Align α-glucosidase (EC 3.2.1.20) (characterized)
to candidate BWI76_RS09045 BWI76_RS09045 alpha-glucosidase
Query= CAZy::ABR26230.1 (752 letters) >FitnessBrowser__Koxy:BWI76_RS09045 Length = 787 Score = 292 bits (748), Expect = 4e-83 Identities = 210/673 (31%), Positives = 326/673 (48%), Gaps = 41/673 (6%) Query: 46 ERKEYDTPEFSISDELESILIETNSLKVKINKND-LSVSFLDKNGN---IINEDYNGG-- 99 E + P + +++ +++ I T+ L+V +++ L + D+ G + N+ Sbjct: 70 ELSGFSLPAWQLTEHSDALTIATDQLRVTVHQPLWLEWRYRDEAGEWQPLANDRPTSAYL 129 Query: 100 AKFNETDVRCYKKLREDH-FYGFGEKAGYLDKKGERLEMWNTDEFMTHNQTTKLLYESYP 158 A + V Y R+D FYG GEKAG L + G+R EM N D + +T LY+ P Sbjct: 130 ANAHGDGVAHYLSRRKDERFYGLGEKAGDLQRNGKRYEMRNLDAMGYNAASTDPLYKHIP 189 Query: 159 FFIGMNDYHTYGIFLDNSFRSFFDMGQESQEYYF----FGAYGGQMNYYFIYGEDIKEVV 214 F I +YG+F DN + D+G E Y+ + A G ++YY G+ + ++ Sbjct: 190 FTITQRSDVSYGLFYDNLSSCWLDLGNEIDNYHTAYRRWQAEAGDIDYYLFSGKRVLDIT 249 Query: 215 ENYTYLTGRISLPPLWVLGNQQSRYSYTP----QERVLEVAKTFREKDIPCDVIYLDIDY 270 + + LTG+ P W LG S YT Q +++ + E IPCD L Y Sbjct: 250 KAFVRLTGKTLFGPKWSLGYSGSTMHYTDAPDAQNQLMNFIRLCDEHAIPCDSFQLSSGY 309 Query: 271 --MEGYR-VFTWNKETFKNHKEMLKQLKEMGFKVVTIVDPGVKRDYDYHVYREGIEKGYF 327 + G R VF WN + K M + + G K+ + P + +D+ Y E E+G F Sbjct: 310 TSINGKRYVFNWNNDKVPQPKVMSQAFHDAGLKLAANIKPCLLQDHPR--YHEVAERGLF 367 Query: 328 VKDKYG-ITYVGKVWPGEACFPDFLQEEVRYWWGEK-HREFINDGIDGIWNDMNEPAVFE 385 ++D W E DF + WW E + + GID WND NE V++ Sbjct: 368 IRDSQADAPERSSFWDDEGSHLDFTNPQTVAWWQEGVTTQLLELGIDSTWNDNNEYEVWD 427 Query: 386 TPTKTMPEDNIHILDGEKVLHKEAHNVYANYMAMATRDGFLRIRPNERPFVLTRAAFSGI 445 E H G ++ K V M A+ + R P +RP++++R+ +G+ Sbjct: 428 G------EARCHGF-GHEIAIKHIRPVMPLLMMRASLEAQQRFAPQKRPYLISRSGCAGM 480 Query: 446 QRYAAMWTGDNRSLYEHLLMMMPMLMNIGLSGQPFVGADVGGFEGDCHE-ELFIRWIEAA 504 QRY W+GDNR+ +E L M + + LSG VG DVGGF GD + ELF+RW++ Sbjct: 481 QRYVQTWSGDNRTNWETLRYNTRMGLGMSLSGLFNVGHDVGGFSGDKPDPELFVRWVQNG 540 Query: 505 VFTPFLRVHSAIGTKDQ---EPWSFGKRAEDISRKYIKMRYELLPYLYDLFYIASQKGYP 561 V P +HS DQ E W + + I R I++RY LLPYLY L + A P Sbjct: 541 VMHPRFTIHS--WNDDQTVNEAWMYPEVTPAI-RSAIELRYRLLPYLYTLLWQAHADDEP 597 Query: 562 IMRPLVFEYQKDENTHKIYDEFMFGEGLLVAPVYLPSKERREVYLP--EGIWYDYWTGKG 619 ++RP +++ D T D+F+ G LLVA V P +R V+LP + WYD+++ + Sbjct: 598 MLRPTFLDHEHDAQTFAECDDFLLGRDLLVASVVEPGARQRRVWLPANQDGWYDFYSHQW 657 Query: 620 FKGKNYYLVDAPIEVIPLFVKEG-GILLKQQPQSFIGEK-KLEELTVEIYKGK-EGHYLH 676 + G + ++DAP+E +PL V+ G G+ L ++ + EK EL + KG L Sbjct: 658 YAGGQWIVLDAPLEKLPLLVRAGAGLPLSERIRHVCAEKDDTRELKLFPLKGMGTCRGLL 717 Query: 677 YEDDGKSFDYTKG 689 +EDDG+S+ Y G Sbjct: 718 FEDDGESWGYRNG 730 Lambda K H 0.320 0.141 0.432 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: 1593 Number of extensions: 102 Number of successful extensions: 10 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: 752 Length of database: 787 Length adjustment: 41 Effective length of query: 711 Effective length of database: 746 Effective search space: 530406 Effective search space used: 530406 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