Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_047094318.1 AAV99_RS11970 ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >NCBI__GCF_001013305.1:WP_047094318.1 Length = 240 Score = 132 bits (333), Expect = 5e-36 Identities = 85/228 (37%), Positives = 129/228 (56%), Gaps = 15/228 (6%) Query: 4 LEVQDLHKRYG----SHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59 +E++ + K +G + + LKGV +K GD ++I+G SGSGKST + + L+ P G Sbjct: 7 IELEGITKTFGKGPAAFQALKGVDMKIDRGDFVAIMGPSGSGKSTTMNILGCLDVPTDGI 66 Query: 60 ILLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVL 119 E++ + D + L R R L VFQ FNL + TA+EN+ E P+ Sbjct: 67 FRFRGIEVQALTR--------DQRSLLRRRY-LGFVFQGFNLLARTTALENV-ELPLLYR 116 Query: 120 GMSKTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSA 179 G +K + R AE L+KVG+ P +SGG+QQRVAIARAL +P+V+L DEPT Sbjct: 117 GETKKQRRIAAERSLDKVGLLPWASHTPAELSGGQQQRVAIARALVTDPDVLLADEPTGN 176 Query: 180 LDPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVV 227 LD E ++++++ L+ G T+++VTHE A E + +V G+V Sbjct: 177 LDTERSLEIMELLTDLSDTGITVLMVTHEEEMA-EYARTIVHFRDGLV 223 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: 139 Number of extensions: 8 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: 240 Length adjustment: 24 Effective length of query: 230 Effective length of database: 216 Effective search space: 49680 Effective search space used: 49680 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