Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate PfGW456L13_3150 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3150 Length = 372 Score = 288 bits (736), Expect = 2e-82 Identities = 160/355 (45%), Positives = 237/355 (66%), Gaps = 22/355 (6%) Query: 3 IKLEVKNLYKIFGEHPQRAFK-YIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMG 61 + ++ ++++KIFG+ A +++GL+K QIL+ G +GV D SL + GEIF IMG Sbjct: 11 VLIDCQSVWKIFGKAAPAAMNAVVQQGLTKTQILQNYGCVVGVSDVSLQVRRGEIFCIMG 70 Query: 62 LSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHM 121 LSGSGKST++RLLN+LI P+ G++++ G +++ ++ A+LREVR + I MVFQS AL+P+ Sbjct: 71 LSGSGKSTLIRLLNKLITPSAGKIVVKGKELSSLNAAQLREVRARHIGMVFQSVALLPNR 130 Query: 122 TVLDNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAI 181 TVL+NTAFG+E+ G+ ER + A AL +VGL ++ YP ELSGGM+QRVGLARA+ Sbjct: 131 TVLENTAFGLEVQGVGKAERYKVAEQALAKVGLSDWMSRYPSELSGGMQQRVGLARAITA 190 Query: 182 NPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNG 241 +P+++LMDE FSALDPLIR ++QDE +L + ++ VFI+HDLDEA+RIGDRIAIM++G Sbjct: 191 DPEVILMDEPFSALDPLIRRQLQDEFRQLTKELGKSAVFITHDLDEAIRIGDRIAIMKDG 250 Query: 242 EVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRSPVGLIR-KTPGFGPRSAL 300 ++QVGT +EI+ NPA+DYV F G+ + A + +PV + PG + Sbjct: 251 AIIQVGTAEEIVLNPADDYVAEFVAGISRLHLVRANSV--MTPVESFKVANPGCDIARLI 308 Query: 301 KLLQDEDREYGYVIERGNKFVGVVSIDSLKAALSQAQGIEAALIDDPLVVDAQTP 355 K D D N+ +G +++ S + AL A++D+ +VV TP Sbjct: 309 KTSVDADI---------NELIG-LTMKSERDAL--------AVVDNGVVVGIITP 345 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: 417 Number of extensions: 19 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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