Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate GFF3087 HP15_3030 histidine/lysine/arginine/ornithine transporter subunit
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Marino:GFF3087 Length = 256 Score = 329 bits (843), Expect = 4e-95 Identities = 160/244 (65%), Positives = 201/244 (82%) Query: 7 QDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEE 66 +D++K + EVLKG+SL+ GDV+S+IGSSGSGKSTFLRCINLLE P +G I+++ + Sbjct: 10 RDIYKTFDQLEVLKGISLETRKGDVVSLIGSSGSGKSTFLRCINLLETPTSGDIIVHGDP 69 Query: 67 LKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTEA 126 ++ N+ G AD KQ++ +R++LSMVFQ FNLWSHMT +ENI+EAPVHVL + K EA Sbjct: 70 IRFTTNRKGERIPADNKQVELIRAKLSMVFQSFNLWSHMTVLENIIEAPVHVLKVPKKEA 129 Query: 127 REKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVG 186 E+AE YLNKVG+ RKD YP MSGG+QQR AIARALAMEPEVMLFDEPTSALDPELVG Sbjct: 130 IERAEAYLNKVGIYERKDYYPAQMSGGQQQRAAIARALAMEPEVMLFDEPTSALDPELVG 189 Query: 187 DVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERLQ 246 +VLKVMQ LA+EGRTM+VVTHEM FAR+VS+Q++FLH+GV+EE G P +V +P SER++ Sbjct: 190 EVLKVMQGLAEEGRTMIVVTHEMAFARDVSSQVLFLHQGVIEEQGTPEKVFDHPDSERMK 249 Query: 247 QFLS 250 QFL+ Sbjct: 250 QFLT 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: 224 Number of extensions: 4 Number of successful extensions: 1 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: 256 Length adjustment: 24 Effective length of query: 230 Effective length of database: 232 Effective search space: 53360 Effective search space used: 53360 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