Align arginine/ornithine transport protein (characterized)
to candidate GFF1141 PGA1_c11560 putative arginine transport system permease protein
Query= CharProtDB::CH_107317 (229 letters) >FitnessBrowser__Phaeo:GFF1141 Length = 238 Score = 112 bits (279), Expect = 8e-30 Identities = 69/219 (31%), Positives = 107/219 (48%), Gaps = 37/219 (16%) Query: 45 LAWCGDLYATVVRGIPDLVLILLIFYG-GQGLL---------NWVAPQLGYDDYI----- 89 L+W G Y VVRG+PD+ L QG+ +W AP +D++ Sbjct: 10 LSWLGKAYIAVVRGVPDIAFFLFFVIALDQGIEYLRHQVKCPDWDAPVRQGNDFVVCDIA 69 Query: 90 ------------DLNPFVSGVGTLGFIFGAYLSETFRGAFMAIPKGQGEAGYGYGMSHRQ 137 ++ F V T +FGA+ + GA A+P+ Q E YGM+HRQ Sbjct: 70 KMPLSSSDQWIHEVYGFSLAVVTFAIVFGAFAANVLFGAMRAVPRAQIETAEAYGMTHRQ 129 Query: 138 VFFRIQVPQMIRLAIPGFTNNWLVLVKATALISVVGLQDMMFKAKQASDATREPFT---- 193 F+RI VPQM A+PG +N W+VL+KAT L+ ++G++D+++ A++ + FT Sbjct: 130 AFWRILVPQMWTYALPGLSNLWMVLIKATPLLFLLGVEDIVYWARELGGSKTARFTDYPH 189 Query: 194 ------YYLAVAGLYLLVTSVSLLLLRLLERRYSVGVKT 226 Y+L + YL T +S ++L + R S G T Sbjct: 190 GDWRMWYFLGLLVFYLAFTKLSEVVLERIRTRLSHGQAT 228 Lambda K H 0.328 0.144 0.442 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: 136 Number of extensions: 8 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: 229 Length of database: 238 Length adjustment: 23 Effective length of query: 206 Effective length of database: 215 Effective search space: 44290 Effective search space used: 44290 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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