Align β-glucosidase (BglX;STM2166) (EC 3.2.1.21) (characterized)
to candidate GFF1345 PS417_06840 beta-D-glucoside glucohydrolase
Query= CAZy::AAL21070.1 (765 letters) >FitnessBrowser__WCS417:GFF1345 Length = 763 Score = 994 bits (2570), Expect = 0.0 Identities = 491/768 (63%), Positives = 608/768 (79%), Gaps = 8/768 (1%) Query: 1 MKWLCSVGVAVSLAMQPALAENLFGNHPLTPEARDAFVTDLLKKMTVDEKIGQLRLISVG 60 MK LC +G+ +LA P AE P + +DAFV+DLLK+MT+DEKIGQLRLIS+G Sbjct: 1 MKKLCLLGLVATLATHPVWAET----KPAALKDKDAFVSDLLKQMTLDEKIGQLRLISIG 56 Query: 61 PDNPKEAIREMIKDGQVGAIFNTVTRQDIRQMQDQVMALSRLKIPLFFAYDVVHGQRTVF 120 P+ P+E IR+ I G++G FN++TR + R MQD M SRLKIP+FFAYDV+HG RT+F Sbjct: 57 PEMPRELIRKEIAAGRIGGTFNSITRPENRPMQDAAMR-SRLKIPMFFAYDVIHGHRTIF 115 Query: 121 PISLGLASSFNLDAVRTVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDTYL 180 PISL LASS+++DA+ GR++A EAA D L++T+APMVD+SRDPRWGR SEGFGEDTYL Sbjct: 116 PISLALASSWDMDAIGRSGRIAAQEAAADSLDITFAPMVDISRDPRWGRTSEGFGEDTYL 175 Query: 181 TSIMGETMVKAMQGKSPADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSSQRLFNDYMPPY 240 S + E MVKA QG SPA+ S+M SVKHFA YGAVEGG++YN VDMS +++ DY+PPY Sbjct: 176 VSRIAEVMVKAFQGVSPANADSIMASVKHFALYGAVEGGRDYNVVDMSPVKMYQDYLPPY 235 Query: 241 KAGLDAGSGAVMVALNSLNGTPATSDSWLLKDVLRDEWGFKGITVSDHGAIKELIKHGTA 300 A + AGSG VMVALNS+NG PAT+++WL+ D+LR +WGFKG+ VSDHGAI ELIKHG A Sbjct: 236 HAAIKAGSGGVMVALNSINGVPATANTWLMNDLLRKDWGFKGLAVSDHGAIFELIKHGVA 295 Query: 301 ADPEDAVRVALKAGVDMSMADEYYSKYLPGLIKSGKVTMAELDDATRHVLNVKYDMGLFN 360 D +A ++A+KAG+DMSM D Y K LPGL+KSG++ +++D+A R VL KYDMGLF Sbjct: 296 KDGREAAKLAIKAGIDMSMNDSLYGKELPGLLKSGEIEQSDIDNAVREVLGAKYDMGLFK 355 Query: 361 DPYSHLGPKESDPVDTNAESRLHRKEAREVARESVVLLKNRLETLPLKKSGTIAVVGPLA 420 DPY +G E DP DT AESRLHR EAR++AR S+VLLKN+ TLPLKKS TIA+VGPLA Sbjct: 356 DPYLRIGKAEDDPADTYAESRLHRAEARDIARRSLVLLKNQNNTLPLKKSATIALVGPLA 415 Query: 421 DSQRDVMGSWSAAGVANQSVTVLAGIQNAVGDGAKILYAKGANITNDKGIVD---FLNLY 477 + D+MGSW+AAG QSVT+L G+ +G+ KI+YA+GANIT DK +VD FLN Sbjct: 416 KAPIDMMGSWAAAGKPEQSVTLLDGLNAVIGEKGKIIYARGANITQDKAVVDYLNFLNFD 475 Query: 478 EEAVKIDPRSPQAMIDEAVQAAKQADVVVAVVGESQGMAHEASSRTNITIPQSQRDLITA 537 V D R Q MIDEAV+AAK+ADVVVA VGES+GM+HE+SSRT++ IPQSQRDLI A Sbjct: 476 APEVVDDTRPAQVMIDEAVKAAKEADVVVAAVGESRGMSHESSSRTDLNIPQSQRDLIKA 535 Query: 538 LKATGKPLVLVLMNGRPLALVKEDQQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPI 597 LKATGKPLVLVLMNGRPL++++E+QQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPI Sbjct: 536 LKATGKPLVLVLMNGRPLSILEENQQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPI 595 Query: 598 SFPRSVGQIPVYYSHLNTGRPYNPEKPNKYTSRYFDEANGPLYPFGYGLSYTTFTVSDVT 657 +FPRSVGQIP YY+HL GRP+ P KP YTS+YFD+ GPL+PFGYGLSYTTF++SD+ Sbjct: 596 TFPRSVGQIPTYYNHLTIGRPFTPGKPGNYTSQYFDDTTGPLFPFGYGLSYTTFSLSDMA 655 Query: 658 LSSPTMQRDGKVTASVEVTNTGKREGATVIQMYLQDVTASMSRPVKQLKGFEKITLKPGE 717 LSS T+ + GK+ ASV V NTGK +G TV+Q+Y+QDV SM RP+K+LK F+K+ LK GE Sbjct: 656 LSSTTLNKTGKLDASVTVKNTGKVDGETVVQLYIQDVAGSMIRPIKELKNFQKVMLKAGE 715 Query: 718 RKTVSFPIDIEALKFWNQQMKYDAEPGKFNVFIGVDSARVKQGSFELL 765 +T+ F I E LKF+N Q+K+ AEPG+FNV IG+DS V+Q +FELL Sbjct: 716 ERTLHFTITEEDLKFYNTQLKFAAEPGEFNVQIGLDSQDVQQQTFELL 763 Lambda K H 0.316 0.132 0.380 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: 1596 Number of extensions: 58 Number of successful extensions: 3 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: 765 Length of database: 763 Length adjustment: 40 Effective length of query: 725 Effective length of database: 723 Effective search space: 524175 Effective search space used: 524175 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 55 (25.8 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