Align Trehalase 1; Alpha,alpha-trehalase; SaTreH1; EC 3.2.1.28 (characterized)
to candidate BPHYT_RS31605 BPHYT_RS31605 glucoamylase
Query= SwissProt::Q4J7W0 (558 letters) >FitnessBrowser__BFirm:BPHYT_RS31605 Length = 596 Score = 232 bits (591), Expect = 4e-65 Identities = 177/582 (30%), Positives = 277/582 (47%), Gaps = 44/582 (7%) Query: 10 IGNGLTSALVD-NGSIVWLTFPRFDSPSVFGKLLDDNA-GEFSIRPVEDKFKVSQSYLVP 67 +G+G T+ALV +GSI WL +PRFD + F LL N G +S+ P + S+ Y Sbjct: 11 LGDGETAALVGKDGSIDWLCWPRFDDDACFAALLGTNDHGHWSLSPAGEVTGQSRRYQED 70 Query: 68 N-VLSTTFKSSNGKAEIVDLMPIGEK-----AIIRKVRTEIPLSFKIIPMFNYGLYRPII 121 ++ T F++++G+ I+D MP+ + I+ +R + + + F+YG P Sbjct: 71 TLIMETDFQTADGEVRIIDFMPVRKTFSSLVRIVAGLRGTVKVRSTLRLRFDYGALPPW- 129 Query: 122 RRKDDGIQFLNPVSRECLSLLSDVPTDEIKPPGTTLYLVYSSD-----CAYGPLDKGKQL 176 DG + V ++L S + + V +Y + G Sbjct: 130 -SVADGDDMIAKVGPNLVALRSPLRLHVTSDSTVANFDVSQGQRIAFVLSYARSEDGPPE 188 Query: 177 ENDLENSFNLTIDYWKDKIRSNDEV---W----RTSVGVLLGLIYSPSGSSIAAATTSLP 229 D E + T +W+ I D W R S+ L LI+ SG +AA TTSLP Sbjct: 189 PVDAEAALISTQHFWRGWIGRFDNSKTDWPFQVRRSLITLKALIHRRSGGLVAAPTTSLP 248 Query: 230 EAVGDSRNWDYRFVWVRDSSMISEALLYSGYVVEARRILNFMLALVNFTAKPLLHPLYAV 289 EA G NWDYR+ W+RD+S ALL +GY EA N++L + + + +Y V Sbjct: 249 EAPGGEMNWDYRYCWLRDASFTLTALLNAGYHEEAEGWRNWLLRAIAGSPDNM-RIMYRV 307 Query: 290 DGSDPPPEIEIPWLSGYMNSRPVRVGNAAASQIQLDIEGFLVDAIYKYYKY---TSDRVF 346 DG+ PE + L GY ++PVR+GNAA+SQ QLD+ G L+D + + +SD+ F Sbjct: 308 DGARHLPEWTVDTLPGYRFAKPVRIGNAASSQHQLDVYGELLDCLDLAGRGGVPSSDQEF 367 Query: 347 VEENWDKIKYIGDWVSKNWMLKDAGMWEDRGDPKHYTHSKVMMWVALDRIEKIMNVKIHE 406 E + + + + W +G+WE R +P+HYT+SKVM+WVA DR + Sbjct: 368 AIE-----QRLVEHLETIWQTVGSGVWESRAEPRHYTYSKVMVWVAFDRFVSRHSRSNLV 422 Query: 407 KDEIKEWV--MRNCVKD-----------GSFVRSSDSNDVDANLLTLPLYDFIDVKDPIF 453 E+ + + +R + D G+F + S +DA+LL LPL F+ V DP Sbjct: 423 SREVLDRITALRQTLHDEICREGWNEGLGTFTQHYGSQALDASLLLLPLVGFLPVGDPRM 482 Query: 454 LKTLKRIEDELYVDGFVKRYSQDFMGEAKHPFALATIWLARVYIRLGRKERAMELLDKVL 513 T+ IE EL G ++R + G + F + W+A GR A E +++L Sbjct: 483 DSTIATIERELSEGGLIRREKPNADGPKEGAFLACSGWMAECMKLQGRDREAREQFERLL 542 Query: 514 KPSGTLYLIGEHIDVENMEYTGNYPQAFVHAQLLLALKEVKG 555 + + L+ E +V GN+PQA H ++ A + G Sbjct: 543 AAANDVGLLAEEYNVPGGHLAGNFPQALTHLAIVNAALALSG 584 Lambda K H 0.320 0.138 0.418 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: 828 Number of extensions: 38 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: 558 Length of database: 596 Length adjustment: 36 Effective length of query: 522 Effective length of database: 560 Effective search space: 292320 Effective search space used: 292320 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