Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate WP_002722555.1 RSPH17029_RS02005 ABC transporter permease subunit
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >NCBI__GCF_000015985.1:WP_002722555.1 Length = 420 Score = 294 bits (753), Expect = 3e-84 Identities = 176/399 (44%), Positives = 235/399 (58%), Gaps = 27/399 (6%) Query: 2 RAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEADS 61 R+ QV +A +L DNT NL+ G FGFL AG+ I+Q L+DYT + Sbjct: 24 RSLTIQVFVFFLFMAGAAWLVDNTMRNLEALGKDFDFGFLWNRAGYDISQRLVDYTNDST 83 Query: 62 YARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQ 121 + R L+GLLNTLL+ +G + AT++G ++GV RLS+NWI+ +L TVYVEVFRN+P LL Sbjct: 84 HGRAMLVGLLNTLLIALLGCMAATVIGVLVGVLRLSRNWIVGRLMTVYVEVFRNVPLLLW 143 Query: 122 ILFWYFAVFLSMPGPRAAHN-----------FGDTFFVSSRGLNMPAALVAEGF-WP--- 166 IL Y + P P A F D V++R +P + + W Sbjct: 144 ILLIYAVFSEATPAPNAFRPNPETGIADRSMFLDAIAVTNRYTALPNPVFSRELGWLDLG 203 Query: 167 --FVISVVLAIVAIVLMTRWANKRF--------EATGEPFHKFWVGLALFLVIPALSALL 216 +V VLA++ ++ + N+ EATGE +W L L + +P A+L Sbjct: 204 LFYVNMDVLAVIGAIIAGWFINRSVKARATRIQEATGERPATWWSSLLLLVGLPV--AVL 261 Query: 217 FGAPVHWEMPELKGFNFVGGWVLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEA 276 H E PEL+GFNFVGG + +AL LAL++YT AFIAEIVR GI +VS GQ+EA Sbjct: 262 LALGFHLEFPELRGFNFVGGLNVSNSFMALWLALSLYTGAFIAEIVRGGILAVSRGQSEA 321 Query: 277 ARSLGLRNGPTLRKVIIPQALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLN 336 A +LGLR G T+ VI+PQALRVIIPPL SQYLNL KNSSLA +GY ++ G LN Sbjct: 322 AFALGLRPGRTMNLVILPQALRVIIPPLISQYLNLTKNSSLAIAVGYLDLRGTLGGITLN 381 Query: 337 QTGQAIEVIAITMSVYLAISISISLLMNWYNKRIALIER 375 QTG+ +E + + M +YLAIS+ IS +MN YN + L ER Sbjct: 382 QTGRELECVLLMMLIYLAISLVISGVMNVYNSAVKLKER 420 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: 399 Number of extensions: 22 Number of successful extensions: 3 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: 420 Length adjustment: 31 Effective length of query: 344 Effective length of database: 389 Effective search space: 133816 Effective search space used: 133816 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 Apr 10 2024. 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