Align Trehalase; Alpha,alpha-trehalase; EC 3.2.1.28 (characterized)
to candidate HSERO_RS00970 HSERO_RS00970 glucoamylase
Query= SwissProt::Q978S7 (623 letters) >FitnessBrowser__HerbieS:HSERO_RS00970 Length = 629 Score = 273 bits (699), Expect = 1e-77 Identities = 175/592 (29%), Positives = 309/592 (52%), Gaps = 29/592 (4%) Query: 34 GFIGNNRTAMLVAMNGYIDWGCLPNFNSNAVFSSILDKNKGGYFAIFPSDTTDVYVDQYY 93 G IGN + LV G I W CLP F+ + VF+++LD G F + + +Q+Y Sbjct: 44 GVIGNCAFSALVDKMGRIVWCCLPRFDGDPVFNALLDPTDNGALWAFQLENFS-HSEQWY 102 Query: 94 KEMTNVLVTEFVKNGKIILRLTDFMPDSEY-GKISFP-EVHRFVESFSEPIDITIDFKPT 151 + T VL T + +TD P + G+ P ++ R + S + + +P Sbjct: 103 EPNTAVLRTRLYDTLGQGIEITDLAPRFQSRGRFFRPLQLVRRIHPLSGAPRMRVVLRPK 162 Query: 152 FNYGQDKPIIEKDQHGFIFTTDKESIGISSEFPLRKNSDRIFGNVK-MEPRSSSWIIA-- 208 F++G+++P+ + + + ++++ ++++ P+ I G + R ++I+ Sbjct: 163 FDWGREEPLQTRGSNHIRYVGQEQTLRLNTDAPI----SYIVGETAFVVSRPYNFILGPD 218 Query: 209 --LYG-IHHLFRTTDYKSYLRLQETTDYWRKWASSSSYAGAYHSMVMRSALALKVLFYEP 265 L+G I+ R + QETT YWR W+ + + + V+R+A+ LK+ YE Sbjct: 219 ETLHGGINDTARDFE-------QETTAYWRNWSRALATPLEWQDAVIRAAITLKLSVYED 271 Query: 266 TGLMVAAPTASLPEAIGGERNWDYRFTWIRDTAYVIEALSSIGYKYEATEFLYDMMDMIT 325 TG ++AA T S+PEA G +RNWDYR+ W+RD +V+ AL+S+ ++L + +++ Sbjct: 272 TGAIIAAMTTSVPEAPGSQRNWDYRYCWLRDAFFVVRALNSLSELGTMEDYLRWLTNVVV 331 Query: 326 RD--NRIRTIYSIDDSNDLEERIIDY-EGYRGSRPVRIGNKAVDQLQIDQYGSIV----R 378 R ++ +Y I L E+I+D+ GY+ +PVR+GN+A + Q D YG+IV + Sbjct: 332 RSGGGHVQPLYGIGLEEALPEQILDHLPGYQHHQPVRVGNQAYEHFQHDVYGNIVLGAAQ 391 Query: 379 AIHSMAKAGGIVNSYLWDFVEQVMAKIEYLWKYPDSSIWEFRTEPKQYVYSKVMSWAAFD 438 A H M + + + +E V + ++ PD+ +WE RT + + S +MSWAA D Sbjct: 392 AFHDM-RLHHRAGAEHFQHLEAVGERAYEVYSQPDAGMWELRTRSRIHTSSALMSWAACD 450 Query: 439 SAISMAKDLGLSAPIKQWKSIQDEIKKEVLEKGFDTDTNSFVQYYGSKNIDAALLRLPIL 498 +A + L + W EI +L + ++ ++ + +G +++DA++L + + Sbjct: 451 RLAKIAARVDLPERARYWGDRAKEIGDRILTEAWNEQRQAYAESFGGRDLDASVLLMVEV 510 Query: 499 GFIPANDEKFLGTLSRIEKELMVDGYLFKRYREDDGLKGDEGSFLMLTFWYIEDLILMKR 558 G I D +F+ T+ +EK L DG +RY D E +F + TFW I+ L + R Sbjct: 511 GLISPTDPRFISTVEALEKSL-CDGPYMRRYEAPDDFGRPETAFNICTFWRIDALARIGR 569 Query: 559 LKKAREVLESVLEKANHLGLYSEEIDEKSGDFLGNFPQALSHLGVIRVAPKL 610 ++ARE+ +++L+ NHLGL SE+ + GNFPQ S +G+I A +L Sbjct: 570 KEQAREIFQAMLDARNHLGLLSEDTHPVTRQMWGNFPQTYSMVGIINCAMRL 621 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: 877 Number of extensions: 30 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: 629 Length adjustment: 38 Effective length of query: 585 Effective length of database: 591 Effective search space: 345735 Effective search space used: 345735 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: 54 (25.4 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