Align Trehalase; Alpha,alpha-trehalase; EC 3.2.1.28 (characterized)
to candidate Echvi_2045 Echvi_2045 Glucoamylase and related glycosyl hydrolases
Query= SwissProt::Q978S7 (623 letters) >FitnessBrowser__Cola:Echvi_2045 Length = 596 Score = 307 bits (787), Expect = 7e-88 Identities = 199/597 (33%), Positives = 309/597 (51%), Gaps = 32/597 (5%) Query: 34 GFIGNNRTAMLVAMNGYIDWGCLPNFNSNAVFSSILDKNKGGYFAIFPSDTTDVYVDQYY 93 G IGN + N I W C P F+S+ +F +LD+ KGG F+I P + Q Y Sbjct: 10 GLIGNCAYIAHIEKNTNISWLCFPRFDSDFIFGGMLDREKGGEFSILPEENAFT-TQQEY 68 Query: 94 KEMTNVLVTEFV-KNGKIILRLTDFMPDSEYGKISFPEVH------RFVESFSEPIDITI 146 E TN+L T + NG+ +TDF P ++F H R VE S I I Sbjct: 69 LENTNILKTTVILDNGEEAYSVTDFAPRF----MNFERYHKPLMVIRKVEPISGEPKIKI 124 Query: 147 DFKPTFNYGQDKPIIEKDQHGFIFTTDKESIGISSEFPLRKNSDRIFGNVKMEPRSSS-- 204 + KP N G K + + F +G E L N N ME R+ Sbjct: 125 NCKPVTNRGNKKLKPSMNSNHIEF------LGAEQEVRLTANCSV---NYIMEDRAFRLQ 175 Query: 205 ---WIIALYGIHHLFRTTDYKSYLRLQETTDYWRKWASSSSYAGAYHSMVMRSALALKVL 261 ++ YG L + + LQ TT YWR+W S+S Y +V+RSALALK+ Sbjct: 176 RPIYLFFTYG-QPLEAPVESTAERFLQATTQYWREWVKSTSIPHFYQKLVVRSALALKIH 234 Query: 262 FYEPTGLMVAAPTASLPEAIGGERNWDYRFTWIRDTAYVIEALSSIGYKYEATEFLYDMM 321 +E TG ++AA T SLPE+ G RNWDYR+ WIRD+ Y + +S+G+ E + + Sbjct: 235 QFEDTGAIIAASTTSLPESPGSTRNWDYRYCWIRDSYYTLNVFNSLGHFQELERYFEYIQ 294 Query: 322 DMITRDN-RIRTIYSIDDSNDLEERIIDYEGYRGSRPVRIGNKAVDQLQIDQYGSIVRAI 380 ++ T N R + +YSI S LEE + D GY G++PVR GN+A +Q D YG ++ ++ Sbjct: 295 NLPTNANGRYQPLYSITGSALLEEELSDLSGYLGNQPVRFGNQAYTHIQNDLYGQVLVSL 354 Query: 381 HSMAKAGGIVNS---YLWDFVEQVMAKIEYLWKYPDSSIWEFRTEPKQYVYSKVMSWAAF 437 + + S + F+ ++ KIE D+ +WEFR +++ Y+ + WA Sbjct: 355 LPLYADKRFIESEKSHSAPFIHNLLDKIEETMNEKDAGLWEFRNLAQEHCYTFIFHWAGS 414 Query: 438 DSAISMAKDLGLSAPIKQWKSIQDEIKKEVLEKGFDTDTNSFVQYYGSKNIDAALLRLPI 497 +AI +A L S+ ++ + ++ + E +E + + ++ Q G+KN+DA+ L+L Sbjct: 415 CAAIKIADRLQDSSMKEKAEKLRLQ-SIEKIEACYVPEMKAYAQAIGTKNMDASTLQLIT 473 Query: 498 LGFIPANDEKFLGTLSRIEKELMVDGYLFKRYREDDGLKGDEGSFLMLTFWYIEDLILMK 557 +G+ + E+ L +EK+L+ YLF RY+ D E +FL+ FWYIE L + Sbjct: 474 MGYFGNDIERANNHLKMLEKDLLAKDYLFYRYKHMDDFGVPETTFLICAFWYIEALACVN 533 Query: 558 RLKKAREVLESVLEKANHLGLYSEEIDEKSGDFLGNFPQALSHLGVIRVAPKLEEAL 614 RL +A E E++ + NHL L+SE++D ++G GNFPQA SH+G++ A ++ + L Sbjct: 534 RLDEAVEGFETLTKYCNHLQLFSEDVDHETGSQWGNFPQAYSHVGLMNAAYRIGQKL 590 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: 955 Number of extensions: 40 Number of successful extensions: 5 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: 596 Length adjustment: 37 Effective length of query: 586 Effective length of database: 559 Effective search space: 327574 Effective search space used: 327574 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