Align Sucrose-6-phosphate hydrolase; Sucrase; Invertase; EC 3.2.1.26 (characterized)
to candidate Echvi_2806 Echvi_2806 Beta-fructosidases (levanase/invertase)
Query= SwissProt::P27217 (466 letters) >FitnessBrowser__Cola:Echvi_2806 Length = 498 Score = 130 bits (326), Expect = 1e-34 Identities = 133/459 (28%), Positives = 184/459 (40%), Gaps = 69/459 (15%) Query: 28 PQWHLAPVNGLLNDPNGFCQVAGRYHLFYQWNPLACDHTYKCWGHWSSADLLHWRHEPIA 87 PQ+H +P +NDPNG + G YHLFYQ P + WGH S DLLHW H PIA Sbjct: 41 PQYHFSPPQQWMNDPNGMVYLDGEYHLFYQHYPDSNVWGPMHWGHAVSEDLLHWDHLPIA 100 Query: 88 LMPDEEYDRNGCYSGSAVEFEGALT---------LCYTGNVKFPDGGRTAWQCLATENAD 138 L PD +SGSAV G + + + G++ Q +A N Sbjct: 101 LYPD---SLGYIFSGSAVIDHGNTSGLGKNGQDPMVAIFTYHHDENGQS--QGIAFSNDK 155 Query: 139 G---TFRKLGPVLPLPEGYTGHVRDPKVWRQD-----GRWYMVLGAQDVQQRGKVLLFTA 190 G T + PVL P RDPKV D G+W M L +D K+ +++ Sbjct: 156 GRSWTKYRNNPVLESPG--IPDFRDPKVSWYDRGNGSGKWIMTLAVKD-----KISFYSS 208 Query: 191 SDLREWRLVGEIAGHDVNGLANAGYMWECPDLFPLADTH------LLICCPQGLAREAQR 244 +L +W + A G +WECPDLFPL LL+ G Sbjct: 209 PNLIDWTHESDFNPE----WAAYGGVWECPDLFPLKTNSGNEKWMLLVSINPGGPNGGS- 263 Query: 245 FLNTYPAVWMAGRFDAERGIFDHGPLHELDSGFEFYAPQT---MQADDGRRLLVGWMGVP 301 + G FD + + + LD G + YA T + +DGRRL +GWM Sbjct: 264 -----ATQYFIGNFDGQNYTAEGESIKWLDYGTDNYAGVTWSNIPPEDGRRLFIGWMSNW 318 Query: 302 DGDEMHQPTRAQGWIHQMTCVREL----EWQAGTLYQRPLRELVALRGEAQGWCGQTLPL 357 + T W T REL + + RP++EL LR + G T L Sbjct: 319 QYANIVPTTE---WRSANTIPRELALITDHGVERVASRPIKELEQLRQTTEIIQGSTHAL 375 Query: 358 APMELAFDLSPDS------TLGLDFAGALQLTVNRDGLRLSRRGLQTAEMHHRYWRG--- 408 +L +S TL + + +T + L R + + Sbjct: 376 KDPLFELELEKESGESARITLKNELGEKVMITFEDNQLIFDRTESGKISFEEGFGKRITA 435 Query: 409 -----EARRLRIFIDRSSVEIFINDGEGVMSSRFFPGYP 442 +R++ DRSS+EIFINDG VM+ FP P Sbjct: 436 PITDITIETIRMYADRSSLEIFINDGALVMTEIIFPNAP 474 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: 787 Number of extensions: 46 Number of successful extensions: 5 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: 466 Length of database: 498 Length adjustment: 34 Effective length of query: 432 Effective length of database: 464 Effective search space: 200448 Effective search space used: 200448 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