Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_086511129.1 BZY95_RS17245 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_002151265.1:WP_086511129.1 Length = 380 Score = 298 bits (763), Expect = 2e-85 Identities = 161/362 (44%), Positives = 234/362 (64%), Gaps = 13/362 (3%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MATL+L ++ K + + +K ++L+++D EF++ VGPSGCGKSTL+ IAGLE+ + G Sbjct: 1 MATLQLHDIVKRFDD--TEVIKGVDLEVNDREFVVFVGPSGCGKSTLLRMIAGLESATSG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 IL+D ++ + P +R +AMVFQSYALYP M+V DN+ F LK+ +P E +V + Sbjct: 59 DILIDGVRMNEVGPAERGLAMVFQSYALYPHMTVEDNMGFSLKLAGVPKEERRRKVREAA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +LQ+E LL RKP LSGGQ+QRVA+GRA+ R P I+LFDEPLSNLDA LRV+MR E+ Sbjct: 119 SILQLEPLLERKPKALSGGQRQRVAIGRAIVRNPSIFLFDEPLSNLDAALRVQMRIELAR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +H+ L T +YVTHDQIEAMT+ DK+ V++ G+++Q G+P ++Y++P N FVA FIGSP Sbjct: 179 LHEELDATMIYVTHDQIEAMTMADKIVVLQGGVVEQVGSPMELYHHPRNRFVAGFIGSPK 238 Query: 241 MNFIPL-RLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIIL-ANGEA 298 MNF+ + R+ + L G C +P + +GL+D + LGIRPE + L G Sbjct: 239 MNFLEVERVSAAATGVEVRLPDGDT-CTVP--VDGSGLDDDALTLGIRPEHLQLDPQGPL 295 Query: 299 NGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFD 358 +G ++V E G T ++V + +T V +V VG++L F+ LFD Sbjct: 296 SG------RIEVIERLGGVTSLYVRMQNTLVTVSADGNVDSRVGDSLRFGFERDCAHLFD 349 Query: 359 AK 360 + Sbjct: 350 GE 351 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: 435 Number of extensions: 22 Number of successful extensions: 3 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: 380 Length adjustment: 30 Effective length of query: 356 Effective length of database: 350 Effective search space: 124600 Effective search space used: 124600 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 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