Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_052367418.1 U743_RS01940 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >NCBI__GCF_000733765.1:WP_052367418.1 Length = 413 Score = 144 bits (363), Expect = 3e-39 Identities = 80/230 (34%), Positives = 134/230 (58%), Gaps = 11/230 (4%) Query: 23 SLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLVANKDGALKAADP 82 S + A G+V ++G SGSGKST +R +N L +P +G I LN ++ + ++ Sbjct: 48 SFEVAEGEVFVVMGLSGSGKSTLVRMLNRLIEPSSGSIKLNGRDITQASRRE-------- 99 Query: 83 KQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTEAREKAEHYLNKVGVAHR 142 ++ R +SMVFQ F L H T ++N ++V GM K E KA L+ VG+ Sbjct: 100 -LIEIRRRSISMVFQSFALMPHQTVLQNAAFG-LNVAGMKKEEREAKAMEALDAVGLKSN 157 Query: 143 KDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVL-KVMQALAQEGRT 201 ++YP +SGG +QRV +ARALA +PEV+L DE SALDP + ++ ++++ +++ RT Sbjct: 158 ANSYPDELSGGMKQRVGLARALATDPEVLLMDEAFSALDPLIRTEMQDELLRLQSEQART 217 Query: 202 MVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERLQQFLSG 251 +V +TH++ A V +++ + G + + G P E++ P +E ++ F G Sbjct: 218 VVFITHDLDEAMRVGDRIAIMQGGWIVQIGTPEEIVRAPANEYVRSFFRG 267 Lambda K H 0.317 0.131 0.366 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: 220 Number of extensions: 12 Number of successful extensions: 4 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: 254 Length of database: 413 Length adjustment: 28 Effective length of query: 226 Effective length of database: 385 Effective search space: 87010 Effective search space used: 87010 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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