Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate 17340 b3270 putative transport system permease protein (VIMSS)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__Keio:17340 Length = 367 Score = 503 bits (1296), Expect = e-147 Identities = 233/355 (65%), Positives = 290/355 (81%) Query: 8 PDMPPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRA 67 P P +S + W+R N+FSSW N+LLT+ +L++ ++PPL+ WA L ANWVG+TRA Sbjct: 9 PPRPASHNSSRAMVWVRKNLFSSWSNSLLTIGCIWLMWELIPPLLNWAFLQANWVGSTRA 68 Query: 68 DCTKEGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRFPRKAIYGLS 127 DCTK GACWVFI +RFGQFMYG YP D RWR++L + + ++ +AP+F P + Y + Sbjct: 69 DCTKAGACWVFIHERFGQFMYGLYPHDQRWRINLALLIGLVSIAPMFWKILPHRGRYIAA 128 Query: 128 FLVLYPISAWCLLHGGVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNM 187 + V+YP+ W L++GG F L+ V T QWGGL LTL+IA+VGI GALP GI+LALGRRS+M Sbjct: 129 WAVIYPLIVWWLMYGGFFALERVETRQWGGLTLTLIIASVGIAGALPWGILLALGRRSHM 188 Query: 188 PAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILFQSAYIAE 247 P +R++ V FIEFWRGVPLITVLFMSSVMLPLF+ EG + DKL+RAL+GVILFQSAY+AE Sbjct: 189 PIVRILSVIFIEFWRGVPLITVLFMSSVMLPLFMAEGTSIDKLIRALVGVILFQSAYVAE 248 Query: 248 VVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVII 307 VVRGGLQA+PKGQYEAA ++ LGYW++ GLVILPQALKLVIPG+VNT IALFKDTSLVII Sbjct: 249 VVRGGLQALPKGQYEAAESLALGYWKTQGLVILPQALKLVIPGLVNTIIALFKDTSLVII 308 Query: 308 IGLFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTG 362 IGLFDL +SV+QA DP WLGM+TEGYVFAAL++WIFCF MSRYS +LE++ +TG Sbjct: 309 IGLFDLFSSVQQATVDPAWLGMSTEGYVFAALIYWIFCFSMSRYSQYLEKRFNTG 363 Lambda K H 0.330 0.144 0.469 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: 698 Number of extensions: 27 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: 365 Length of database: 367 Length adjustment: 30 Effective length of query: 335 Effective length of database: 337 Effective search space: 112895 Effective search space used: 112895 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 (21.9 bits) S2: 49 (23.5 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