Align Sucrose-6-phosphate hydrolase; Sucrase; Invertase; EC 3.2.1.26 (characterized)
to candidate AO356_28590 AO356_28590 glycosyl hydrolase family 32
Query= SwissProt::P27217 (466 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28590 Length = 500 Score = 251 bits (640), Expect = 5e-71 Identities = 176/498 (35%), Positives = 242/498 (48%), Gaps = 59/498 (11%) Query: 3 LPSRLPAILQAVMQGQPQALADSHYPQWHLAPVNGLLNDPNGFCQVAGRYHLFYQWNPLA 62 +P+ L QA+ G + + D + P +HLAP G +NDPNG G YH+FYQ +P Sbjct: 12 MPASLEHAQQALRDGLSRLIHD-YRPDYHLAPPTGWMNDPNGVVFFRGEYHVFYQHHPFD 70 Query: 63 CDHTYKCWGHWSSADLLHWRHEPIALMPDEEYDRNGCYSGSAVEFEGALTLCYTGNVKFP 122 WGH SADL+HW+H PIAL P +++DR+GC+SGSAV L L YTG+ Sbjct: 71 AKWGPMYWGHAKSADLVHWQHLPIALAPGDDFDRDGCFSGSAVVCGDTLALIYTGHTWLG 130 Query: 123 DGGRTAW----QCLATENADGTFRKLGPVL-PLPEGYTGHVRDPKVWRQDGRWYMVLGAQ 177 + G QCLAT F K G V+ P+ H RDPKVW++DG WY++ GA+ Sbjct: 131 EVGDERLIRQVQCLATSVDGVRFVKHGAVIEDAPQAAIMHFRDPKVWQEDGYWYLIAGAR 190 Query: 178 DVQQRGKVLLFTASDLREWRLVGEIAGHDVNGLANAGYMWECPDLFPLADTHLLICCPQG 237 + + L+ ++DLR W + ++ G GYMWECPDLF L +L+ PQG Sbjct: 191 -LGDTPLLPLYRSTDLRAWEFLDYVS----RGTDGDGYMWECPDLFRLDGRDVLLYSPQG 245 Query: 238 LAREAQRFLNTYPAVWMAGRFDAERGIFDHGPLHELDSGFEFYAPQTMQADDGRRLLVGW 297 + LN Y + G D+E F GP ELD+G +FYA QT+ A DGRRL+ W Sbjct: 246 MQPAGYERLNKYQTGYRIGHLDSE-WHFSGGPFIELDNGHDFYAAQTLVAADGRRLVWAW 304 Query: 298 MGVPDGDEMHQPTRAQGWIHQMTCVRELEWQAGTLYQRPLRELVALR----------GEA 347 + D E P++A W + RELE Q L P RELVALR GE+ Sbjct: 305 L---DMWESPMPSQAHHWCGMLGLPRELELQGDRLGVFPARELVALRQAPLPSIAPWGES 361 Query: 348 -QGW----CGQTLPL-----------APMELAFDLSPD---STLGLDFAGALQLTVNRDG 388 W G L + + +A S D TL A +L ++R Sbjct: 362 GSRWVPQVSGDRLEIHVHLDLLDCTEGHLGIALRCSADEQEQTLLYYDASLRRLVLDRSR 421 Query: 389 LRLSRRGLQTAEMHHRYWRGEARRLRIFIDRSSVEIFINDGEGVMSSRFFP--------- 439 G ++ + + LR+F+DRSS+E+F G +SSR +P Sbjct: 422 SGAQVSGQRSVPIEPAQTQ---LHLRVFLDRSSIEVFEQSGRFSLSSRLYPRPDSLGVKL 478 Query: 440 ---GYPGQLIFSGATPVA 454 G G + S A P+A Sbjct: 479 LASGTGGHVAISNAWPLA 496 Lambda K H 0.324 0.140 0.475 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: 920 Number of extensions: 56 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 466 Length of database: 500 Length adjustment: 34 Effective length of query: 432 Effective length of database: 466 Effective search space: 201312 Effective search space used: 201312 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 52 (24.6 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