Align β-glucosidase (BglX;STM2166) (EC 3.2.1.21) (characterized)
to candidate Pf1N1B4_3261 Periplasmic beta-glucosidase (EC 3.2.1.21)
Query= CAZy::AAL21070.1 (765 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3261 Length = 763 Score = 962 bits (2488), Expect = 0.0 Identities = 478/768 (62%), Positives = 602/768 (78%), Gaps = 8/768 (1%) Query: 1 MKWLCSVGVAVSLAMQPALAENLFGNHPLTPEARDAFVTDLLKKMTVDEKIGQLRLISVG 60 MK LC +G+ VSLA LA P E +DAF++ L+K+MT+DEKIGQLRLIS+G Sbjct: 1 MKKLCLLGLFVSLASHTVLAATT----PAPIENKDAFISHLMKQMTLDEKIGQLRLISIG 56 Query: 61 PDNPKEAIREMIKDGQVGAIFNTVTRQDIRQMQDQVMALSRLKIPLFFAYDVVHGQRTVF 120 P+ P+E IR+ I G +G FN++TR + R MQD M SRLKIP+FFAYDV+HG RT+F Sbjct: 57 PEMPREMIRKEIAAGNIGGTFNSITRAENRPMQDAAMR-SRLKIPMFFAYDVIHGHRTIF 115 Query: 121 PISLGLASSFNLDAVRTVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDTYL 180 PI L LASS+++DA+ GR++A EAA D L++T+APMVD+SRDPRWGR SEGFGEDTYL Sbjct: 116 PIPLALASSWDMDAIGRSGRIAAKEAAADSLDITFAPMVDISRDPRWGRTSEGFGEDTYL 175 Query: 181 TSIMGETMVKAMQGKSPADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSSQRLFNDYMPPY 240 S + MVKA QG S+M SVKHFA YGAVEGG++YN VDMS +++ DY+PPY Sbjct: 176 VSRIAGVMVKAFQGTGANAADSIMASVKHFALYGAVEGGRDYNVVDMSPVKMYQDYLPPY 235 Query: 241 KAGLDAGSGAVMVALNSLNGTPATSDSWLLKDVLRDEWGFKGITVSDHGAIKELIKHGTA 300 +A +DAG+G VMVALNS+NG PAT+++WL+ D+LR EWGFKG+ VSDHGAI ELIKHG A Sbjct: 236 RAAIDAGAGGVMVALNSINGVPATANTWLMNDLLRKEWGFKGLAVSDHGAIFELIKHGVA 295 Query: 301 ADPEDAVRVALKAGVDMSMADEYYSKYLPGLIKSGKVTMAELDDATRHVLNVKYDMGLFN 360 AD +A ++A+KAG+DMSM D Y K LPGL+K+G++ ++D+A R VL KYDMGLF Sbjct: 296 ADGREAAKLAIKAGIDMSMNDTLYGKELPGLLKAGEIEQKDIDNAVREVLAAKYDMGLFK 355 Query: 361 DPYSHLGPKESDPVDTNAESRLHRKEAREVARESVVLLKNRLETLPLKKSGTIAVVGPLA 420 DPY +G E DP DT AESRLHR EAR+VAR S+VLLKN+ ETLPLKK+ IA+VGPLA Sbjct: 356 DPYLRIGKAEDDPADTYAESRLHRAEARDVARRSLVLLKNQGETLPLKKTAKIALVGPLA 415 Query: 421 DSQRDVMGSWSAAGVANQSVTVLAGIQNAVGDGAKILYAKGANITNDKGIVD---FLNLY 477 + D+MGSW+AAG QSVT+ G+ +A+G + ++YA+GANIT+DK I+D FLN Sbjct: 416 KAPIDMMGSWAAAGRPEQSVTLFDGMTHALGAQSTLIYARGANITSDKKILDYLNFLNFD 475 Query: 478 EEAVKIDPRSPQAMIDEAVQAAKQADVVVAVVGESQGMAHEASSRTNITIPQSQRDLITA 537 V DPR +IDEAV+AA+QADVVVA VGES+GM+HE+SSRT++ IP +QR+LI A Sbjct: 476 APEVVDDPRPANVLIDEAVKAAQQADVVVAAVGESRGMSHESSSRTDLNIPAAQRELIKA 535 Query: 538 LKATGKPLVLVLMNGRPLALVKEDQQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPI 597 LKATGKPLVLVLMNGRPL++++E++QADAILETWF+GTEGGNAIADVLFGDYNPSGKLPI Sbjct: 536 LKATGKPLVLVLMNGRPLSILEENEQADAILETWFSGTEGGNAIADVLFGDYNPSGKLPI 595 Query: 598 SFPRSVGQIPVYYSHLNTGRPYNPEKPNKYTSRYFDEANGPLYPFGYGLSYTTFTVSDVT 657 + PRSVGQIP YY+HL+ GRP+ P KP YTS+YF++ GPL+PFG+GLSYT F+++D+ Sbjct: 596 TVPRSVGQIPTYYNHLSIGRPFTPGKPGNYTSQYFEDTTGPLFPFGFGLSYTQFSLTDMA 655 Query: 658 LSSPTMQRDGKVTASVEVTNTGKREGATVIQMYLQDVTASMSRPVKQLKGFEKITLKPGE 717 LSS T+ + GK+ ASV V NTGKR+G TV+Q+Y+QDVT SM RPVK+LK F+K+ +K GE Sbjct: 656 LSSTTLNKTGKLDASVVVKNTGKRDGETVVQLYIQDVTGSMIRPVKELKNFQKVLVKAGE 715 Query: 718 RKTVSFPIDIEALKFWNQQMKYDAEPGKFNVFIGVDSARVKQGSFELL 765 +K V F I + LKF+N Q+KY AEPGKFNV IG+DS V Q SFELL Sbjct: 716 QKVVHFTITEDDLKFYNAQLKYAAEPGKFNVQIGLDSQDVTQQSFELL 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: 1574 Number of extensions: 66 Number of successful extensions: 4 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 Apr 09 2024. 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