Align Alpha,alpha-trehalose phosphorylase; TPase; EC 2.4.1.64 (characterized)
to candidate CA265_RS24655 CA265_RS24655 family 65 glycosyl hydrolase
Query= SwissProt::Q8L164 (774 letters) >FitnessBrowser__Pedo557:CA265_RS24655 Length = 772 Score = 454 bits (1167), Expect = e-131 Identities = 264/747 (35%), Positives = 414/747 (55%), Gaps = 29/747 (3%) Query: 13 EDWVIRETQFSIDTNYRNETIFTLANGYIGMRGTFEERYSGPKNTSFNGTYINGFY--EI 70 ++W I E F N +E+IF+L NG +G R FEE Y+G + G Y+ G Y + Sbjct: 8 DEWNIIEEGFDPHLNKISESIFSLGNGRMGQRANFEETYTGE---TLPGNYVAGVYYPDK 64 Query: 71 HDIVYPEGGYG--FAKIGQTMLNVADSKIIKLYVDGEEFDLLQGKILFYERVLDMKKGFV 128 + + + GY FAK+ LN A+ I++ +DGE DL ++ ++RVL+M G++ Sbjct: 65 TRVGWWKNGYPEYFAKV----LNAANWIGIEVKLDGEILDLATAEVSDFKRVLNMHAGYL 120 Query: 129 ERKVKWESPTGKILEVKIKRIVSLNRQHLAAISFTMQPVNFTGKIRFVSAIDGNVSNIND 188 ER + +GK L+VK R S+ + AI +++ P+NF G++ + IDG+V N + Sbjct: 121 ERTFTAKLKSGKTLKVKSTRFCSIADDEVGAIRYSITPLNFDGRLTLMPFIDGDVKNQD- 179 Query: 189 SEDVRVGSNLKGKVLKTIDKSVEGLKGWIVQKTQKSNFSYACAIDNVLVADSKYEVSNSL 248 SN K + + G + +I +T+K+ F C N+ + + +++ + Sbjct: 180 -------SNYDEKFWDKVADEISGTEAYIKLRTKKTEFE-VCTGSNIELYKNAEKLAINP 231 Query: 249 E----EDGVKVIVDLEAEKGTSYTLNKFISYYTSKDFDENKLVALALEEIEKAKNDGFET 304 E E V LE + +L K + +S+++ + L+ I KA GF+T Sbjct: 232 EAVRKEKFVGQTFSLEVKANEEISLVKIAANLSSENYPKESLLKETKSIIAKASAKGFDT 291 Query: 305 IEKEQEEFLNSFWKDADVIIEGDKALQQGIRFNEFHLLQS-VGRDGKTNIAAKGLTGGGY 363 + KEQ E S W+++D+IIEGD + QQ IRFN F L Q+ G+D + NI KG TG Y Sbjct: 292 LLKEQTEAWASKWEESDIIIEGDVSAQQAIRFNIFQLFQTYTGKDDRLNIGPKGFTGEKY 351 Query: 364 EGHYFWDSDIYIMPFFLYTKP-EIAKALVMYRYNLLDAARSRAKELGHK--GALYPWRTI 420 G +WD++ Y +PF+L T P E++K L++YR+ L A A +LG K ALYP T+ Sbjct: 352 GGSTYWDTEAYCVPFYLATAPQEVSKNLLVYRHKQLGKAIENAAKLGFKDGAALYPMVTM 411 Query: 421 DGPECSAYFPAGTAQYHINADIVYALKRYVEATNDVDFLYDYGCEILFETARFWEDLGAY 480 +G EC + + H N I +A+ Y+ T D +L D+G E+L ARFW+ + Sbjct: 412 NGEECHNEWEITFEEIHRNGAIAFAIFNYIRYTGDESYLSDFGLEVLIGIARFWKQRVNW 471 Query: 481 IPLKGNKFCINCVTGPDEYTALVDNNAYTNYMAKMNLEYAYDIANKMKKEVPQKYQKVAS 540 K ++ + VTGP+EY V+NN YTN +A ++YA + A +K + P+KY + Sbjct: 472 SNDK-QQYVMLGVTGPNEYENNVNNNWYTNILATWCMKYATEAAEIVKTQQPEKYNSLLK 530 Query: 541 KLNLKDEEIVAWKKAADNMYLPYSKELDIIPQDDSFLYKERITVDEIPEDQFPLLLHWHY 600 LN +E W + MY P ++L I Q D +L KE+ V ++P + P+ W + Sbjct: 531 SLNFDQKEFADWADIIEKMYYPQDEKLGIFLQQDGYLDKEQTLVKDLPASERPINQKWSW 590 Query: 601 LNIYRYQICKQPDVLLLMFLQREKFTKDELKKNYDYYEPITTHDSSLSPAIFSILANEIG 660 I R KQ DVL ++ E + D LK+N+D+YEP T H+SSLSP + SILA ++ Sbjct: 591 DRILRSCFIKQADVLQGLYFFEEDYDLDTLKRNFDFYEPRTVHESSLSPCVHSILAAKLN 650 Query: 661 YTDKAYKYFMMTARMDLDDYNDNVKDGIHAASMAGTWSAVVNGFGGMRVYTNELHFEPRL 720 +AY++++ TAR+DLDDYN++ +DG+H SMAGTW +VV GF GMRV +L F P L Sbjct: 651 DEARAYEFYLRTARLDLDDYNNDTEDGLHITSMAGTWMSVVEGFAGMRVREGKLQFNPFL 710 Query: 721 PKEWNLLSFNVRYKGRKINVKLTKENV 747 P +W SF + ++G + + +T+ + Sbjct: 711 PGKWKSFSFTIGFRGATLKINITESGI 737 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: 1690 Number of extensions: 94 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 774 Length of database: 772 Length adjustment: 41 Effective length of query: 733 Effective length of database: 731 Effective search space: 535823 Effective search space used: 535823 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: 55 (25.8 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