Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_00010 (365 letters) >MicrobesOnline__882:209027 Length = 368 Score = 250 bits (638), Expect = 5e-71 Identities = 141/349 (40%), Positives = 205/349 (58%), Gaps = 31/349 (8%) Query: 4 LKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTIELD 63 +++ + K FE + IDLE+++ EF+ +GPSGCGK+T+LRLI+G E +G I L Sbjct: 8 IELRGVTKNFEDTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVITLK 67 Query: 64 GRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARILEL 123 G+ + + P R + VFQ YAL+PHM+VR+N+ F L + K ++ R+V +A R++ L Sbjct: 68 GQRMDDAPPEARQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALRMVHL 127 Query: 124 GSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLHKEL 183 + DR+P+QLSGGQ+QRVAI RA+V NP + L DEP S LD LR Q +LE+ L ++L Sbjct: 128 EAHADRRPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHLQRQL 187 Query: 184 QATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMGFLQ 243 T ++VTHDQ EA ++ +VVV+N G+IEQIGSP E+Y PANL+VA F+G ++ L Sbjct: 188 GITFVFVTHDQEEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVG--EINILN 245 Query: 244 ATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPE---------------HL 288 A + A H G+ G T I R + G V + +RPE HL Sbjct: 246 AVIAANHGDGLYDAVIEGVTFPI-RSQRTFAPGDKVNVLLRPEDLRVYTLTEDRPAGPHL 304 Query: 289 T--------LGAEGQVLVTTDVTERLGSDTFCH-----VNVDSGESLTV 324 T GA ++VT RL + F + +N + GE++TV Sbjct: 305 TGRIEESVYKGATVDLIVTLSDGRRLMAAEFFNEDDVDINYNPGETVTV 353 Lambda K H 0.319 0.136 0.381 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: 324 Number of extensions: 13 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: 365 Length of database: 368 Length adjustment: 30 Effective length of query: 335 Effective length of database: 338 Effective search space: 113230 Effective search space used: 113230 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: 49 (23.5 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