Align Alpha,alpha-trehalose phosphorylase; TPase; EC 2.4.1.64 (characterized)
to candidate N515DRAFT_1906 N515DRAFT_1906 alpha,alpha-trehalose phosphorylase
Query= SwissProt::Q8L164 (774 letters) >FitnessBrowser__Dyella79:N515DRAFT_1906 Length = 1036 Score = 538 bits (1386), Expect = e-157 Identities = 294/751 (39%), Positives = 443/751 (58%), Gaps = 13/751 (1%) Query: 29 RNETIFTLANGYIGMRGTFEERYSGPKNTSFNGTYINGFYEIHDIVYPEGGYGFAKIGQT 88 ++E++F LANG +G+RG EE S P SF ++ +E I Y E GFA T Sbjct: 43 QDESLFALANGALGVRGGLEEGDS-PSQASF----LSAAWERTPIEYHERFPGFAAHTDT 97 Query: 89 MLNVADSKIIKLYVDGEEFDLLQGKILFYERVLDMKKGFVERKVKWESPTGKILEVKIKR 148 + VAD+ I+L + L +G+ L +ER LD+++G R ++W SP G+ LE++ +R Sbjct: 98 RIPVADATRIQLRLGDVPVRLAEGEWLDFERRLDLREGCYRRFLRWRSPAGETLEIEAER 157 Query: 149 IVSLNRQHLAAISFTMQPVNFTGKIRFVSAIDGNVSNINDSEDVRVGSNLKGKVLKTIDK 208 IVSL+ L A+ + ++ V++TG + SAI +D R+G+ L G L T+D Sbjct: 158 IVSLDEPGLLALRYRVRSVDYTGPVTLESAISTARDAAEQGDDPRIGTRLDGG-LHTVDA 216 Query: 209 SVEGLKGWIVQKTQKSNFSYACAIDNVLVADSKYEVSNSLEEDGVKVIVDLEAEKGTSYT 268 + E W+ Q+T S ACA + +L + GV G + T Sbjct: 217 AAEPDFAWVRQQTTHSGIRLACAQAHRAQDGGLDCHFANLAQHGVVHSYTGMLTPGQAVT 276 Query: 269 LNKFISYYTSK---DFDENKLVALALEEIEKAKNDGFETIEKEQEEFLNSFWKDADVIIE 325 L K+++Y ++ D ++ L+A +E A + + + + Q + L W AD+ I+ Sbjct: 277 LEKYVAYAWTEPHGDDADDALLARTRGILEAAAHLRYAGLLERQRQALAPLWDGADLAID 336 Query: 326 GDKALQQGIRFNEFHLLQSVGRDGKTNIAAKGLTGGGYEGHYFWDSDIYIMPFFLYTKPE 385 GD A +Q +RFN FHL QS RDG+ + AAKGLTG GYEGHYFWD++ +I+P PE Sbjct: 337 GDAATEQALRFNLFHLFQSSCRDGQGSAAAKGLTGEGYEGHYFWDAEAFILPVLATVAPE 396 Query: 386 IAKALVMYRYNLLDAARSRAKELGH-KGALYPWRTIDGPECSAYFPAGTAQYHINADIVY 444 +A+ +++YR+ +LD +R A+EL H +GALY WRTI G ECSAY+P G+AQYHINA I + Sbjct: 397 LARGMLLYRHRILDRSRRHARELNHPRGALYAWRTISGDECSAYYPGGSAQYHINAAIAW 456 Query: 445 ALKRYVEATNDVDFLYDYGCEILFETARFWEDLGAYIPLKGNKFCINCVTGPDEYTALVD 504 A+ YV+A+ D DFL D+G EILFETAR W D+G + +G+ FCI+ VTGPDEY+ALVD Sbjct: 457 AISLYVDASGDTDFLRDHGAEILFETARVWLDIGHFNARRGDAFCIHEVTGPDEYSALVD 516 Query: 505 NNAYTNYMAKMNLEYAYDIANKMKKEVPQKYQKVASKLNLKDEEIVAWKKAADNMYLPYS 564 NN YTN MA+ +L A A M P +Y + +++ L ++E+ W++AA+ MYLP Sbjct: 517 NNHYTNRMAQRHLRDAAATALWMAGAAPVEYGALCARIGLGEDEVAQWRRAAEAMYLPED 576 Query: 565 KELDIIPQDDSFLYKERI---TVDEIPEDQFPLLLHWHYLNIYRYQICKQPDVLLLMFLQ 621 L + PQDD FL + R+ + + + PLLL H L IYR+Q+CKQ D LL + L Sbjct: 577 PRLGVFPQDDGFLDRPRLPDHLAAKPGDGKHPLLLRLHPLTIYRHQVCKQADTLLALMLA 636 Query: 622 REKFTKDELKKNYDYYEPITTHDSSLSPAIFSILANEIGYTDKAYKYFMMTARMDLDDYN 681 + + ++N+DYYE +T HDS+LS + F ++A E+G KA++YF + R+DLDD + Sbjct: 637 GDGVERAAKRRNFDYYESVTVHDSTLSASTFGVIAAEVGLAAKAWRYFQDSLRVDLDDSH 696 Query: 682 DNVKDGIHAASMAGTWSAVVNGFGGMRVYTNELHFEPRLPKEWNLLSFNVRYKGRKINVK 741 N G+H A+MAG+W +V GFGG R + PRLP W+ F +R+ ++ V+ Sbjct: 697 GNAAHGVHMAAMAGSWLGLVWGFGGFRTIDGQPALAPRLPAAWHGYRFGLRWGRAQLRVE 756 Query: 742 LTKENVVFALLEGEPIEIYYFDKKILLEKGE 772 + V + LL G+ + + ++ + G+ Sbjct: 757 VDASGVRYTLLRGDTLAFRHDGREHTIHAGQ 787 Lambda K H 0.318 0.137 0.407 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: 1573 Number of extensions: 57 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: 774 Length of database: 1036 Length adjustment: 43 Effective length of query: 731 Effective length of database: 993 Effective search space: 725883 Effective search space used: 725883 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 (21.7 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