Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate RR42_RS02580 RR42_RS02580 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__Cup4G11:RR42_RS02580 Length = 242 Score = 94.4 bits (233), Expect = 3e-24 Identities = 81/247 (32%), Positives = 123/247 (49%), Gaps = 21/247 (8%) Query: 125 WYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIVLMTRW 184 W++ VFL +AA N ++ S GL + AL G ++I++V+ V VL T Sbjct: 5 WHWGVFLE----QAAQNETYLDWMIS-GLKVTIAL---GLSSWIIALVIGSVLGVLRTV- 55 Query: 185 ANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELK--GFNFVGGWVLIPE 242 NK + + +F IP L L ++ MPEL G +F + Sbjct: 56 PNKWLSGLAATY------VEIFRNIPLLVQLFIW---YFVMPELLPGGESFKQMNPFAQQ 106 Query: 243 LLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIP 302 LA L L +TAA + E VRSGI S+ GQ A ++G T R V++P + RVI+P Sbjct: 107 FLAAMLCLGTFTAARVCEQVRSGINSLPPGQRNAGLAMGFTLAQTYRYVLLPMSFRVIVP 166 Query: 303 PLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLL 362 PLTS++LN+ KNS++A+ IG E+ + +++ T + E +Y I+I + LL Sbjct: 167 PLTSEFLNIFKNSAVASTIGLLELAAQ-GRQLVDYTARPYESFIAVTIMYALINIVVMLL 225 Query: 363 MNWYNKR 369 M W R Sbjct: 226 MRWVEGR 232 Score = 58.9 bits (141), Expect = 1e-13 Identities = 29/76 (38%), Positives = 45/76 (59%) Query: 60 DSYARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPL 119 ++Y + GL T+ + I+A ++G ++GV R N +S LA YVE+FRNIP L Sbjct: 18 ETYLDWMISGLKVTIALGLSSWIIALVIGSVLGVLRTVPNKWLSGLAATYVEIFRNIPLL 77 Query: 120 LQILFWYFAVFLSMPG 135 +Q+ WYF + +PG Sbjct: 78 VQLFIWYFVMPELLPG 93 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: 239 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 242 Length adjustment: 27 Effective length of query: 348 Effective length of database: 215 Effective search space: 74820 Effective search space used: 74820 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