Align Sucrose-6-phosphate hydrolase; Sucrase; Invertase; EC 3.2.1.26 (characterized)
to candidate AO353_25135 AO353_25135 glycosyl hydrolase family 32
Query= SwissProt::P27217 (466 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25135 Length = 489 Score = 253 bits (646), Expect = 1e-71 Identities = 174/475 (36%), Positives = 236/475 (49%), Gaps = 44/475 (9%) Query: 3 LPSRLPAILQAVMQGQPQALADSHYPQWHLAPVNGLLNDPNGFCQVAGRYHLFYQWNPLA 62 + S L +A+ G + + D + P +H+AP G +NDPNG G YH+FYQ P Sbjct: 1 MSSSLDLAQRALSDGLSRVIHD-YRPGYHIAPPAGWMNDPNGVVYFRGEYHVFYQHYPFE 59 Query: 63 CDHTYKCWGHWSSADLLHWRHEPIALMPDEEYDRNGCYSGSAVEFEGALTLCYTGNVKFP 122 WGH SADL+HW+H PIAL P +++DR+GC+SGSAV L L YTG+ Sbjct: 60 AKWGPMYWGHAKSADLVHWQHLPIALAPGDDFDRDGCFSGSAVVCGDTLALIYTGHTWLG 119 Query: 123 DGGR----TAWQCLATENADGTFRKLGPVLPLPEGYT-GHVRDPKVWRQDGRWYMVLGAQ 177 + G QCLAT F K G V+ P T H RDPKVW++D WY++ GA+ Sbjct: 120 EAGDERSIRQVQCLATSIDGIRFVKHGAVIETPPQDTIMHFRDPKVWKEDDCWYLIAGAR 179 Query: 178 DVQQRGKVLLFTASDLREWRLVGEIAGHDVNGLANAGYMWECPDLFPLADTHLLICCPQG 237 + + L+ ++DL W +G ++G G GYMWECPDLF L +L+ PQG Sbjct: 180 -LGDIPLLPLYRSTDLHAWEFLGYVSG----GSEGDGYMWECPDLFRLNGRDVLLYSPQG 234 Query: 238 LAREAQRFLNTYPAVWMAGRFDAERGIFDHGPLHELDSGFEFYAPQTMQADDGRRLLVGW 297 + + LN Y + GR D+E F GP ELD+G +FYA QT+ A DGRRLL W Sbjct: 235 MQPQGYERLNKYQTGYRVGRLDSE-WHFTGGPFIELDNGHDFYAAQTLLAADGRRLLWAW 293 Query: 298 MGVPDGDEMHQPTRAQGWIHQMTCVRELEWQAGTLYQRPLRELVALRG---EAQGWCGQT 354 + D E P++A W + RELE +A L P REL ALR W ++ Sbjct: 294 L---DMWESPMPSKAHHWCGMLGLPRELELRADRLCVYPARELTALRKAPLPGTPWWDES 350 Query: 355 LPLAPMELAFDLSPDSTLGLDFAG------ALQLTVNRDG----------------LRLS 392 E+ D+ + + LD G + L + DG L S Sbjct: 351 GTRWVPEVKGDML-EIHVHLDLLGCTDGHLGIALRCSDDGYEETLLYYDASLQRLVLDRS 409 Query: 393 RRGLQTAEMHHRYW--RGEARRLRIFIDRSSVEIFINDGEGVMSSRFFPGYPGQL 445 R G Q E LR+F+DRSS+E+F +G +SSR +P PG L Sbjct: 410 RSGAQATGQRSVSIDPTQERLELRVFLDRSSIEVFDENGRFSLSSRLYP-QPGSL 463 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: 892 Number of extensions: 54 Number of successful extensions: 7 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: 489 Length adjustment: 34 Effective length of query: 432 Effective length of database: 455 Effective search space: 196560 Effective search space used: 196560 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: 51 (24.3 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