Align α-glucosidase (SusB;Aglu;BFO_2272) (EC 3.2.1.20) (characterized)
to candidate 6936934 Sama_1108 alpha-glucosidase (RefSeq)
Query= CAZy::AEW20125.1 (708 letters) >FitnessBrowser__SB2B:6936934 Length = 676 Score = 498 bits (1283), Expect = e-145 Identities = 285/714 (39%), Positives = 399/714 (55%), Gaps = 69/714 (9%) Query: 13 LFSFLVSAPFTMRAEELKSPDGNLLMRFEVNGEGTPVYELTYKRKPVIKPSRLGLEI-EG 71 L + S P + LKSP+G + +R V+ + P Y + + KPVI S+LG + Sbjct: 7 LLAMAASLPLQAKTLSLKSPNGEIELR--VSDDDAPHYAVLFHGKPVIGASKLGFDFTNA 64 Query: 72 FSLRKAFTLKGVETVTFDETWTPVWGEVKAIRNHYNEMTATLHQADGDRTMVIRFRLYDD 131 + R F + + T D +W WGE + I + +NE+ + D + +RFR +DD Sbjct: 65 ANFRGGFDITDSQRATVDSSWEQPWGEARIIEDKHNELVVSFTHPDSKQAYKVRFRAFDD 124 Query: 132 GLGFRYEFPQQKSLNYFVIKEEYSEFAM--AGDHKAFWIPG-DYDTQEYDYTESRLTEIR 188 G+GFRYE LN I E +EFA+ A +A+WIPG ++ EY Y S+L + Sbjct: 125 GVGFRYEVNANTPLN---IGRELTEFAIEDADKAEAWWIPGRGWNRYEYLYQHSKLADAA 181 Query: 189 GLMQTAITPNTSQTPFSPTGVQTALMMKSDDGLYINLHEAALVDYPCMSLNLDDQTLTFQ 248 + QTPF+ +K+ DG++I +HEAALVDY M+LN + TF Sbjct: 182 LV----------QTPFT---------LKNKDGVHIAIHEAALVDYAAMTLN-QRRPGTFV 221 Query: 249 SWLTPDAQGKKGYMQTPCHTPWRTVIVSDDARRILASHLTLNLNEPCKLDDVSWIRPVKY 308 + LTP + G +TPWRT+ ++ +A ++ SHL LNLNEP +L DVSW+ P KY Sbjct: 222 AELTPWSDGVAVKTNGTFNTPWRTLHIAPNATGLINSHLILNLNEPNQLGDVSWVEPGKY 281 Query: 309 IGVWWEMISGKSTWAYTNDLPSVHLDVTDYTKMKPNGTHAANNEKVRRYIDFAAKHGFDQ 368 +G+WW M K+TW H A + ++Y+ FAA +GFD Sbjct: 282 VGIWWGMHINKNTWG-------------------SGSQHGATTAETKKYLRFAADNGFDG 322 Query: 369 VLVEGWNIGWE-DWFGNSKDYVFDFVTPYPDFDLKALNEYAHSKGVKLMMHHETSSSVRN 427 VLVEGWNIGW+ DWF N +F F P+ DFD+KA+ +Y G +L+ HHETS SV N Sbjct: 323 VLVEGWNIGWDGDWFHNGD--LFSFTKPFADFDIKAIADYGREVGARLIGHHETSGSVSN 380 Query: 428 YERQMEKAYKLMNDYGYNAVKSGYV---GNI-------IPRGEYHYGQWMVNHYLYAVKK 477 Y +Q + A+ L G VK+GYV GNI + R E+H GQ+MV YL VK Sbjct: 381 YRKQWDGAFSLYQKMGVAQVKTGYVADGGNIKRIDENGLERFEWHDGQFMVGEYLDNVKT 440 Query: 478 AAEHRIMVNAHEAVRPTGLCRTYPNLIGNEAARGGEYESFGG--NKVFHTTILPFTRLMG 535 AA+++I +N HE ++ TGL RTYPN + E ARG EY ++G N H +L FTR++ Sbjct: 441 AAKYQISINTHEPIKDTGLRRTYPNWLAREGARGQEYNAWGNPPNPPEHIAMLSFTRMLA 500 Query: 536 GPMDYTPGIFETRLEKVNPGNNSYVHSTLARQLALYVTMYSPLQMAADLPENYERFMDAF 595 GPMD+TPGIF+ + N STLA+QLALYV +YSP+QMAADLPENY + DAF Sbjct: 501 GPMDFTPGIFDMSFNGLGDNTNR-PQSTLAKQLALYVVLYSPIQMAADLPENYLKRPDAF 559 Query: 596 QFIKDVAIDWDDSKYLEAEPGRYITVARKAK-----GTNNWFVGCTANEDGHLSNVSLDF 650 QFIKDV DW+ S L+ G ++ +ARK + N+W++G +E+ V LDF Sbjct: 560 QFIKDVPTDWEQSIALDGAVGDFVVMARKERKARQYSGNDWYLGAVTDENARDVTVKLDF 619 Query: 651 LDPGRKYTATIYADAPTAHYEKNPQAYTIKQMKVTNKSKLTLRAASGGGYAISI 704 L+PG+ + A IY D A ++ P IK+ V L+L A GGG A+ + Sbjct: 620 LEPGKTFEAQIYQDGKDAEWKWRPYEMDIKKQTVRKGDTLSLHLAEGGGAAVRL 673 Lambda K H 0.319 0.135 0.417 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: 1437 Number of extensions: 72 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 708 Length of database: 676 Length adjustment: 39 Effective length of query: 669 Effective length of database: 637 Effective search space: 426153 Effective search space used: 426153 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 (21.7 bits) S2: 54 (25.4 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