Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate PP_0868 PP_0868 ABC transporter ATP-binding subunit
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Putida:PP_0868 Length = 385 Score = 197 bits (501), Expect = 4e-55 Identities = 127/351 (36%), Positives = 199/351 (56%), Gaps = 23/351 (6%) Query: 44 VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103 V SL + EGEI V +G SG GKST ++++NRLI PT GQV I+G D + + LR Sbjct: 21 VDSVSLTVNEGEICVFLGPSGCGKSTTLKMINRLITPTSGQVFINGEDTTGLDEVTLR-- 78 Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLE--NYAHSY 161 + I V Q L P+MT+ +N L G + ++ E+A + + + LE Y Y Sbjct: 79 --RHIGYVIQQIGLFPNMTIEENITVVPRLLGWDKQKCHERARELMHMIKLEPKQYLQRY 136 Query: 162 PDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFI 221 P ELSGG +QR+G+ RALA + +LLMDE F A+DP+ R +Q+E ++Q +T++ + Sbjct: 137 PRELSGGQQQRIGVIRALAADAPVLLMDEPFGAVDPINREMIQNEFFEMQRALNKTVIMV 196 Query: 222 SHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDIS----QVFSAK 277 SHD+DEA+++GD+IAI + G+++Q+ PD +L +PA+D+V F G D + + A+ Sbjct: 197 SHDIDEAIKLGDKIAIFRAGKLLQLDHPDTLLAHPADDFVSNFV-GQDSTLKRLLLVRAE 255 Query: 278 DIARRTPNGLIRKTPGFGPRSALKLLQDEDREYGYVIERGNKFVGAVSIDSLKTALTQQQ 337 D A P+ +P AL+LL + DR Y V + NK +G V + + +QQ Sbjct: 256 DAADNAPS----VSPETPVGDALELLDEHDRRYVVVTDAQNKALGYVR----RRDMHRQQ 307 Query: 338 GLDAALIDAPLAVDA--QTPLSELLSHVGQAPCA-VPVVDEDQQYVGIISK 385 G + P A L LLS + + A +PV+D +Q ++G +++ Sbjct: 308 GTCGDFL-RPFNATASHDEHLRILLSRMYEFNRAWLPVLDAEQVFLGEVTQ 357 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: 386 Number of extensions: 13 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: 385 Length adjustment: 31 Effective length of query: 369 Effective length of database: 354 Effective search space: 130626 Effective search space used: 130626 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