Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate GFF1457 HP15_1422 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Marino:GFF1457 Length = 240 Score = 237 bits (605), Expect = 1e-67 Identities = 127/248 (51%), Positives = 171/248 (68%), Gaps = 13/248 (5%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 + VQ++HK +G EVLKGVSL G+V+S+IG SGSGKST L CIN +E + GKIL++ Sbjct: 2 ISVQNVHKSFGDLEVLKGVSLDVKKGEVVSVIGGSGSGKSTLLYCINAIEPINKGKILVD 61 Query: 64 NEELKLV-ANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122 + ++ NKD ++R +L MVFQ +N + HMT +EN AP V MS Sbjct: 62 DVDVHAKETNKD------------KLRQKLGMVFQQWNSFPHMTVLENAALAPRIVKKMS 109 Query: 123 KTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDP 182 K EA E A+ L VG+ + D YP MSGG+QQR+AIARALAM+P+ ML DE TSALDP Sbjct: 110 KEEAIEIAKKELEHVGLGDKFDVYPTKMSGGQQQRLAIARALAMKPDYMLLDEVTSALDP 169 Query: 183 ELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQS 242 ELVG+VL ++ LA+EG TM+ VTHEMGFAR+VS+++ + H+GV+ E G R+V+ +PQ+ Sbjct: 170 ELVGEVLDTLRLLAEEGMTMICVTHEMGFARDVSDRVAYFHEGVIAEIGEARQVITDPQN 229 Query: 243 ERLQQFLS 250 Q+FLS Sbjct: 230 PLTQKFLS 237 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: 183 Number of extensions: 7 Number of successful extensions: 2 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 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