Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_086510097.1 BZY95_RS11680 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_002151265.1:WP_086510097.1 Length = 368 Score = 303 bits (776), Expect = 5e-87 Identities = 170/363 (46%), Positives = 233/363 (64%), Gaps = 13/363 (3%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA++ L +NK +G +K+++L I +GEF++ VGPSGCGKSTL+ IAGLE+I+ G Sbjct: 1 MASVTLDKINKVFGS--THIIKDVDLAIGEGEFVVFVGPSGCGKSTLLRLIAGLESITDG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 + + D ++ + P++R + MVFQSYALYP M+V +N+AFGLK+ K + E V + Sbjct: 59 ELSIGDQVVNELPPRERGVGMVFQSYALYPHMTVYENMAFGLKLAKTAKETVHERVMATA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++LQ+E LL RKP LSGGQ+QRVAMGRA+AR P+I LFDEPLSNLDA LRV+MR E+ Sbjct: 119 RILQLEELLERKPKALSGGQRQRVAMGRAMAREPRILLFDEPLSNLDASLRVQMRNEIAR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +H+RL +T VYVTHDQ+EAMTL DK+ V+ G ++Q G+P+++Y PA FVA FIGSP Sbjct: 179 LHKRLGSTMVYVTHDQVEAMTLADKIVVLDGGRVEQVGSPQELYQRPATKFVAGFIGSPT 238 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAG--LEDREVILGIRPEQIILANGEA 298 MNF+P RL D + +G LP QDA + + LGIRPE + L+ EA Sbjct: 239 MNFLPARLLGADATGCRIGATGLTELALP---QDASGHAQGAALTLGIRPEHLRLS--EA 293 Query: 299 NGLPTIRAEVQVTEPTGPDTLVFV--NLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLL 356 G E+ E G + V++ +T + R VG+ +TL DP V L Sbjct: 294 QGSEGF--EIVNVEYLGNEVYVYLEPKEGETLLIQRGEAPTTWRVGQRVTLAPDPEHVHL 351 Query: 357 FDA 359 FDA Sbjct: 352 FDA 354 Lambda K H 0.319 0.138 0.393 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: 413 Number of extensions: 22 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: 386 Length of database: 368 Length adjustment: 30 Effective length of query: 356 Effective length of database: 338 Effective search space: 120328 Effective search space used: 120328 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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