Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate RR42_RS34785 RR42_RS34785 ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Cup4G11:RR42_RS34785 Length = 287 Score = 184 bits (467), Expect = 2e-51 Identities = 110/293 (37%), Positives = 172/293 (58%), Gaps = 13/293 (4%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60 M FLQQ++NGL+LG +Y L+A+G T+VYGI+ + NFAHG YM GA+V+ + + SL Sbjct: 1 MTLFLQQVLNGLTLGGVYSLVALGLTLVYGILHVPNFAHGAFYMAGAYVS---YYLMTSL 57 Query: 61 GIT-WVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQ 119 G+ W+ + A+ + AV +R+ + PLR++P L +I+AIG+ +FL+ Q Sbjct: 58 GMNYWLAMG------AAAIAVAVLSMLADRLVFHPLRNAPELHDMIAAIGIMLFLEAGAQ 111 Query: 120 ILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRA 179 + GA + P G + + G +S RL I LM +TRT G A Sbjct: 112 AMWGADFHRM-PTPYGQMVEVMG-LSAPAQRLLIIAAAFGLMVLLHLFLTRTVTGSTIVA 169 Query: 180 CEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAA 239 Q+++ A L+G++ RV L F + ALAA+A + I ++ +G L KAF Sbjct: 170 MAQNREGAALVGIDATRVTLLVFAISGALAAIAATLYAPI-NLVYPSMGNLVITKAFVII 228 Query: 240 VLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGL 292 +LGG+GS+PGA++GG++IG+ E+F Y+ +++KD+ F +LVL+L RP GL Sbjct: 229 ILGGMGSIPGAIVGGLIIGMAESFGGFYVSTDYKDIIAFALLVLILSIRPQGL 281 Lambda K H 0.329 0.144 0.425 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: 276 Number of extensions: 12 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: 301 Length of database: 287 Length adjustment: 26 Effective length of query: 275 Effective length of database: 261 Effective search space: 71775 Effective search space used: 71775 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