Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate WP_011842476.1 RSPH17029_RS18140 ABC transporter permease subunit
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >NCBI__GCF_000015985.1:WP_011842476.1 Length = 398 Score = 329 bits (844), Expect = 7e-95 Identities = 174/376 (46%), Positives = 249/376 (66%), Gaps = 6/376 (1%) Query: 2 RAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEADS 61 R V+Q+ AV LG++L+ N NL + I +GFGFL + + F I + LI Y+ D+ Sbjct: 27 RTVVYQIALAAAVALLGFYLYQNVVENLARQNIATGFGFLGQVSQFEIGETLIAYSARDT 86 Query: 62 YARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQ 121 Y R +GL+NTL V+ G+++AT++GF +G+AR+S NW++ +LAT YVE+ RNIP +LQ Sbjct: 87 YGRALAVGLMNTLSVSAAGIVVATVIGFSVGIARVSSNWLLQRLATAYVEIVRNIPVILQ 146 Query: 122 ILFWYFAVFLSMPGPRAAHNFGDTFFVSSRGLN--MPAALVAEGFWPFVISVVLAIVAIV 179 ++FW AV ++P PR A F+S+RGL MP+A A W + ++V I + Sbjct: 147 VIFWA-AVIRNLPAPRQAVELWGMGFLSNRGLTFAMPSAHAAH-LW-MLAALVAGIALAI 203 Query: 180 LMTRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVL 239 L + A + EATG W + L + +P L L FGAP PE +GFNF GG + Sbjct: 204 LASHKAKRHREATGRYIDMLWPCVGLIVGLPLLVWLGFGAPHEISFPERRGFNFAGGATI 263 Query: 240 IPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRV 299 PE +AL +++Y++ FIAEIVR+GI++ GQ EAARS+ LR LR V++PQALRV Sbjct: 264 SPEFVALMTGISLYSSGFIAEIVRAGIQATPRGQVEAARSIALRPRFILRYVVLPQALRV 323 Query: 300 IIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISI 359 I+PPLTSQY++L KNSS+A IGYP++V++ TV+NQTGQA+E IA+ M VYL +S+ Sbjct: 324 IVPPLTSQYVSLIKNSSIAVVIGYPDLVNI-GNTVMNQTGQAVEAIAVMMLVYLIVSLVT 382 Query: 360 SLLMNWYNKRIALIER 375 SLLMN+YN+ +A+ ER Sbjct: 383 SLLMNFYNRLVAIKER 398 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: 434 Number of extensions: 25 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: 375 Length of database: 398 Length adjustment: 30 Effective length of query: 345 Effective length of database: 368 Effective search space: 126960 Effective search space used: 126960 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