Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate BWI76_RS05950 BWI76_RS05950 polar amino acid ABC transporter inner membrane subunit
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__Koxy:BWI76_RS05950 Length = 250 Score = 98.6 bits (244), Expect = 2e-25 Identities = 73/225 (32%), Positives = 108/225 (48%), Gaps = 23/225 (10%) Query: 156 PAALVAEGF----WPFVISVVLAIVAIVLMT--RWANKRFEATGEPFHKFWVGLALFLVI 209 P + GF W V ++LA V +L+ R R G WV +LF Sbjct: 15 PLQWIISGFLTTVWVSVAGMILATVLAILLLALRLGGGR---PGRWLVAAWV--SLFRNT 69 Query: 210 PALSALLFGAPVHWEMPELKGFNFVGG-----------WVLIPELLALTLALTVYTAAFI 258 P L LLF W + L +F+ W L PE L L V+T+AF+ Sbjct: 70 PLLVQLLFWYFAAWNLLPLGARDFINDDHSWSILPGNVWWLTPEFLCSMWGLGVFTSAFL 129 Query: 259 AEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIPPLTSQYLNLAKNSSLA 318 E + SG+++VSHGQ EAA S G LR +++PQ L P+ QYLNL K SSLA Sbjct: 130 IEEIASGLRAVSHGQREAALSQGFTPWQELRHILLPQGLANAWQPIIGQYLNLMKLSSLA 189 Query: 319 AGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLLM 363 +GIG+ E+ + + + A+E A+ ++YLA+ + + + + Sbjct: 190 SGIGFAEL-TYQVRQIESYNAHALEAFAVGTALYLALGVVMGVAL 233 Score = 53.1 bits (126), Expect = 8e-12 Identities = 27/66 (40%), Positives = 39/66 (59%) Query: 69 GLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQILFWYFA 128 G L T+ V+ G+ILAT+L ++ RL L +V +FRN P L+Q+LFWYFA Sbjct: 22 GFLTTVWVSVAGMILATVLAILLLALRLGGGRPGRWLVAAWVSLFRNTPLLVQLLFWYFA 81 Query: 129 VFLSMP 134 + +P Sbjct: 82 AWNLLP 87 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: 278 Number of extensions: 19 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 250 Length adjustment: 27 Effective length of query: 348 Effective length of database: 223 Effective search space: 77604 Effective search space used: 77604 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: 48 (23.1 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