Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate BWI76_RS16585 BWI76_RS16585 trehalose synthase
Query= CAZy::AAS80455.1 (528 letters) >FitnessBrowser__Koxy:BWI76_RS16585 Length = 541 Score = 210 bits (534), Expect = 1e-58 Identities = 150/510 (29%), Positives = 228/510 (44%), Gaps = 105/510 (20%) Query: 2 WWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGYD 61 W A+IYQ+ F D N DG GD+ G+ +L Y++ +G +W++PFY +P D GYD Sbjct: 4 WHTRAIIYQIDSALFYDFNSDGCGDIAGITAKLRYIRRMGATVIWITPFYLTPFLDEGYD 63 Query: 62 VADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKRD 121 V+D+ VDP FG L D +E+A LG++V+++L+ HTS HPWF +R SR+SP RD Sbjct: 64 VSDHLQVDPRFGQLADIIAFIEQARELGMQVIIELLIQHTSDAHPWFQRARRSRSSPFRD 123 Query: 122 WYIWKDPAPDGGPPNNWQSFFGG---PAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREA 178 +Y+W D D PP F G WT DE GQY+ H F +PDLN +P V + Sbjct: 124 YYLWADSDDDDTPP-----MFPGVEESIWTWDEEAGQYFRHMFYRHEPDLNLASPAVIKE 178 Query: 179 IYEVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPET 238 + ++ FWL+ GV GFR+D L + + G + + G+W Sbjct: 179 VENIIIFWLKLGVSGFRLDAAAHLTK------QAGRGEEKRGLW---------------- 216 Query: 239 YAYVREMRQVLDEFSEPGRERVMVGEIYLPYPQLVRYY--QAGCHLPFNFHLIFRGLPDW 296 + +R++++ + + +++GE+ + Q Y+ ++ NF L Sbjct: 217 --ILEHLRRLVERHNP---QAILLGEVDVDVEQYRDYFGDNNRLNMVLNFWLNKYFYVSL 271 Query: 297 RPENLARIVEEYESLLTRWD---WPNWVLGNHDQ-------------------------- 327 +N ++ + + D + NW L NHD+ Sbjct: 272 ASQNARPLINAIKKTIVPPDACCFANW-LRNHDELDLEGIGNKNKQTVLEAFAPDEKMNV 330 Query: 328 ------PRLASRLGEAQARVA--AMLLFTLRGTPTWYYGDEIGMKNGEIPPEKVQDPAAL 379 RLA L + R+A +LF+L G P YGDEIGM D AL Sbjct: 331 YQRGIRRRLAPMLNGNRQRLAFCHAVLFSLPGVPIMRYGDEIGM----------GDDLAL 380 Query: 380 RQKDRLGEHNLPPGRDPERTPMQWDDTPFAGFSTVEPWLPVNP-------DYKTRNVAAQ 432 + R RTPMQW + GFS +P V P Y+ NVA Sbjct: 381 EE------------RYAVRTPMQWAGSAGGGFSAADPDTFVAPMIDRGPFRYQKVNVADS 428 Query: 433 EQDPRSMLHLVRRLIALRKD-PDLLYGAYR 461 S+LH + + R + P++ +R Sbjct: 429 LLHRHSLLHRIMDIANTRSEFPEIAVAPFR 458 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: 883 Number of extensions: 41 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: 528 Length of database: 541 Length adjustment: 35 Effective length of query: 493 Effective length of database: 506 Effective search space: 249458 Effective search space used: 249458 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: 52 (24.6 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