Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 138 bits (347), Expect = 2e-37 Identities = 80/237 (33%), Positives = 138/237 (58%), Gaps = 17/237 (7%) Query: 19 LKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLVANKDGALK 78 ++ S + G++ I+G SGSGKST +R +N L +P +G++L++ E++ + N D +K Sbjct: 46 VQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDI-VAMNDDQLVK 104 Query: 79 AADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTEAREKAEHYLNKVG 138 R++LSMVFQ F L HMT ++N + + G+ K ++A L +VG Sbjct: 105 VR--------RAKLSMVFQSFALMPHMTVLQNAAFG-LEMDGVDKQTREQRALQALEQVG 155 Query: 139 VAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDP----ELVGDVLKVMQA 194 + ++ P +SGG QQRV +AR LA++P+++L DE SALDP E+ ++LK+ Sbjct: 156 LEAWAESMPDELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQ-- 213 Query: 195 LAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERLQQFLSG 251 A+ RT+V ++H++ A + +++ + G V + G P E+L NP + ++ F G Sbjct: 214 -AKAKRTIVFISHDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRG 269 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: 255 Number of extensions: 15 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: 415 Length adjustment: 28 Effective length of query: 226 Effective length of database: 387 Effective search space: 87462 Effective search space used: 87462 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 Apr 09 2024. 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