Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate Echvi_2842 Echvi_2842 Alpha-glucosidases, family 31 of glycosyl hydrolases
Query= BRENDA::Q8RDL1 (751 letters) >FitnessBrowser__Cola:Echvi_2842 Length = 808 Score = 562 bits (1448), Expect = e-164 Identities = 286/695 (41%), Positives = 431/695 (62%), Gaps = 12/695 (1%) Query: 3 QRTVEGIVVRSEGKKLELRVITDKIVNIFVTDKEEKRRDTIAIEKKKYDIPDFNVEESKD 62 ++T GI ++ + + T KIV + V+ + ++ + P N+ E D Sbjct: 23 EQTPHGIAGITDKAYFNICLYTAKIVRVQVSRTVPFTPNPYSVVASPEETP-VNLHEEAD 81 Query: 63 KVLVLTKDLKVEIDKKTFFITFKDKDGDVINEDYGE-GVKLGDSEVRCYKKLR-EDHFYG 120 +++ TKDLK+ ++K + +T+ D++G+++N+D GV +EV YKKL+ + F G Sbjct: 82 FLILETKDLKIVLNKNEWALTYYDQNGNLLNQDDPAFGVSWLGTEVTNYKKLQPHEKFIG 141 Query: 121 FGEKAGYLDKKGEKFEMWNTDEFMTHNQTTKLLYESYPFFIGMNKKHTYGIFLDNSFRSF 180 GEK G +D+ G+ F WNTD F + LY S PF+IG++++ YGIF DN+ ++ Sbjct: 142 LGEKTGGIDRAGQAFVNWNTDYF-AYGVNDDPLYMSIPFYIGIHQELAYGIFFDNTHKTT 200 Query: 181 FNMGEESEEYYYFGAYGGQMNYYFIYGNDIKEVVENYTYLTGRIELPPLWALGNQQSRYS 240 FN G + + YF A G M+YYF G+ + E++ YT LTG++ LPP WALG QQ RYS Sbjct: 201 FNFGASNRRFSYFSADDGDMDYYFFQGDSVSEIIGGYTSLTGKLALPPKWALGFQQCRYS 260 Query: 241 YTPQEKVLEVAKTFREKDIPCDVIYLDIDYMEGYRVFTWNKGTFKNYKEMLKNLKSMGFK 300 Y P+ +V +AKTFR+KD+P DVIYLDI +M+ Y+VFT++ F N K M+K L + GF+ Sbjct: 261 YYPESEVFTLAKTFRDKDMPADVIYLDIHHMKKYKVFTFDGEKFPNPKAMIKALNAKGFR 320 Query: 301 VVTIVDPGVKRDYEYFVYREGIENDYFVKDKYGITYVGKVWPGEACFPDFLQDKVRKWWG 360 VV I+DPG+K + +Y Y EG++ D F+K G TY G+VWPG FPDF K R+WW Sbjct: 321 VVVIMDPGIKVEKDYLPYEEGMDQDLFLKYPDGETYEGQVWPGWCAFPDFTAAKTREWWA 380 Query: 361 EKIANFVRDGIDGIWNDMNEPAVFETPTKTMPEDNIHILDGEKISHREAHNVYANYMALA 420 EK+A + G+DG W DMNEPA + T + + +GE++SHR+A N+Y MA A Sbjct: 381 EKMAFYTDAGVDGFWTDMNEPASWGQHTPNLINFD---YEGEQVSHRKARNIYGMQMARA 437 Query: 421 TKEGLLKERTNERPFILTRAAFAGIQRYAAMWTGDNRSLYEHLLMMMPMLMNVGLSGQPF 480 + G ERPFILTRA F+GIQR+AA WTGDN + EH+L + ++ ++G+SG F Sbjct: 438 AQNG-ASTNGQERPFILTRAGFSGIQRFAAAWTGDNVASEEHMLAGIRLVNSLGISGVSF 496 Query: 481 AGADVGGFEGDCSEELFIRWIEAAVFTPFLRVHSAIGTKDQEPWSFGKKAEDIARKFIKI 540 AG DVGGF G+ S+ LF RW+ A F P R HS I + D EPW+FG++ E+I++ ++K+ Sbjct: 497 AGYDVGGFCGEASKSLFARWMSIAAFAPLYRAHSMINSNDAEPWAFGEEVEEISKNYLKL 556 Query: 541 RYELLPYIYDLFYEASKKGYPVMRPLVFEYQEDENTH--KIYDEFMLGQNLLIAPVYLPS 598 RY++LP Y FY++++ G PV + L +Y D++ + + ++++ LL+ PV Sbjct: 557 RYKMLPLWYSAFYKSTQDGLPVAKSLAIDYCFDDHVYDARFQNQYICCDALLVVPVE-SH 615 Query: 599 KDRREVYLPSGIWYDYFMGERYEGGNYYLVEAPIDTIPVFVKEGAIIVKQKPLSYVEEDR 658 K+ + YLP G WY + + Y+G V+ PI+ +PVFVK G+I+ Q P+S+ E Sbjct: 616 KEITKAYLPEGQWYYLYNDDSYKGAQEIYVDTPINYLPVFVKGGSILPLQSPVSHTAEQH 675 Query: 659 IEEKVVEIYRG-NRGRYVHYEDDGKTFDYKKGVYN 692 + +Y+G Y+HYEDDG T DY+KG ++ Sbjct: 676 DGILRLHVYKGEGTSSYIHYEDDGVTLDYQKGKHH 710 Lambda K H 0.320 0.141 0.426 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: 1773 Number of extensions: 81 Number of successful extensions: 7 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: 751 Length of database: 808 Length adjustment: 41 Effective length of query: 710 Effective length of database: 767 Effective search space: 544570 Effective search space used: 544570 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: 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