Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate AO356_27105 AO356_27105 amino acid transporter
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27105 Length = 253 Score = 339 bits (869), Expect = 4e-98 Identities = 173/255 (67%), Positives = 211/255 (82%), Gaps = 3/255 (1%) Query: 1 MYKLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKI 60 MYKL V LHK YG+HEVLKGVSL+A GDVIS+IG+SGSGKSTFLRCIN LE P+ G + Sbjct: 1 MYKLTVDGLHKSYGTHEVLKGVSLQAKTGDVISLIGASGSGKSTFLRCINFLETPNDGAM 60 Query: 61 LLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLG 120 L+ + + +V N G L+ AD ++LQR+R+RL+MVFQHFNLW HMT +ENI AP VLG Sbjct: 61 SLDGKPICMVKNHAG-LRVADDRELQRLRTRLAMVFQHFNLWGHMTVLENITIAPRRVLG 119 Query: 121 MSKTEAREKAEHYLNKVGVAHR-KDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSA 179 +SK +A ++A YL+KVG+ R D +P +SGG+QQRVAIARALAMEPEVMLFDEPTSA Sbjct: 120 VSKKDAEDRARRYLDKVGLPARIADQFPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSA 179 Query: 180 LDPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVN 239 LDPE+VG+VLKV+Q LA+EGRTM++VTHEMGFAR+VSNQL+FLH+G+VEE G P E+L N Sbjct: 180 LDPEVVGEVLKVIQGLAEEGRTMIMVTHEMGFARKVSNQLLFLHQGLVEEQGGP-EILDN 238 Query: 240 PQSERLQQFLSGSLK 254 P+SERLQQFLS LK Sbjct: 239 PRSERLQQFLSNGLK 253 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: 238 Number of extensions: 9 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: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 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 17 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