Align sucrose-6-phosphate hydrolase (ScrB) (EC 3.2.1.26) (characterized)
to candidate Pf1N1B4_5116 Sucrose-6-phosphate hydrolase (EC 3.2.1.B3)
Query= CAZy::CAG25843.1 (469 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5116 Length = 489 Score = 258 bits (659), Expect = 3e-73 Identities = 173/473 (36%), Positives = 231/473 (48%), Gaps = 50/473 (10%) Query: 10 ILQAVMKGQSKALADAHYPCWHLAPVTGLMNDPNGFCWSGGRYHLFYQWNPLACDHKYKC 69 I Q + + D + P +HLAP G MNDPNG + G YH+FYQ +P Sbjct: 7 IAQHALSDGLSRVTDDYRPGYHLAPPAGWMNDPNGVVYFRGEYHVFYQHHPFDAKWGPMY 66 Query: 70 WGHWSSTDLLHWQHEPLALMPDKEYDRNGCYSGSAVNNQGVLTLCYTGNVKF----DDGS 125 WGH S DL+HWQH P+AL P ++DR+GC+SGSAV L L YTG+ D+ Sbjct: 67 WGHAKSADLVHWQHLPIALAPGDDFDRDGCFSGSAVVCGDTLALIYTGHTWLGEVGDERY 126 Query: 126 RTAWQCLATENNQGGFDKLGPVI-PLPDGYTGHVRDPKVWKHNSQWYMVLGAQDKEKRGK 184 QCLAT + F K G VI P H RDPKVW+ + WY++ GA+ + Sbjct: 127 IRQVQCLATSTDGIQFVKHGAVIDTAPQDTIMHFRDPKVWQEDDGWYLIAGARLGDV-PL 185 Query: 185 VLLYSSVDLYTWSFHGEIAGNGLNEIDNAGYMWECPDFFALDGEYILLCCPQGMVREHER 244 + LY S DL++W F ++ + GYMWECPD F L+G +LL PQGM E Sbjct: 186 LPLYRSTDLHSWEFLDYVSSGS----EGDGYMWECPDLFRLNGRDVLLYSPQGMQPEGYE 241 Query: 245 YLNTYPCAWLHGQFDYETGKFTHGAFSELDAGFEFYAPQTMEAPDGRRLLVGWMGVPDGE 304 LN Y + G+ D + FT G F ELD G +FYA QT+ A DGRRL+ W+ D Sbjct: 242 RLNKYQTGYRVGRLDSQ-WHFTGGPFIELDNGHDFYAAQTLLAADGRRLVWAWL---DMW 297 Query: 305 EMLQPTRKHHWQHQMTCFRELSFQQGKLFQMPIRELAQLREAE----HFWQGKADH-APH 359 E P++ HHW + REL +L P REL LR A +W+G P Sbjct: 298 ESPMPSQAHHWCGMLGVPRELELHADRLCVYPARELTALRMAPLPGVSWWEGSGSRWVPE 357 Query: 360 VEIERLEMDI------IPSGELYLNFGNALALHLNDDG---------IQLQR-------- 396 V + LE+ + SG L +AL +DDG LQR Sbjct: 358 VNGDMLEIHVHLDLRGCTSGHL------GIALRCSDDGHEETLLYYDASLQRLVLDRSRA 411 Query: 397 -RSLAGQEKLTRYWRGSVTSLKILCDSSSVEIFINNGEGVMSNRYFPHHPASL 448 + GQ ++ L++ D SS+E+F NG +S+R +P P SL Sbjct: 412 GAQVTGQRSVSIDPTQERLELRVFLDRSSIEVFDENGRFSLSSRLYP-RPDSL 463 Lambda K H 0.321 0.138 0.463 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: 862 Number of extensions: 43 Number of successful extensions: 7 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: 469 Length of database: 489 Length adjustment: 34 Effective length of query: 435 Effective length of database: 455 Effective search space: 197925 Effective search space used: 197925 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 (21.9 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