Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_046009788.1 OLEAN_RS14330 proline/glycine betaine ABC transporter ATP-binding protein ProV
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >NCBI__GCF_000967895.1:WP_046009788.1 Length = 398 Score = 141 bits (355), Expect = 2e-38 Identities = 88/278 (31%), Positives = 154/278 (55%), Gaps = 41/278 (14%) Query: 2 YKLEVQDLHKRYGSHEV------------------------LKGVSLKAAAGDVISIIGS 37 YKLEV++L+K +G+ ++ SL+ G++ I+G Sbjct: 3 YKLEVKNLYKVFGNKPKKAIQMLESGATKDTIFSQTGMTVGVQNASLQIKEGEIFVIMGL 62 Query: 38 SGSGKSTFLRCINLLEQPHAGKILLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQ 97 SGSGKST +R +N L +P G++L++ E++ + K +L+A R+++SMVFQ Sbjct: 63 SGSGKSTLVRLLNRLIEPTLGQVLIDGEDITRLDKK--SLRAV-------RRNKVSMVFQ 113 Query: 98 HFNLWSHMTAMENIMEAPVHVLGMSKTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQR 157 F L H+T ++N + + G K EKA + LN+VG+ +YP +SGG QQR Sbjct: 114 SFALLPHLTVLDNAAFG-LELSGEPKDVRYEKAMNALNQVGLEAYALSYPDELSGGMQQR 172 Query: 158 VAIARALAMEPEVMLFDEPTSALDP----ELVGDVLKVMQALAQEGRTMVVVTHEMGFAR 213 V +ARALA +P+++L DE SALDP E+ +++ + +A + RT++ ++H++ A Sbjct: 173 VGLARALANDPDILLMDEAFSALDPLIRAEMQDELVNLQKA---QRRTIIFISHDLDEAM 229 Query: 214 EVSNQLVFLHKGVVEESGNPREVLVNPQSERLQQFLSG 251 + +++ + G + + G P E+L NP ++ ++ F G Sbjct: 230 RIGDRIAIMQGGKIIQVGQPDEILQNPANDYVKSFFKG 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: 11 Number of successful extensions: 5 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: 398 Length adjustment: 27 Effective length of query: 227 Effective length of database: 371 Effective search space: 84217 Effective search space used: 84217 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