Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate AO356_28385 AO356_28385 ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28385 Length = 293 Score = 125 bits (314), Expect = 1e-33 Identities = 91/309 (29%), Positives = 160/309 (51%), Gaps = 24/309 (7%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60 ME+F + LI GL G +Y L+AIG+ ++Y G+ NFA G + + A +TF+++ Sbjct: 1 MEFFFEVLIGGLLAGVMYALVAIGFVLIYKASGVFNFAQGAMVLFSA----LTFVSLLER 56 Query: 61 GIT-WVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQ 119 G+ W LA ++ L A +L VER+ RPL + + ++ +G+S ++ + Q Sbjct: 57 GVPFW--LAFVISLAAMVLIAV----AVERVVLRPLVNRSPITLFMATLGLSYVIEGFAQ 110 Query: 120 ILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRA 179 L GA+ L+ + + L G + +S + V L+ + L +T LG + RA Sbjct: 111 ALWGAQVHGLE-LGISDEPLELGGMLLSQFDIFAAVTAAFLVLLLSWLFNKTRLGLSLRA 169 Query: 180 CEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGV---IDFYIGFLAGVKAF 236 D A +G+ + RV +V+ A+A G++ L++G + F + L +KA Sbjct: 170 VADDPLAALAVGIRLQRV----WVVVWAVAGFVGLVAGLLWGARLGVQFSLS-LVVLKAL 224 Query: 237 TAAVLGGIGSLPGAMLGGVVIG----LIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGL 292 ++GG S+ GA++GG++IG L E + ++GS ++ + + +L L+ RP GL Sbjct: 225 PVLIIGGFTSISGAIVGGLIIGASEKLAEVYLGPFIGSGIENWFPYVLALLFLLVRPAGL 284 Query: 293 LGRPEIEKV 301 G IE+V Sbjct: 285 FGERAIERV 293 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: 289 Number of extensions: 22 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: 293 Length adjustment: 26 Effective length of query: 275 Effective length of database: 267 Effective search space: 73425 Effective search space used: 73425 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