Align α-glucosidase (BT0339;BT_0339) (EC 3.2.1.20) (characterized)
to candidate WP_013429643.1 CALKRO_RS03030 alpha-xylosidase
Query= CAZy::AAO75446.1 (748 letters) >NCBI__GCF_000166775.1:WP_013429643.1 Length = 772 Score = 384 bits (987), Expect = e-111 Identities = 211/577 (36%), Positives = 315/577 (54%), Gaps = 30/577 (5%) Query: 174 RYDGLPIAFCKRTGKKERATLSFESRPDECFAGTGERFFKMDLSGQTLFLKNQDGQGVNN 233 +Y G I T +E+ +LS EC G GERF +GQ + + N+DG G N+ Sbjct: 135 KYLGYAIMPDNTTYMREQLSLSV----GECVYGLGERFTPFVKNGQVIDMWNEDG-GTNS 189 Query: 234 RRTYKNIPFYLSSRMYGTFYHTCAHSKLSLAGHSTRSVQFLSDQAMLDAFVIAGDTMEEI 293 YKNIPFY+++R YG F + +A + VQF + L+ F+I G M+ + Sbjct: 190 DLAYKNIPFYITNRGYGVFVNDPGRVSFEVATENVERVQFSVEGEYLEYFIIGGSNMKNV 249 Query: 294 LRGYRDLTGYPSMPPLWSFGVWMSRMTYFSADE--VNEICDRMRAEHYPCDVIHLDTGWF 351 L Y LTG P +PP WSFG+W++ S DE V D M + P V H D W Sbjct: 250 LENYTKLTGRPQLPPAWSFGLWLTTSFTTSYDEKTVTNFIDGMIEKDIPLHVFHFDCFWM 309 Query: 352 RTDWLCEWKFNEERFPDPKGFIQRLKKNGYRVSLWQLPYVAEDAEQIEEAKANEYIAPLT 411 + +++++ FP+P ++RLK+ G ++ +W PYV++ ++ +E K Y Sbjct: 310 KDMHWVDFEWDRRVFPEPSQMLKRLKEKGVKICVWINPYVSQFSKLFDEGKEKGYFL--- 366 Query: 412 KQQDTDGSNFSALDYA---GTIDFTYPKATEWYKGLLKQLLDMGVTCIKTDFGENIHMDA 468 + +G + D+ +DFT P+A WY LK+L+ MGV C KTDFGE I D Sbjct: 367 --KKPNGDVWQTDDWQPGMAIVDFTNPEACRWYSEKLKELIKMGVDCFKTDFGERIPTDV 424 Query: 469 VY-KGMKPELLNNLYALLYQKAAYEITKEVTGDG--IVWARAAWAGCQRYPLHWGGDSCS 525 VY G P+ ++N Y LY K YE +E G G +V+AR+A AG Q++P+HWGGD + Sbjct: 425 VYFDGSDPQKMHNYYTYLYNKTVYETLQETFGKGNAVVFARSATAGSQKFPVHWGGDCLA 484 Query: 526 SWDGMAGSLKGGLHFGLSGFAFWSHDVPGFHTLPNFMNSIVAEDVYMRWTQFGVFTSHIR 585 S++ MA +L+GGL L GF FWSHD+ GF S D+Y RW FG+ +SH R Sbjct: 485 SYESMAETLRGGLSLSLCGFGFWSHDIGGFE-------STATPDLYKRWVAFGLLSSHSR 537 Query: 586 YHGTNK-REPWHYPAIAPLVKKWW-KLRYSLIPYIIEQSKLAVESGWPLLQALILHHPED 643 HG + + PW Y A V +++ KL+ L+PYI + A E G P+L+ ++L P+D Sbjct: 538 LHGNSAYKVPWLYDEEAVDVLRFFTKLKCKLMPYIFSAAVEATERGIPVLRPMVLEFPDD 597 Query: 644 KLCWHIDDEYYFGNDFLVAPVMNSENRRDIYLPEGQWVNFFTGERLQGGRWLKEVYVPLE 703 C ++D +Y G+ LVAP+ + + + Y+PEG W N TGE+++GG+W KE + Sbjct: 598 PACVYLDRQYMLGDSLLVAPIFSEDGYVEYYVPEGIWTNILTGEKVEGGKWRKEKH-GYF 656 Query: 704 EMPVYVRENAVIPIYPEEVNCTDEMDLGKSIALRIDH 740 +P+ R N VIPI + + D ++A+ I H Sbjct: 657 SLPLLARPNTVIPI--GSCDTRPDYDYADNVAMNIYH 691 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: 1671 Number of extensions: 64 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 24 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