Align α-glucosidase (BT0339;BT_0339) (EC 3.2.1.20) (characterized)
to candidate 17717 b3656 predicted alpha-glucosidase (NCBI)
Query= CAZy::AAO75446.1 (748 letters) >FitnessBrowser__Keio:17717 Length = 772 Score = 348 bits (894), Expect = e-100 Identities = 185/526 (35%), Positives = 291/526 (55%), Gaps = 24/526 (4%) Query: 202 ECFAGTGERFFKMDLSGQTLFLKNQDGQGVNNRRTYKNIPFYLSSRMYGTFYHTCAHSKL 261 E G GERF + +GQT+ N+DG G + + YKNIPFY+++R YG + Sbjct: 160 ETVYGLGERFTALVRNGQTVETWNRDG-GTSTEQAYKNIPFYMTNRGYGVLVNHPQCVSF 218 Query: 262 SLAGHSTRSVQFLSDQAMLDAFVIAGDTMEEILRGYRDLTGYPSMPPLWSFGVWMSRMTY 321 + VQF + L+ FVI G T + +L Y TG P++PP WSFG+W++ Sbjct: 219 EVGSEKVSKVQFSVESEYLEYFVIDGPTPKAVLDRYTRFTGRPALPPAWSFGLWLTTSFT 278 Query: 322 FSADE--VNEICDRMRAEHYPCDVIHLDTGWFRTDWLCEWKFNEERFPDPKGFIQRLKKN 379 + DE VN D M + P V H D W + C+++++ FPDP+G I+RLK Sbjct: 279 TNYDEATVNSFIDGMAERNLPLHVFHFDCFWMKAFQWCDFEWDPLTFPDPEGMIRRLKAK 338 Query: 380 GYRVSLWQLPYVAEDAEQIEEAKANEYIAPLTKQQDTDGSNFSALDYAGTI---DFTYPK 436 G ++ +W PY+ + + +E + Y+ + DGS + + + DFT P Sbjct: 339 GLKICVWINPYIGQKSPVFKELQEKGYLL-----KRPDGSLWQWDKWQPGLAIYDFTNPD 393 Query: 437 ATEWYKGLLKQLLDMGVTCIKTDFGENIHMDAV-YKGMKPELLNNLYALLYQKAAYEITK 495 A +WY LK L+ MGV C KTDFGE I D + G P+ ++N YA +Y + + + K Sbjct: 394 ACKWYADKLKGLVAMGVDCFKTDFGERIPTDVQWFDGSDPQKMHNHYAYIYNELVWNVLK 453 Query: 496 EVTGD--GIVWARAAWAGCQRYPLHWGGDSCSSWDGMAGSLKGGLHFGLSGFAFWSHDVP 553 + G+ +++AR+A G Q++P+HWGGD ++++ MA SL+GGL GLSGF FWSHD+ Sbjct: 454 DTVGEEEAVLFARSASVGAQKFPVHWGGDCYANYESMAESLRGGLSIGLSGFGFWSHDIG 513 Query: 554 GFHTLPNFMNSIVAEDVYMRWTQFGVFTSHIRYHGTNK-REPWHY-PAIAPLVKKWWKLR 611 GF + VY RW FG+ +SH R HG+ R PW Y +V+ + +L+ Sbjct: 514 GF-------ENTAPAHVYKRWCAFGLLSSHSRLHGSKSYRVPWAYDDESCDVVRFFTQLK 566 Query: 612 YSLIPYIIEQSKLAVESGWPLLQALILHHPEDKLCWHIDDEYYFGNDFLVAPVMNSENRR 671 ++PY+ ++ A G P+++A+++ P+D C ++D +Y G++ +VAPV Sbjct: 567 CRMMPYLYREAARANARGTPMMRAMMMEFPDDPACDYLDRQYMLGDNVMVAPVFTEAGDV 626 Query: 672 DIYLPEGQWVNFFTGERLQGGRWLKEVYVPLEEMPVYVRENAVIPI 717 YLPEG+W + + + L G RW K+ + L +PVYVR+N ++ + Sbjct: 627 QFYLPEGRWTHLWHNDELDGSRWHKQQHGFL-SLPVYVRDNTLLAL 671 Lambda K H 0.322 0.139 0.449 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: 1715 Number of extensions: 84 Number of successful extensions: 8 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: 748 Length of database: 772 Length adjustment: 40 Effective length of query: 708 Effective length of database: 732 Effective search space: 518256 Effective search space used: 518256 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 (21.9 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