Align α-glucosidase (BT0339;BT_0339) (EC 3.2.1.20) (characterized)
to candidate BWI76_RS27590 BWI76_RS27590 alpha-xylosidase
Query= CAZy::AAO75446.1 (748 letters) >FitnessBrowser__Koxy:BWI76_RS27590 Length = 772 Score = 361 bits (926), Expect = e-104 Identities = 191/522 (36%), Positives = 295/522 (56%), Gaps = 24/522 (4%) Query: 206 GTGERFFKMDLSGQTLFLKNQDGQGVNNRRTYKNIPFYLSSRMYGTFYHTCAHSKLSLAG 265 G GERF + +GQT+ N+DG G + ++YKNIPFYL++R YG + + Sbjct: 164 GLGERFTALVRNGQTVDTWNEDG-GTSTEQSYKNIPFYLTNRGYGVLVNHPERVSFEIGS 222 Query: 266 HSTRSVQFLSDQAMLDAFVIAGDTMEEILRGYRDLTGYPSMPPLWSFGVWMSRMTYFSAD 325 VQF + L+ FVI G T +E+L Y TG P++PP WSFG+W++ + D Sbjct: 223 EKVSKVQFSVEGEHLEYFVIDGPTPKEVLNRYTRFTGRPALPPAWSFGLWLTTSFTTNYD 282 Query: 326 E--VNEICDRMRAEHYPCDVIHLDTGWFRTDWLCEWKFNEERFPDPKGFIQRLKKNGYRV 383 E VN D M + P V H D W + C+++++ FPDP+G I+RLK+ G +V Sbjct: 283 EATVNRFIDGMAERNLPLHVFHFDCFWMKAFQWCDFEWDPLTFPDPEGMIKRLKEKGLKV 342 Query: 384 SLWQLPYVAEDAEQIEEAKANEYIAPLTKQQDTDGSNFSALDYAGTI---DFTYPKATEW 440 +W PY+ + + +E + Y+ + DGS + + + DFT P+A +W Sbjct: 343 CVWINPYIGQRSPVFKELQEKGYLL-----KRPDGSLWQWDKWQPGLAIYDFTNPQACQW 397 Query: 441 YKGLLKQLLDMGVTCIKTDFGENIHMDAV-YKGMKPELLNNLYALLYQKAAYEITKEVTG 499 Y LK L+ MGV C KTDFGE I D + G P+ ++N YA +Y + + + KE G Sbjct: 398 YADKLKGLVAMGVDCFKTDFGERIPTDVQWFDGSDPQKMHNHYAFIYNELVWNVLKETVG 457 Query: 500 D--GIVWARAAWAGCQRYPLHWGGDSCSSWDGMAGSLKGGLHFGLSGFAFWSHDVPGFHT 557 + +++AR+A G Q++P+HWGGD ++++ MA SL+GGL G+SGF FWSHD+ GF Sbjct: 458 EKEAVLFARSASVGAQQFPVHWGGDCYANYESMAESLRGGLSIGMSGFGFWSHDIGGFE- 516 Query: 558 LPNFMNSIVAEDVYMRWTQFGVFTSHIRYHGTNK-REPWHYP-AIAPLVKKWWKLRYSLI 615 + VY RW FG+ +SH R HG+ R PW Y +V+ + +L+ ++ Sbjct: 517 ------NTAPAHVYKRWCAFGLLSSHSRLHGSKSYRVPWAYDDESCDVVRHFTQLKCRMM 570 Query: 616 PYIIEQSKLAVESGWPLLQALILHHPEDKLCWHIDDEYYFGNDFLVAPVMNSENRRDIYL 675 PY+ Q+ LA E G P+L++++L P D C ++D +Y G+ LVAPV + +L Sbjct: 571 PYLYRQAALANEFGTPMLRSMMLEFPHDPACDYLDRQYMLGDSVLVAPVFSEAGDVQFWL 630 Query: 676 PEGQWVNFFTGERLQGGRWLKEVYVPLEEMPVYVRENAVIPI 717 PEG+W + + + QG RW K+ + L +PVYVR+N ++ + Sbjct: 631 PEGRWTHLWRNDEAQGSRWHKQNHDVL-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: 1697 Number of extensions: 82 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