Align Trehalase; Alpha,alpha-trehalase; EC 3.2.1.28 (characterized)
to candidate CA265_RS04150 CA265_RS04150 glycosyl hydrolase
Query= SwissProt::Q978S7 (623 letters) >FitnessBrowser__Pedo557:CA265_RS04150 Length = 594 Score = 310 bits (793), Expect = 1e-88 Identities = 203/593 (34%), Positives = 312/593 (52%), Gaps = 22/593 (3%) Query: 34 GFIGNNRTAMLVAMNGYIDWGCLPNFNSNAVFSSILDKNKGGYFAIFPSDTTDVYVDQYY 93 G IGN V N I W C P F+S VF S+LD+ KGG F+I P + QYY Sbjct: 10 GIIGNCAFIAHVNKNTDISWLCWPRFDSPFVFGSLLDEKKGGEFSILPQGEFTSH--QYY 67 Query: 94 KEMTNVLVTEFV-KNGKIILRLTDFMPDSE-YGKISFPEVH-RFVESFSEPIDITIDFKP 150 E TNVL TE ++GK R+TDF P Y + P + R +E ITI KP Sbjct: 68 IENTNVLRTEITAEDGKY--RITDFAPRFHLYDRYFKPLMFIRKIEPLEGSPRITIKCKP 125 Query: 151 TFNYGQDKPIIEKDQHGFIFTTDKESIGISSEFPLRKNSDRIFGNVKMEPRSSSWIIALY 210 +YG+ K + + + E+I +S+ L IF + ++I Y Sbjct: 126 VCDYGKGKMKSSRGSNHIDYLGCDENIRLSTNVSLTY----IFDEKAFVLNEAKYLIMTY 181 Query: 211 GIHHLFRTTDYKSYLRLQETTDYWRKWASSSSYAGAYHSMVMRSALALKVLFYEPTGLMV 270 G +L + L+ET YWR W SS AG Y V+RSAL LK+ YE TG ++ Sbjct: 182 G-QNLEAPVVSTAENFLRETIAYWRLWIKHSSIAGFYQPFVIRSALVLKIHQYEDTGAII 240 Query: 271 AAPTASLPEAIGGERNWDYRFTWIRDTAYVIEALSSIGYKYEATEFLYDMMDMI-TRDNR 329 AA T SLPE+ G RNWDYR+ W+RD+ YV+ +L+ IG+ E + + D+ D R Sbjct: 241 AASTTSLPESPGSTRNWDYRYCWLRDSHYVLTSLNHIGHFEEMERYFNYLSDISHAEDIR 300 Query: 330 IRTIYSIDDSNDLEERIIDY-EGYRGSRPVRIGNKAVDQLQIDQYGSIVRAIHSMAKAGG 388 + +Y I ++ ER +D+ GY+G +P+R+GN+A + +Q D YG ++ ++ + Sbjct: 301 YQPLYGIAGEREITERTLDHLTGYKGEQPIRVGNQAYEHIQNDIYGQVLISMLPLYTDHR 360 Query: 389 IVNSYLWD---FVEQVMAKIEYLWKYPDSSIWEFRTEPKQYVYSKVMSWAAFDSAISMAK 445 V S D ++E V++KIE D+ IWEFR + YS + WA +A+ MAK Sbjct: 361 FVFSERSDSVRWIESVLSKIERTIDEKDAGIWEFRNIANVHCYSNLFQWAGAQAALKMAK 420 Query: 446 DLGLSAPIKQWKSIQDEIKKEVLEKGFDTDTNSFVQYYGSKNIDAALLRLPILGFIPAND 505 +G K+ + + D+ + E +D + + GS ++DA+ L+L ++ ++ Sbjct: 421 TIGNDDFEKRAQVLIDKAAAHI-EACYDPERKVYTNAVGSPHLDASTLQLIMMNYLDPAS 479 Query: 506 EKFLGTLSRIEKELMVDGYLFKRYREDDGLKGDEGSFLMLTFWYIEDLILMKRLKKAREV 565 ++ L +EKEL + LF RY D + +FL+ FWY+E L + R +A + Sbjct: 480 DRAKDHLIALEKELKTEDGLFYRYLHADDFGKPKTTFLICAFWYVEALACVGRTDEAIKE 539 Query: 566 LESVLEKANHLGLYSEEIDEKSGDFLGNFPQALSHLGVI----RVAPKLEEAL 614 E++++ NHL L+SE++D K+G GNFPQA SH+G++ R+A KL+ + Sbjct: 540 FENIIKYCNHLLLFSEDVDAKTGSQWGNFPQAYSHVGLMNAAYRIAIKLDRPI 592 Lambda K H 0.320 0.137 0.409 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: 954 Number of extensions: 55 Number of successful extensions: 7 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: 623 Length of database: 594 Length adjustment: 37 Effective length of query: 586 Effective length of database: 557 Effective search space: 326402 Effective search space used: 326402 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: 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