Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_012673982.1 SULAZ_RS08155 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >NCBI__GCF_000021545.1:WP_012673982.1 Length = 262 Score = 139 bits (351), Expect = 4e-38 Identities = 83/249 (33%), Positives = 143/249 (57%), Gaps = 12/249 (4%) Query: 3 KLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILL 62 K++V++L K +G EVLK VS + +V ++G SGSGKST ++ I L +P +GKI + Sbjct: 4 KIKVENLVKAFGKKEVLKNVSFEVKEREVFVLMGGSGSGKSTVIKHIIGLLKPTSGKIYI 63 Query: 63 NNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122 + ++ + + + L R ++ +FQ L+ + EN+ + M Sbjct: 64 DGVDITTLKDFE----------LIEFRKKIGYLFQEGALFDSLKVWENVGFYYLENTKMP 113 Query: 123 KAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDP 182 + E R+ A LA VG+ +D YP +SGG ++RV++ARA++ PE++L+DEPTS LDP Sbjct: 114 QDEIRKLATQKLALVGLKDIEDLYPSQLSGGMRKRVSLARAISYNPEIILYDEPTSGLDP 173 Query: 183 ELVGDVLKVMQALAQE-GRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQ 241 + ++ L E G T +VVTH++ A +++++ +HKGV+ G P+E+ +P Sbjct: 174 VTSAMIDNLILKLRDELGVTSIVVTHDLESAFNIADRIAMIHKGVIYAIGTPQEIKNHPD 233 Query: 242 SERLQQFLS 250 +QQF++ Sbjct: 234 PV-VQQFIN 241 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: 149 Number of extensions: 6 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: 262 Length adjustment: 24 Effective length of query: 230 Effective length of database: 238 Effective search space: 54740 Effective search space used: 54740 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: 47 (22.7 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