAILDRS-AGHFRLGPYGVS 108 P P + + +TT L+S GS++++C PR DSP++F +L+ S G F + P Sbjct: 11 PALPTDARGMIGNMKTTALVSLRGSIDFMCFPRIDSPAIFAGLLEPSRGGAFTIEPTFEG 70 Query: 109 VPSARRYLPGSLIMETTWQTHTGWLIVRDALVMGKWHDIERRSRTHRRTPMDWDAEHILL 168 + YLP + ++ T + T G + D + + E S P+ + ++ Sbjct: 71 ANVKQMYLPDTNVLLTRFMTPEGVCELLDFMPVP-----EDGSGADAAAPLP----NCVI 121 Query: 169 RTVRCVSGTVELMMSCEPAFDYHRLGATWEYSAEAYGEAIARANTEPDAHPTLRLTTNLR 228 R VR V G + M CEP FDY R T + A AN ++ LRL + L Sbjct: 122 RVVRIVHGRMAFRMRCEPRFDYARGAHTAHIDKNGGVDFHAAANAGSESGTQLRLNSTLP 181 Query: 229 IGLEGREARARTRMKEGDDVFVALSWTKHPPPQTYD-EAADKMWQTTECWRQWINIGNFP 287 + L+ A A + G+ + +++D EAA + T WR W + Sbjct: 182 LALDHGAAHAEFELSHGETAGFVFGDAEGLREKSFDCEAA--LTDTIRYWRSWSAQSTYR 239 Query: 288 DHPWRAYLQRSALTLKGLTYSPTGALLAASTTSLPETPRGERNWDYRYAWIRDSTFALWG 347 +R + RSALTLK L+ S GA++AA T LPE G R WDYR+ WIRD+ F+++ Sbjct: 240 GR-YREVVMRSALTLKLLSSSEHGAIVAAPTFGLPEALDGSRRWDYRFTWIRDAAFSVYA 298 Query: 348 LYTLGLDREADDFFAFIADVSGANNNERHPLQVMYGVGGERSLVEAELHHLS-GYDHARP 406 L LG EA F +IA S +++ L VMY + G+ E E+ LS G A Sbjct: 299 LLRLGYTGEARHFMTWIAGRSRLCDSDGS-LNVMYTIDGKEPPEETEITALSNGNGVAGV 357 Query: 407 VRIGNGAYNQRQHDIWGSILDSFYLHAKSREQVPENLWPVLKRQVEEAIKHWREPDRGIW 466 +GN A +Q Q D++G++LD+ YL+ K + + W + R V+ ++HWREPD GIW Sbjct: 358 PLVGNAARDQVQLDVYGALLDAIYLYNKYGAAISHDGWRDVTRTVDYVVEHWREPDHGIW 417 Query: 467 EVRGEPQHFTSSKVMCWVALDRGAKLAERQGEKSYAQQWRAIADEIKADILEH-GVDSRG 525 E R + S++MCWV +DR +LAE++ + ++W D I ADI EH + Sbjct: 418 EFRNGLRPLLHSRLMCWVTVDRALRLAEKRSLPAPLKRWFDTRDAIHADIHEHFWNEELN 477 Query: 526 VFTQRYGDEALDASLLLVVLTRFLPPDDPRVRNTVLAIADELTEDGLVLRYRVHETDDGL 585 F Q + LDAS L++ L RF+ P DPR T+ AI EL D L+ RY T DGL Sbjct: 478 AFVQTPDSQRLDASALMMPLVRFIGPTDPRWLGTLDAIGSELKVDPLIFRYTRGTTLDGL 537 Query: 586 SGEEGTFTICSFWLVSALVEIGEVGRAKRLCERLLSFASPLLLYAEEIEPRSGRHLGNFP 645 G EG F+ CSFW AL G V + + E++L++A+ + L++EE+ SG LGNFP Sbjct: 538 PGIEGGFSACSFWYAEALARAGRVDEGRLVFEKMLAYANHVGLFSEEV-ATSGEALGNFP 596 Query: 646 QAFTHLALINAVVHVIR 662 QA THLALI+A + R Sbjct: 597 QALTHLALISAAYQLDR 613 Lambda K H 0.319 0.134 0.425 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: 1198 Number of extensions: 59 Number of successful extensions: 6 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: 680 Length of database: 623 Length adjustment: 38 Effective length of query: 642 Effective length of database: 585 Effective search space: 375570 Effective search space used: 375570 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 (21.8 bits) S2: 54 (25.4 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