Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >NCBI__GCF_900141795.1:WP_074200832.1 Length = 227 Score = 123 bits (308), Expect = 4e-33 Identities = 87/230 (37%), Positives = 125/230 (54%), Gaps = 18/230 (7%) Query: 4 LEVQDLHKRY----GSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59 LE ++L K Y VLKGVSL + ++I+GSSGSGKST L + L++P G+ Sbjct: 6 LEGRNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGE 65 Query: 60 ILLNNEELKLVANKDGALKAADPKQLQRMRSR-LSMVFQHFNLWSHMTAMENIMEAPVHV 118 +LL + + R+R+R + V+Q +L +TA EN+M P+ + Sbjct: 66 VLLLGQPFSKLGEAARG----------RLRNRHMGFVYQFHHLLPELTAEENVM-MPLLI 114 Query: 119 LGMSKAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTS 178 S+A AR+KA L VG+S R P +SGGE+QRVA+ARAL EP+ +L DEPT Sbjct: 115 RRESEATARDKALALLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTG 174 Query: 179 ALDPELVGDVLKVMQALAQE-GRTMVVVTHEMGFAREVSNQLVFLHKGVV 227 LD VL +M L Q G ++VVTH++ A + L L G++ Sbjct: 175 NLDSRSAEQVLSLMDDLNQRFGTALLVVTHDVNIAARMDRTLT-LRDGMI 223 Lambda K H 0.317 0.131 0.364 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: 145 Number of extensions: 12 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: 254 Length of database: 227 Length adjustment: 23 Effective length of query: 231 Effective length of database: 204 Effective search space: 47124 Effective search space used: 47124 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 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