Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_019866319.1 METMI_RS0110850 phosphate ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >NCBI__GCF_000384075.1:WP_019866319.1 Length = 277 Score = 121 bits (304), Expect = 1e-32 Identities = 90/258 (34%), Positives = 139/258 (53%), Gaps = 24/258 (9%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQ--PHA---G 58 + V++L YG + L G++++ V + IG SG GKST LRCIN + H G Sbjct: 31 IRVENLKLFYGEKQALHGINMEMPKKKVTAYIGPSGCGKSTLLRCINRMNDLVDHVTIEG 90 Query: 59 KILLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHV 118 KILL+NE + D ++ A +R R+ MVFQ N + + EN+ + + Sbjct: 91 KILLDNENIY-----DKSVNVA------ALRRRVGMVFQKPNPFPK-SIFENVAYG-LRI 137 Query: 119 LGMS-KAEAREKAELYLAKVGV-SHRKDAYPGH---MSGGEQQRVAIARALAMEPEVMLF 173 G++ K E E L + KD + MSGG+QQR+ IARA+A+EPEV+L Sbjct: 138 QGINDKRILEETVENALRGAALWDEMKDRLNDNALGMSGGQQQRLVIARAIAIEPEVLLL 197 Query: 174 DEPTSALDPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNP 233 DEP SALDP + +++ L +E T+V+VTH M A VS+ F++ G + E G Sbjct: 198 DEPASALDPISTLKIEELINEL-KEKYTIVIVTHNMQQAARVSDYTAFMYMGELIEMGTT 256 Query: 234 REVLVNPQSERLQQFLSG 251 E+ NP+ ++ + +++G Sbjct: 257 SELFTNPKKKQTEDYITG 274 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: 153 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: 277 Length adjustment: 25 Effective length of query: 229 Effective length of database: 252 Effective search space: 57708 Effective search space used: 57708 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