Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate H281DRAFT_06049 H281DRAFT_06049 trehalose synthase
Query= CAZy::AAS80455.1 (528 letters) >FitnessBrowser__Burk376:H281DRAFT_06049 Length = 1153 Score = 248 bits (632), Expect = 1e-69 Identities = 181/557 (32%), Positives = 262/557 (47%), Gaps = 124/557 (22%) Query: 1 MWWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGY 60 +W+K+A+IYQV+ +SF D N DGVGD G+ +L Y+ LGV+A+WL PFY SP +D GY Sbjct: 41 LWYKDAIIYQVHIKSFFDANNDGVGDFPGLIAKLDYIAELGVNAIWLLPFYPSPRRDDGY 100 Query: 61 DVADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLES-RASRNSPK 119 D+ADY +V P +G L D R ++EAHA G++V+ +LV NHTS +HPWF + RA S Sbjct: 101 DIADYRNVHPDYGQLSDVKRFIQEAHARGIRVITELVINHTSDQHPWFQRARRAKPGSNH 160 Query: 120 RDWYIWKDPAP----------DGGPPNNWQSFFGGPAWTLDEATGQYYLHQFLPEQPDLN 169 R++Y+W D D P N WT D G YY H+F QPDLN Sbjct: 161 RNFYVWSDTDQKYQETRIIFIDSEPSN----------WTHDPVAGAYYWHRFYSHQPDLN 210 Query: 170 WRNPEVREAIYEVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLH 229 + NP V + ++MRFWL G+DG R+D + L E R+ N Sbjct: 211 FDNPAVLREVLQIMRFWLDMGIDGLRLDAVPYLVE----REGTNN--------------- 251 Query: 230 IFTEDQPETYAYVREMRQVLD-EFSEPGRERVMVGEIYLPYPQLVRYY---QAGCHLPFN 285 E+ PET+A ++++R +D E+ R+++ E +P+ V+ Y + CH+ F+ Sbjct: 252 ---ENLPETHAILKKIRATIDAEYP----NRMLLAEAN-QWPEDVKEYFGDEDECHMAFH 303 Query: 286 FHLIFRGLPDWRPEN---LARIVEEYESLLTRWDWPNWVLGNHDQ--------------- 327 F L+ R E+ + I+ + L W + L NHD+ Sbjct: 304 FPLMPRIYMSIASEDRFPITDIMRQTPDLAETNQWAIF-LRNHDELTLEMVTDSERDYLW 362 Query: 328 ----------------PRLASRLGEAQARVAAM--LLFTLRGTPTWYYGDEIGMKNGEIP 369 RLA + + R+ + LL ++ GTP YYGDE+GM Sbjct: 363 NTYASDRRARLNLGIRRRLAPLMERDRRRIELINSLLLSMPGTPVIYYGDELGM------ 416 Query: 370 PEKVQDPAALRQKDRLGEHNLPPGRDPERTPMQWDDTPFAGFSTVEPWLPVNP------- 422 G++ RD RTPMQW GFS +P V P Sbjct: 417 ----------------GDNIHLGDRDGVRTPMQWSSDRNGGFSRADPEQLVLPPVMGSLY 460 Query: 423 DYKTRNVAAQEQDPRSMLHLVRRLIALRKDPDLL-YGAYRTYR-AREGVYAYLR----GE 476 + NV AQ +DP S+L+ RR++A R+ G R + + AYLR Sbjct: 461 GFDAVNVEAQSRDPHSLLNWTRRMLATRRAKQTFGRGTIRFLKPENRKILAYLREMPNEP 520 Query: 477 GWLVALNLTEKEKALEL 493 L NL+ +A+EL Sbjct: 521 PILCVANLSRAPQAVEL 537 Lambda K H 0.321 0.141 0.466 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: 1841 Number of extensions: 102 Number of successful extensions: 6 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: 528 Length of database: 1153 Length adjustment: 41 Effective length of query: 487 Effective length of database: 1112 Effective search space: 541544 Effective search space used: 541544 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: 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