Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_053938866.1 WG78_RS16145 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >NCBI__GCF_001294205.1:WP_053938866.1 Length = 242 Score = 216 bits (551), Expect = 3e-61 Identities = 113/248 (45%), Positives = 162/248 (65%), Gaps = 13/248 (5%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 + ++++ K YG +VL S + G+V+ + G SGSGKST ++C+N LE G I+++ Sbjct: 2 ISIKNISKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNGLEAFQKGDIIVD 61 Query: 64 NEELKLVANKDGALKAADPK-QLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122 + DPK L ++RSR+ MVFQ+F L+ H++ +N+ A + VLG + Sbjct: 62 GTSV------------GDPKTNLPKLRSRVGMVFQNFELFPHLSITQNLTLAQMQVLGRN 109 Query: 123 KTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDP 182 + EA L++VG+ D +PG +SGG+QQRVAIARALAM+P MLFDEPTSALDP Sbjct: 110 RDEATVNGLRLLDRVGLKAHADKHPGQLSGGQQQRVAIARALAMDPIAMLFDEPTSALDP 169 Query: 183 ELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQS 242 E+V +VL VM LAQEG TM+ VTHEMGFAR+V+N+++F+ KG + E + +P+S Sbjct: 170 EMVNEVLDVMVELAQEGMTMMCVTHEMGFARKVANRVIFMDKGAIVEDATKEDFFGSPRS 229 Query: 243 ERLQQFLS 250 ER Q FLS Sbjct: 230 ERAQVFLS 237 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: 171 Number of extensions: 7 Number of successful extensions: 2 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: 242 Length adjustment: 24 Effective length of query: 230 Effective length of database: 218 Effective search space: 50140 Effective search space used: 50140 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: 46 (22.3 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