Align arginine permease (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein
Query= CharProtDB::CH_091699 (590 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 246 bits (629), Expect = 1e-69 Identities = 163/465 (35%), Positives = 246/465 (52%), Gaps = 33/465 (7%) Query: 84 VKRELKQRHIGMIALGGTIGTGLFIGLSTPLTNAGPVGALISYLFMGSLAYSVTQSLGEM 143 ++R LK RHI +IALGG IGTGLF+G++ + AGP L+ Y G +A+ + + LGEM Sbjct: 10 LQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGP-SVLLGYAIAGLMAFLIMRQLGEM 68 Query: 144 ATFIPVTSSFTVFSQRFLSPAFGAANGYMYWFSWAITFALELSVVGQVIQFWTYKVPLAA 203 PV SF+ F+ ++ S G +G+ YW + + EL+ VG +Q+W P A Sbjct: 69 VVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPDFPTWA 128 Query: 204 WISIFWVIITIMNLFPVKYYGEFEFWVASIKVLAIIGFLIYCFCMVCGAGVTGPVG--FR 261 +IF+V+I ++NL VK YGE EFW A +KV+AI+ +I + G+G GP Sbjct: 129 TAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVS-MIGFGAWLLGSGHGGPDASVAN 187 Query: 262 YWRNPGAWGPGIISKDKNEGRFLGWVSSLINAAFTFQGTELVGITAGEAANPRKSVPRAI 321 W+ G + G+ G V +L F+F G ELVGITA EA NPR+S+P+A Sbjct: 188 LWQYGGFFPNGV----------TGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKAT 237 Query: 322 KKVVFRILTFYIGSLLFIGLLVPYNDPKLTQSTSYVSTSPFIIAIENSGTKVLPHIFNAV 381 +VV+RIL FYIG+L + L P+ K+ Q SPF++ + ++ I N V Sbjct: 238 NQVVYRILIFYIGALAVLLSLYPWQ--KVVQ-----GGSPFVMIFHELDSDLVATILNIV 290 Query: 382 ILTTIISAANSNIYVGSRILFGLSKNKLAPKFLSRTTKGGVPYIAVFVTAAFGALAYMET 441 +LT +S NS +Y SR+LFGL+ AP+ L + ++ GVP A+ V+A L + Sbjct: 291 VLTAALSVYNSCVYANSRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLIN 350 Query: 442 STGGDKVFEWLLNITGVAGFFAWLFISISHIRFMQALKYRGISRDELPFKAKL-MPGLAY 500 F L+ + A W ISI+H++F +A GI+ PF L P Y Sbjct: 351 YLMPGGAFGLLMALAVSALVINWASISITHLKFRKAKLAAGIT----PFYKSLGHPLTNY 406 Query: 501 YAATFMTIIIIIQGFTAFAPKFNGVSFAAAYISIFLFLAVWILFQ 545 F+ +I+++ T P V A+I++ +W+ F+ Sbjct: 407 LCLAFIVLILVVMYLT--PPIRISVMLIPAWIAV-----LWVAFK 444 Lambda K H 0.325 0.140 0.438 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: 691 Number of extensions: 45 Number of successful extensions: 5 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: 590 Length of database: 453 Length adjustment: 35 Effective length of query: 555 Effective length of database: 418 Effective search space: 231990 Effective search space used: 231990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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