Align Trehalase; Alpha,alpha-trehalase; EC 3.2.1.28 (characterized)
to candidate RR42_RS02325 RR42_RS02325 glucoamylase
Query= SwissProt::Q978S7 (623 letters) >FitnessBrowser__Cup4G11:RR42_RS02325 Length = 612 Score = 281 bits (720), Expect = 4e-80 Identities = 183/594 (30%), Positives = 303/594 (51%), Gaps = 33/594 (5%) Query: 34 GFIGNNRTAMLVAMNGYIDWGCLPNFNSNAVFSSILDKNKG-GYFAIFPSDTTDVYVDQY 92 G IGN + LV G I W CLP F+ + VF+++LD + G+FAI D + + Q+ Sbjct: 27 GMIGNCAISALVDGRGRIVWCCLPRFDGDPVFNALLDPGENAGHFAIEIEDFHEAH--QW 84 Query: 93 YKEMTNVLVTEFVKNGKIILRLTDFMPDS-EYGKISFP-EVHRFVESFSEPIDITIDFKP 150 Y+ T VL T L +TDF P G+ P + R + + + P Sbjct: 85 YEPNTAVLRTRLTDQHGNSLEITDFAPRFFRIGRYFRPTSLIRRIRPVQGAPRVRVTLAP 144 Query: 151 TFNYGQDKPIIEKDQHGFIFTTDKESIGISSEFPLRKNSDRIFGNVKMEPRSSSWIIA-- 208 F++G+ KP I + + D ++ ++++ PL + + R ++I+ Sbjct: 145 RFDWGRVKPEITRGSSHVRYIGDGSTLRMTTDAPLTYVLSQ---TPFLLTRDLNFILGPD 201 Query: 209 ---LYGIHHLFRTTDYKSYLRLQETTDYWRKWASSSSYAGAYHSMVMRSALALKVLFYEP 265 G+ + R + QETT YW+ W+ + + V+R+A+ LK+ YE Sbjct: 202 ETLQGGVEEIARDFE-------QETTAYWKMWSRRLAVPREWQEAVIRAAITLKLSLYEE 254 Query: 266 TGLMVAAPTASLPEAIGGERNWDYRFTWIRDTAYVIEALSSIGYKYEATEFLYDMMDMI- 324 TG +VAA T S+PEA G RNWDYRF W+RD +VI AL+S+ ++L + +++ Sbjct: 255 TGAIVAAMTTSIPEAPGSGRNWDYRFCWLRDAFFVIRALNSLSEVGTMEDYLRWLSNVVM 314 Query: 325 -TRDNRIRTIYSIDDSNDLEERIIDY-EGYRGSRPVRIGNKAVDQLQIDQYGSIVRAI-- 380 +R+ I+ +Y I +L E ++D+ GYRG PVR+GN+A + Q D YG++V Sbjct: 315 QSRNGHIQPLYGIGLELELPESMLDHLSGYRGMGPVRVGNQAQEHFQHDVYGNVVLGAAQ 374 Query: 381 ----HSMAKAGGIVNSYLWDFVEQVMAKIEYLWKYPDSSIWEFRTEPKQYVYSKVMSWAA 436 H + GG ++ + V + ++ + PD+ +WE RT + + S +MSWAA Sbjct: 375 AFHDHRLLHRGGAAEYHVLETVGEQAVRV---FGTPDAGMWELRTRARVHTSSALMSWAA 431 Query: 437 FDSAISMAKDLGLSAPIKQWKSIQDEIKKEVLEKGFDTDTNSFVQYYGSKNIDAALLRLP 496 D + L L W+ + +K ++ + + + +F + +G + +DA++L + Sbjct: 432 CDRLAKIGDALQLPDRAAYWRQHAEGMKVRIVRESWSEERQAFAESFGGRELDASVLLMA 491 Query: 497 ILGFIPANDEKFLGTLSRIEKELMVDGYLFKRYREDDGLKGDEGSFLMLTFWYIEDLILM 556 +GFI DE+F+ TL +E L DG +RY D E +F + TFW I+ L + Sbjct: 492 EVGFIEPRDERFMSTLKAMEASL-CDGPYMRRYEAPDDFGKPETAFNICTFWRIDALARV 550 Query: 557 KRLKKAREVLESVLEKANHLGLYSEEIDEKSGDFLGNFPQALSHLGVIRVAPKL 610 R ++ARE+ E++L N LGL SE+ +G+ GNFPQ S +G+I A +L Sbjct: 551 GRREEAREIFEAMLAARNPLGLLSEDTHPVTGEMWGNFPQTYSMVGLINGAMRL 604 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: 866 Number of extensions: 39 Number of successful extensions: 6 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: 612 Length adjustment: 37 Effective length of query: 586 Effective length of database: 575 Effective search space: 336950 Effective search space used: 336950 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