Align sucrose-6-phosphate hydrolase (ScrB) (EC 3.2.1.26) (characterized)
to candidate BWI76_RS23410 BWI76_RS23410 glycosyl hydrolase family 32
Query= CAZy::CAG25843.1 (469 letters) >FitnessBrowser__Koxy:BWI76_RS23410 Length = 477 Score = 267 bits (682), Expect = 7e-76 Identities = 166/441 (37%), Positives = 237/441 (53%), Gaps = 39/441 (8%) Query: 27 YPCWHLAPVTGLMNDPNGFCWSGGRYHLFYQWNPLACDHKYKCWGHWSSTDLLHWQHEPL 86 YP +HLA G +NDPNG W G YH FYQ +P + WGH S DL+HW+H P+ Sbjct: 24 YPRYHLAARAGWINDPNGLVWFDGWYHAFYQHHPYSTQWGPMHWGHARSKDLVHWEHLPV 83 Query: 87 ALMPDKEYDRNGCYSGSAVNNQGVLTLCYTGNVKF-----DDGSRTAWQCLATENNQGGF 141 AL P+ D++GC+SGSAV + L L YTG+ KF D+ + QCLAT + F Sbjct: 84 ALAPEGPEDKDGCFSGSAVVDGDTLALIYTGH-KFHGDPSDEANLYQVQCLATSRDGIHF 142 Query: 142 DKLGPVIPLPDGYTGHVRDPKVWKHNSQWYMVLGAQDKEKRGKVLLYSSVDLYTWSFHGE 201 ++ G V+ P G H RDPKVW+ WYM++GA+D + G+V LY S DL W G Sbjct: 143 ERQGIVVDTPPG-MHHFRDPKVWREGDSWYMIVGARDGD-TGQVRLYRSADLRQWQDAGV 200 Query: 202 IAGNGLNEID-NAGYMWECPDFFALDGEYILLCCPQGMVREHERYLNTYPCAWLHGQFDY 260 L+E + GYMWECPDFFAL+G++IL+ PQG+ + R N + +L G++ Sbjct: 201 -----LDEAEKEMGYMWECPDFFALNGKHILMFSPQGLAAKGYRNRNLFQSGYLLGEWQP 255 Query: 261 ETGKFTHGAFSELDAGFEFYAPQTMEAPDGRRLLVGWMGVPDGEEMLQPTRKHHWQHQMT 320 G F E+D G +FYAPQ+ PDGRR+++GW+ D E P ++ W ++ Sbjct: 256 GQAFVREGEFVEMDHGHDFYAPQSFLTPDGRRIVIGWL---DMWESPLPEQQDGWAGMLS 312 Query: 321 CFRELSFQQGKLFQM-PIRELAQLREAEHFWQ-GKADHAPHVEIERLE-MDII------- 370 RELS QM P +E+ +R A W + +E E M++I Sbjct: 313 LPRELSLSADNRLQMRPAKEVESMRGASFPWPVTTLKNQQTTTVENCEAMEVILHWDCAS 372 Query: 371 PSGELY-LNFGNALALHLNDDGIQLQRRSLAGQ--------EKLTRYWRGSVTSLKILCD 421 S E Y L+ G+ L ++++ Q+QR L + G+ L+I D Sbjct: 373 SSAEQYGLSLGDGLRVYVD---AQMQRLVLERHYPQYGLCGTRSVPLTEGADLKLRIFFD 429 Query: 422 SSSVEIFINNGEGVMSNRYFP 442 SSSVE+F+N+GE +S+R +P Sbjct: 430 SSSVEVFVNDGEACLSSRIYP 450 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: 828 Number of extensions: 47 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: 469 Length of database: 477 Length adjustment: 33 Effective length of query: 436 Effective length of database: 444 Effective search space: 193584 Effective search space used: 193584 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