Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate AZOBR_RS08660 AZOBR_RS08660 ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__azobra:AZOBR_RS08660 Length = 399 Score = 415 bits (1066), Expect = e-120 Identities = 213/375 (56%), Positives = 271/375 (72%), Gaps = 1/375 (0%) Query: 1 VRAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEAD 60 VRA +QV+ V VIA+GWFL NT NL R I +GFGFL+R A FGI + LIDY D Sbjct: 26 VRAVFYQVLVVGIVIAVGWFLIHNTLDNLSKRSIATGFGFLDREASFGIGESLIDYHPRD 85 Query: 61 SYARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLL 120 SY R FL+G+LNTL V+ IGV+LAT+LG +IGVARLS NW+I+KLA+ YVE+ RNIPPLL Sbjct: 86 SYGRAFLVGVLNTLKVSIIGVVLATVLGTLIGVARLSSNWLIAKLASTYVEIVRNIPPLL 145 Query: 121 QILFWYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIVL 180 Q+ FWY V SMP R A N F+S RGL +P + ++ +A++ ++ Sbjct: 146 QLFFWYALVSESMPPVRQALNPIPGVFLSQRGLFVPVPSADPVWGTMGFALAIAVIGVIF 205 Query: 181 MTRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVLI 240 + RWA R E TG+PF L+L + +P ++ + GAP ++P+L+GFNFVGG VL Sbjct: 206 LRRWAKARQERTGQPFPIGTASLSLLIGLPLIAYIAGGAPTALDVPKLQGFNFVGGVVLT 265 Query: 241 PELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVI 300 PE A+ + L VYTAAFIAE+VRSGI +V+ GQTEAAR+LG+ +G TLR V++PQALRVI Sbjct: 266 PEFFAILVGLVVYTAAFIAEVVRSGILAVNWGQTEAARALGIDSGKTLRLVVLPQALRVI 325 Query: 301 IPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISIS 360 +PPLTSQYLNL KNSSLA IGYP++VS+ A T LNQTGQAIE +A+ M YL IS+ IS Sbjct: 326 VPPLTSQYLNLTKNSSLALAIGYPDLVSI-ANTTLNQTGQAIEGVAMIMGTYLVISLGIS 384 Query: 361 LLMNWYNKRIALIER 375 + MNWYNKRIAL+ER Sbjct: 385 IFMNWYNKRIALVER 399 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: 481 Number of extensions: 15 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: 375 Length of database: 399 Length adjustment: 30 Effective length of query: 345 Effective length of database: 369 Effective search space: 127305 Effective search space used: 127305 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