Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >MicrobesOnline__882:209027 Length = 368 Score = 216 bits (551), Expect = 6e-61 Identities = 120/290 (41%), Positives = 175/290 (60%), Gaps = 10/290 (3%) Query: 4 LELRNVNKTYGPGLPDT--LKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGA 61 +ELR V K + DT L NI+L+I +GEFL L+GPSGCGK+T++ I+G E G Sbjct: 8 IELRGVTKNF----EDTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGV 63 Query: 62 ILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSK 121 I + + P+ R + VFQ+YAL+P MSVR+N+ FGL++++ P EI V + Sbjct: 64 ITLKGQRMDDAPPEARQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALR 123 Query: 122 LLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLM 181 ++ +E R+P QLSGGQQQRVA+ RA+ P + L DEP S LD KLR +M+ E+K + Sbjct: 124 MVHLEAHADRRPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHL 183 Query: 182 HQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPM 241 ++L T V+VTHDQ EA + D+V VM DG I+Q G+P++IY PANL+VA F+G + Sbjct: 184 QRQLGITFVFVTHDQEEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVGEINI 243 Query: 242 NFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQI 291 + DG A+++ P+ Q +V + +RPE + Sbjct: 244 LNAVIAANHGDGLYDAVIEG----VTFPIRSQRTFAPGDKVNVLLRPEDL 289 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: 390 Number of extensions: 11 Number of successful extensions: 1 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 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