Align alpha,alpha-trehalase (EC 3.2.1.28) (characterized)
to candidate N515DRAFT_1910 N515DRAFT_1910 alpha,alpha-trehalase
Query= BRENDA::D4I261 (536 letters) >FitnessBrowser__Dyella79:N515DRAFT_1910 Length = 560 Score = 196 bits (497), Expect = 3e-54 Identities = 148/442 (33%), Positives = 203/442 (45%), Gaps = 61/442 (13%) Query: 142 LLPLPRPYVVPGGRFSEAYYWDSYFSMLGFAAAGRGELMRSMADNFAWMIDKYGHIPNGN 201 LL LP PYVVPGG F+E Y WDSYF +LG AA RG+L R M DN + ++ YG + N N Sbjct: 110 LLYLPHPYVVPGGFFNEMYGWDSYFIVLGLAADQRGKLARDMVDNALFEVEHYGAVLNAN 169 Query: 202 RTYYLSRSQPPVFAMMV-------ELFEKNNVHEA--QHYLPQLKSEYEFWMDGQATLSS 252 RTYYLSRSQPP M+ + F + +A P ++ W + Sbjct: 170 RTYYLSRSQPPFLTAMMATVLGDPDAFASDAERKAWLAGAYPLAVRNHDVWTREEHRAGD 229 Query: 253 NQAYRHVVMLDDGSVLNRYWDD----------RDTPRDE--------SYREDVETARHSS 294 R+ L DG VL D R P+D+ +D E AR + Sbjct: 230 TGLARYYD-LGDGPVLEAQNSDDFYVKVIKWLRAHPKDDPGYLLKGAQQPDDAEAARLAK 288 Query: 295 -------------------RPSSEVYRDLRAGAASGWDYTSRWLSEPGHLESIQTTSIVP 335 R +++ YR RA SG+D + G T Sbjct: 289 DSCDVRASKVCLGNWHDGYRLTADYYRGDRAMRESGYDTNFHFGPFGG-----STHHYAS 343 Query: 336 IDLNAFLYKLETTIARLSASKGDLDAADRFQQLALRRREAVDKFLWDEPAGLYRDYNWRE 395 +DLN+ LY+ E +A + G D A R+ A R++A+DK+LW G+YRDY++ Sbjct: 344 VDLNSLLYRYELDLADFATKLGKSDEAKRWTDAAAARKQAMDKYLWRAGDGMYRDYDFVA 403 Query: 396 GEQA-TFSAAAVTPLYVGMASLDQASRTAKAVRDHLLA---PGGILCSMNVTGEQWDSPN 451 G+ + T PL+ G AS QA+ AVR L GG+ +G QW+ P Sbjct: 404 GKPSPTPYINTFYPLWAGAASPQQAA----AVRGKLAVFERRGGLSMDNQPSGVQWNDPF 459 Query: 452 GWAPVQWMAIKGFHSYGNELLAQEIASRWLHTVSSTWQQHHKMVEKYNIS-GDAALLGGG 510 GWAP W+AIKG YG A+ +A + TV + EKYN++ G+A + Sbjct: 460 GWAPTNWLAIKGLEDYGFHDDARRLAGNFTATVDRGLADDGTIREKYNMAKGNADVRVSA 519 Query: 511 GEYPLQDGFGWTNGVTRRLLEM 532 G GFGWTNGV +L E+ Sbjct: 520 GYSENVIGFGWTNGVYLKLQEI 541 Lambda K H 0.318 0.134 0.421 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: 881 Number of extensions: 54 Number of successful extensions: 4 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: 536 Length of database: 560 Length adjustment: 36 Effective length of query: 500 Effective length of database: 524 Effective search space: 262000 Effective search space used: 262000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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