Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_046009788.1 OLEAN_RS14330 proline/glycine betaine ABC transporter ATP-binding protein ProV
Query= SwissProt::P17328 (400 letters) >NCBI__GCF_000967895.1:WP_046009788.1 Length = 398 Score = 468 bits (1205), Expect = e-136 Identities = 238/395 (60%), Positives = 304/395 (76%), Gaps = 1/395 (0%) Query: 1 MAIKLEVKNLYKIFGEHPQRAFKYIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIM 60 M+ KLEVKNLYK+FG P++A + +E G +K+ I +TG+++GV++ASL I+EGEIFVIM Sbjct: 1 MSYKLEVKNLYKVFGNKPKKAIQMLESGATKDTIFSQTGMTVGVQNASLQIKEGEIFVIM 60 Query: 61 GLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPH 120 GLSGSGKST+VRLLNRLIEPT GQVLIDG DI ++ LR VRR K++MVFQSFAL+PH Sbjct: 61 GLSGSGKSTLVRLLNRLIEPTLGQVLIDGEDITRLDKKSLRAVRRNKVSMVFQSFALLPH 120 Query: 121 MTVLDNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALA 180 +TVLDN AFG+EL+G R EKA++AL QVGLE YA +YPDELSGGM+QRVGLARALA Sbjct: 121 LTVLDNAAFGLELSGEPKDVRYEKAMNALNQVGLEAYALSYPDELSGGMQQRVGLARALA 180 Query: 181 INPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQN 240 +PDILLMDEAFSALDPLIR EMQDELV LQ +RTI+FISHDLDEAMRIGDRIAIMQ Sbjct: 181 NDPDILLMDEAFSALDPLIRAEMQDELVNLQKAQRRTIIFISHDLDEAMRIGDRIAIMQG 240 Query: 241 GEVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRSPVGLIRKTPGFGPRSAL 300 G+++QVG PDEIL NPANDYV++FF+GVD+S VF+A DIA + V +I++ A+ Sbjct: 241 GKIIQVGQPDEILQNPANDYVKSFFKGVDVSNVFNAGDIATQGDVKVIKQAADVDLSLAM 300 Query: 301 KLLQDEDREYGYVIERGNKFVGVVSIDSLKAALSQAQGIEAALIDDPLVVDAQTPLSELL 360 L +++ EY Y+ + + GV+S + L LS +E A ID + D T ++E++ Sbjct: 301 TQLNNDESEYAYITDENDHLRGVISTEDLANNLSNQSQLENAFIDLESITDT-TQINEVI 359 Query: 361 SHVGQAPCAVPVVDEEHQYVGIISKRMLLQALDRE 395 V +PC VPVVD++++Y G+IS+ LL+ LDRE Sbjct: 360 GQVAASPCPVPVVDKDNKYQGVISQNQLLETLDRE 394 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: 483 Number of extensions: 27 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: 398 Length adjustment: 31 Effective length of query: 369 Effective length of database: 367 Effective search space: 135423 Effective search space used: 135423 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 24 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