Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_018371126.1 BN415_RS08120 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >NCBI__GCF_000341525.1:WP_018371126.1 Length = 377 Score = 332 bits (850), Expect = 1e-95 Identities = 192/376 (51%), Positives = 235/376 (62%), Gaps = 30/376 (7%) Query: 1 MASVTLRNIRKAYDENE--VMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGG 58 M V L + K Y +E + D NLDI D EF+VFVGPSGCGKST +RMIAGLEDI+ G Sbjct: 1 MVQVKLDKVYKRYPNSEHYSVEDFNLDIQDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 Query: 59 DLTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAA 118 + IDG +NDVAP R IAMVFQ+YALYPHMT+Y+NMAFGLKL K EID VR AA Sbjct: 61 EFLIDGQVMNDVAPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYAKDEIDRRVREAA 120 Query: 119 KILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFAR 178 +IL + LDRKP LSGGQRQRVA+GRAI R K+FL DEPLSNLDA LRV MR E A+ Sbjct: 121 EILGLIEFLDRKPADLSGGQRQRVAMGRAIVRDSKIFLMDEPLSNLDAKLRVSMRAEIAK 180 Query: 179 LHDELKTTMIYVTHDQVEAMTLADKIVVLSA----------GNLEQVGSPTMLYHAPANR 228 LH + T IYVTHDQ EAMTLAD+IV++SA G +EQ+GSP LY+ PAN+ Sbjct: 181 LHRRIGATTIYVTHDQTEAMTLADRIVIMSATKNPSGTGTIGRIEQIGSPQELYNTPANK 240 Query: 229 FVAGFIGSPKMNFM-----EGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGI 283 FVAGFIGSP MNF +GV+ S G+++R G +R +E G ++ GI Sbjct: 241 FVAGFIGSPAMNFFKVALKDGVISS--EQGLSLRLPEG--KRKLLEDKGY-NGKELIFGI 295 Query: 284 RPEHLHVGM------AEDGISARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKG 337 RPE + E ++A + E LG + LY S + ++R+ + H G Sbjct: 296 RPEDIKASQLELDAYPESVVTAEVIVSELLGSESMLY--SKLGDTEFVSRVEARDLHNPG 353 Query: 338 ETQKLGATPEHCHLFD 353 E KL H FD Sbjct: 354 EHVKLAFNVNKGHFFD 369 Lambda K H 0.320 0.135 0.384 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: 377 Number of extensions: 19 Number of successful extensions: 2 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: 369 Length of database: 377 Length adjustment: 30 Effective length of query: 339 Effective length of database: 347 Effective search space: 117633 Effective search space used: 117633 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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