Align arginine permease (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter
Query= CharProtDB::CH_091699 (590 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 259 bits (662), Expect = 2e-73 Identities = 157/434 (36%), Positives = 231/434 (53%), Gaps = 21/434 (4%) Query: 84 VKRELKQRHIGMIALGGTIGTGLFIGLSTPLTNAGPVGALISYLFMGSLAYSVTQSLGEM 143 +KR LK RHI +IALGG IGTGLF+G + L +AGP ++ Y G +A+ + + LGEM Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGP-SMILGYAIAGFIAFLIMRQLGEM 69 Query: 144 ATFIPVTSSFTVFSQRFLSPAFGAANGYMYWFSWAITFALELSVVGQVIQFWTYKVPLAA 203 PV SF+ F+ ++ G G+ YW + + EL+ VG+ IQFW +P Sbjct: 70 IVEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIP--T 127 Query: 204 WIS--IFWVIITIMNLFPVKYYGEFEFWVASIKVLAIIGFLIY-CFCMVCGAGVTGPVGF 260 W+S +F+V + ++N VK++GE EFW A IKV+AI+G ++ C+ + G G Sbjct: 128 WVSALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTGGPQASVS 187 Query: 261 RYWRNPGAWGPGIISKDKNEGRFLGWVSSLINAAFTFQGTELVGITAGEAANPRKSVPRA 320 W + G + G +G + S+ F+F G ELVGITA EA+ PRK +P+A Sbjct: 188 NLWSHGGFFPNG----------GMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKA 237 Query: 321 IKKVVFRILTFYIGSLLFIGLLVPYND--PKLTQSTSYVSTSPFIIAIENSGTKVLPHIF 378 I +VV+RIL FY+G+L + L P++ L S S SPF+ G HI Sbjct: 238 INQVVYRILIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHIL 297 Query: 379 NAVILTTIISAANSNIYVGSRILFGLSKNKLAPKFLSRTTKGGVPYIAVFVTAAFGALAY 438 N V+LT +S NS +Y SR+LFGL++ APK L + K GVP A+ ++A L Sbjct: 298 NFVVLTAALSVYNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCV 357 Query: 439 METSTGGDKVFEWLLNITGVAGFFAWLFISISHIRFMQALKYRGISRDELPFKAKLMPGL 498 + E L + + W ISI+HI+F +A+ +G++ FK P Sbjct: 358 VVNYVAPQSALELLFALVVASLMINWALISITHIKFRKAMGEQGVTPS---FKTFWFPFS 414 Query: 499 AYYAATFMTIIIII 512 Y FM +II + Sbjct: 415 NYLCLAFMVMIISV 428 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: 715 Number of extensions: 42 Number of successful extensions: 4 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: 467 Length adjustment: 35 Effective length of query: 555 Effective length of database: 432 Effective search space: 239760 Effective search space used: 239760 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