Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate AO353_04610 AO353_04610 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04610 Length = 393 Score = 684 bits (1765), Expect = 0.0 Identities = 340/375 (90%), Positives = 363/375 (96%) Query: 1 VRAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEAD 60 VRAW+FQ++T+VAVI++GW+LF+NTQTNLQHRGITSGF FLERSAGFGIAQHLIDYTE+D Sbjct: 19 VRAWLFQIITIVAVISMGWYLFNNTQTNLQHRGITSGFSFLERSAGFGIAQHLIDYTESD 78 Query: 61 SYARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLL 120 SYARVF+IGLLNTLLVTFIGVILATILGFI+GVARLS+NWII+KLATVYVE FRNIPPLL Sbjct: 79 SYARVFVIGLLNTLLVTFIGVILATILGFIVGVARLSKNWIINKLATVYVETFRNIPPLL 138 Query: 121 QILFWYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIVL 180 QILFWYFAVFL+MPGPR +HNF DTFFVSSRGLNMPAA +A GFW FVIS+V+AIVAIVL Sbjct: 139 QILFWYFAVFLTMPGPRNSHNFADTFFVSSRGLNMPAAQMANGFWAFVISIVVAIVAIVL 198 Query: 181 MTRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVLI 240 M RWANKRFEATG PFHKFWVGLALFL+IPAL AL+FG P+HWEMP+L+GFNFVGGWVLI Sbjct: 199 MCRWANKRFEATGVPFHKFWVGLALFLLIPALCALIFGVPLHWEMPKLQGFNFVGGWVLI 258 Query: 241 PELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVI 300 PELLALTLALTVYTAAFIAEIVRSGI SVSHGQTEAARSLGLRNGPTLRKVIIPQALRVI Sbjct: 259 PELLALTLALTVYTAAFIAEIVRSGINSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVI 318 Query: 301 IPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISIS 360 IPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISIS Sbjct: 319 IPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISIS 378 Query: 361 LLMNWYNKRIALIER 375 LLMNWYNKRIALIER Sbjct: 379 LLMNWYNKRIALIER 393 Lambda K H 0.328 0.141 0.430 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: 646 Number of extensions: 8 Number of successful extensions: 1 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: 375 Length of database: 393 Length adjustment: 30 Effective length of query: 345 Effective length of database: 363 Effective search space: 125235 Effective search space used: 125235 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 (21.8 bits) S2: 50 (23.9 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