Align β-glucosidase (BglX;STM2166) (EC 3.2.1.21) (characterized)
to candidate Pf1N1B4_3419 Periplasmic beta-glucosidase (EC 3.2.1.21)
Query= CAZy::AAL21070.1 (765 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3419 Length = 763 Score = 870 bits (2248), Expect = 0.0 Identities = 427/735 (58%), Positives = 565/735 (76%), Gaps = 5/735 (0%) Query: 33 ARDAFVTDLLKKMTVDEKIGQLRLISVGPDNPKEAIREMIKDGQVGAIFNTVTRQDIRQM 92 +++AFV+DL+ +MT++EKIGQLRLI++ E IRE I G++G + +V+R R M Sbjct: 26 SKEAFVSDLINQMTLEEKIGQLRLIAIDEKMTPEKIREEIAAGRIGGTYGSVSRFVNRPM 85 Query: 93 QDQVMALSRLKIPLFFAYDVVHGQRTVFPISLGLASSFNLDAVRTVGRVSAYEAADDGLN 152 QD SRLKIP+FF +DV+HG RT+FPI L LASS+++ A+ GR++A EA+ DG++ Sbjct: 86 QDASQQ-SRLKIPMFFGWDVIHGHRTIFPIGLALASSWDIGAIELSGRIAAKEASADGID 144 Query: 153 MTWAPMVDVSRDPRWGRASEGFGEDTYLTSIMGETMVKAMQGKSPADRYSVMTSVKHFAA 212 +T+APM+D++RDPRWGR SEGFGEDTYL S + + MV+A QG SP S+M S KHFA Sbjct: 145 LTFAPMIDIARDPRWGRTSEGFGEDTYLVSRIAKAMVQAYQGASPNAPDSIMASAKHFAL 204 Query: 213 YGAVEGGKEYNTVDMSSQRLFNDYMPPYKAGLDAGSGAVMVALNSLNGTPATSDSWLLKD 272 YGAVEGG++YN+VDM R+ DY+PPY++ ++ G+GA+MVALNS+NG PA S++WL++D Sbjct: 205 YGAVEGGRDYNSVDMGLARMHQDYLPPYRSAIEGGAGAMMVALNSINGVPAASNAWLMQD 264 Query: 273 VLRDEWGFKGITVSDHGAIKELIKHGTAADPEDAVRVALKAGVDMSMADEYYSKYLPGLI 332 +LR WGFKG+ +SDH I +L++HG A + +A R+A+KAGVDMSM D Y L GL+ Sbjct: 265 LLRKAWGFKGLVISDHNGINDLVQHGVAKNHREAARLAIKAGVDMSMNDFSYGPELQGLL 324 Query: 333 KSGKVTMAELDDATRHVLNVKYDMGLFNDPYSHLGPKESDPVDTNAESRLHRKEAREVAR 392 +SG ++ + +D+A R VL KYDMGLF DPY +G DP D NAE RLHR +AREVAR Sbjct: 325 ESGAISQSNIDNAVREVLGAKYDMGLFEDPYRRIGIASEDPADNNAEHRLHRAQAREVAR 384 Query: 393 ESVVLLKNRLETLPLKKSGTIAVVGPLADSQRDVMGSWSAAGVANQSVTVLAGIQNAVGD 452 +++VLLKN LPLKK G IA++GPLA S D+MGSWSA+GVA QSVT+ G++NA+ Sbjct: 385 KTLVLLKNENGLLPLKKEGVIALIGPLAKSAVDIMGSWSASGVAEQSVTIYDGLKNAMTQ 444 Query: 453 GAKILYAKGANITNDKGIVDFLNLYEEAVKI--DPRSPQAMIDEAVQAAKQADVVVAVVG 510 G+ ++YA+GAN+ D+ +V +L Y+ KI D R MIDEAV+AA+QADVV+AVVG Sbjct: 445 GS-LIYARGANLEEDQEVVKYLE-YQGVSKIENDARPAAEMIDEAVKAAQQADVVIAVVG 502 Query: 511 ESQGMAHEASSRTNITIPQSQRDLITALKATGKPLVLVLMNGRPLALVKEDQQADAILET 570 E + M+HEA+SRT++ +P Q +LITALKATGKPLVLVLMNGRPL++ KE +QADAILET Sbjct: 503 EPRSMSHEAASRTSLDLPGRQSELITALKATGKPLVLVLMNGRPLSIGKEQKQADAILET 562 Query: 571 WFAGTEGGNAIADVLFGDYNPSGKLPISFPRSVGQIPVYYSHLNTGRPYNPEKPNKYTSR 630 W++G+EGGNA+ADVLFGDYNPSGKLPI+FPRSVGQIP YYSHLNTGRPY YTS+ Sbjct: 563 WYSGSEGGNAVADVLFGDYNPSGKLPITFPRSVGQIPNYYSHLNTGRPYIAGALRNYTSQ 622 Query: 631 YFDEANGPLYPFGYGLSYTTFTVSDVTLSSPTMQRDGKVTASVEVTNTGKREGATVIQMY 690 YFD+++GPLYPFG+GLSYT F+++D+ LSS T+ + + ASV V N G+R+G TV+Q+Y Sbjct: 623 YFDQSHGPLYPFGFGLSYTDFSLTDMALSSTTLSKTDNLVASVMVKNIGQRDGETVVQLY 682 Query: 691 LQDVTASMSRPVKQLKGFEKITLKPGERKTVSFPIDIEALKFWNQQMKYDAEPGKFNVFI 750 ++DV S+SRPVK+LK F+KI LK GE K V F I+ LKF+N Q++Y AEPG+F V I Sbjct: 683 IRDVVGSVSRPVKELKNFQKIMLKAGEEKAVHFSINENDLKFFNSQLEYAAEPGEFRVQI 742 Query: 751 GVDSARVKQGSFELL 765 G+DS VK+ SFELL Sbjct: 743 GLDSQDVKEQSFELL 757 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: 1403 Number of extensions: 37 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