Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >NCBI__GCF_000017185.1:WP_011974043.1 Length = 238 Score = 137 bits (344), Expect = 3e-37 Identities = 81/231 (35%), Positives = 137/231 (59%), Gaps = 17/231 (7%) Query: 4 LEVQDLHKRYGSHE----VLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59 +E +++ K YG E VL+G++LK G+ ++I+G SG GKST L + LL+ P+ G Sbjct: 18 IEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKGM 77 Query: 60 ILLNNEELKLVANKDGALKAADPKQLQRMRSRLS-MVFQHFNLWSHMTAMENIMEAPVHV 118 + + ++ + + D A+ R ++S +FQ FNL + +TA+EN+ E P+ + Sbjct: 78 VYIKGKKTTMFSENDRAV----------FRRKISGFIFQQFNLINTLTALENV-ELPLVL 126 Query: 119 LGMSKTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTS 178 +K +KA+ L + + HR++ YP +SGG+QQRVAIARAL+ P+++ DEPT Sbjct: 127 DEKNKNYRIKKAKKLLKIINLGHRENYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTG 186 Query: 179 ALDPELVGDVLKVMQAL-AQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVE 228 LD + +V+ +++ L +EG T+++VTHE FA+ S + +VE Sbjct: 187 NLDSKNSREVMDILKELNEKEGITVIMVTHEPEFAKYASRIINMKDGEIVE 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: 165 Number of extensions: 7 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: 238 Length adjustment: 24 Effective length of query: 230 Effective length of database: 214 Effective search space: 49220 Effective search space used: 49220 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