Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate H281DRAFT_03485 H281DRAFT_03485 osmoprotectant transport system ATP-binding protein
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__Burk376:H281DRAFT_03485 Length = 372 Score = 186 bits (471), Expect = 1e-51 Identities = 129/372 (34%), Positives = 200/372 (53%), Gaps = 38/372 (10%) Query: 39 GLSLGVKDA-SLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISD 97 G S V D + + GEI V++G SG GK+T ++++NRLI+P+ G++ IDG D + Sbjct: 13 GASAPVVDGIDMEVGAGEICVLLGPSGCGKTTTLKMINRLIQPSSGKIFIDGRDTDEFEV 72 Query: 98 AELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQVGLE-- 155 ELR ++I V Q L P+MTV +N + L G + +A + + V L+ Sbjct: 73 VELR----RQIGYVIQQIGLFPNMTVEENISVVPRLLGWDKARAKRRAAELMEIVALDPS 128 Query: 156 NYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQ 215 Y YP +LSGG +QRVG+ARALA +P ++LMDE F A+DP+ R +QDE +++Q + + Sbjct: 129 TYLSRYPKDLSGGQQQRVGVARALATDPPVMLMDEPFGAIDPINRELIQDEFLRIQQQVK 188 Query: 216 RTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF---------FR 266 +TI+F+SHD+DEA+++ DRIAI + G + Q TPD IL PA+ ++ F R Sbjct: 189 KTIMFVSHDIDEAVKMADRIAIFRGGRLEQFDTPDTILARPASPFIAGFVGADRALKRLR 248 Query: 267 GVDISQVFSAKDIARRSPVGLIRKTPGFGPRSALKLLQDEDREYGYVIERGNKFVGVVSI 326 V S SA D A R G A LL+ E +++ K G +S Sbjct: 249 LVRASDALSACDCAAR---------VGDSSERARALLERHGVEQIVLLDAAGKPQGYLS- 298 Query: 327 DSLKAALSQAQGIEAALIDDPL------VVDAQTPLSELLSHVGQAPCAVPVVDEEHQYV 380 A LS +G A P+ D ++ +S + S +GQ+ A VD+E ++V Sbjct: 299 ---AAELSAIEGTLMAAHAKPVQGVARHSDDLRSVISSMFS-LGQSWLA--TVDDEGRFV 352 Query: 381 GIISKRMLLQAL 392 G +++ ++ L Sbjct: 353 GYVNQAHIVDML 364 Lambda K H 0.319 0.137 0.378 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: 364 Number of extensions: 14 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: 400 Length of database: 372 Length adjustment: 30 Effective length of query: 370 Effective length of database: 342 Effective search space: 126540 Effective search space used: 126540 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 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