Align ABC transporter for L-Arginine, periplasmic substrate-binding component (characterized)
to candidate Pf6N2E2_2958 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
Query= reanno::BFirm:BPHYT_RS07735 (264 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2958 Length = 260 Score = 248 bits (634), Expect = 7e-71 Identities = 133/257 (51%), Positives = 166/257 (64%), Gaps = 6/257 (2%) Query: 1 MKMNWRNIAALALFAAASATAGTAAAADIKEVHFGVEASYAPFESKSPSGELQGFDIDVG 60 MK ++ALAL AA G A A + KE+ FGV+ SYAPFESK+ G L GFDID+G Sbjct: 1 MKKALLTLSALALCMAA----GVATAKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLG 56 Query: 61 NAVCAKLKAKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPNQM 120 NA+CA+LK KC WVE+ FDG+IP L+A KF+ + S MT+T R +A+DF+ +++ P Sbjct: 57 NAICAELKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKAIDFSSELFSGPTAY 116 Query: 121 IAKKGSGLLPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLASGR 180 + KKGSGL ASLKGK VG QGTIQE YAKA AGV YQ QDQ+YADL SGR Sbjct: 117 VFKKGSGLSEDVASLKGKTVGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYADLTSGR 176 Query: 181 LDAAFQDAEAASKGFLKKPQGAGFEFAGPAVTDEKLLGAGVGFGVRKGDKALKDALNQAL 240 LDAA QD A GFLK P+G G+E + P D +LL + G+RKG+ LK LN+ + Sbjct: 177 LDAAIQDMLQAELGFLKSPKGEGYEVSKP--VDSELLPSKTAIGIRKGNSELKALLNKGI 234 Query: 241 KELKADGTIDRFAAKYF 257 K L DG K+F Sbjct: 235 KALHDDGKYAEIQKKHF 251 Lambda K H 0.317 0.133 0.383 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: 234 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: 264 Length of database: 260 Length adjustment: 25 Effective length of query: 239 Effective length of database: 235 Effective search space: 56165 Effective search space used: 56165 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