Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate BWI76_RS05990 BWI76_RS05990 branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Koxy:BWI76_RS05990 Length = 299 Score = 223 bits (569), Expect = 3e-63 Identities = 123/299 (41%), Positives = 182/299 (60%), Gaps = 10/299 (3%) Query: 4 FLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGIT 63 FLQQ++NG+SLG +Y LIAIGYTMVYG++ +INFAH ++ M+GAF L F +IG Sbjct: 6 FLQQVVNGMSLGGMYALIAIGYTMVYGVLRLINFAHADVMMVGAFTTLFLFSSIG----- 60 Query: 64 WVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQG 123 +P + V L ++ ++G ++R+AYRPLR + +++ LI+AIG+S FL+N +L G Sbjct: 61 -LPFGVAVFLTLALC--GLFGMLIDRVAYRPLRQASKISMLITAIGVSFFLENLFNVLFG 117 Query: 124 ARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQD 183 S+ N T G V ++ V +IT+ L+ L+ RT G A RA D Sbjct: 118 GSSRFFSAPDFFNNTRAFGDVIITNVAWIVPLITVLLLLAILWLLYRTRYGMAIRAVAFD 177 Query: 184 KKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGG 243 L+G++ +R+ISL F +G++LAA+ G+ + Y ID +G L G+KAF AAVLGG Sbjct: 178 VNTVRLMGIDANRIISLVFALGSSLAALGGVFYSISYPTIDPLMGVLIGLKAFAAAVLGG 237 Query: 244 IGSLPGAMLGGVVIGLIEAFWSGYMG--SEWKDVATFTILVLVLIFRPTGLLGRPEIEK 300 IGS+ GA+LGG ++G E +KD F L+LVL+FRP G++G +E+ Sbjct: 238 IGSVTGAVLGGFILGFTEVVAVALFPELGGYKDAFAFMFLILVLLFRPVGIMGDERLER 296 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: 339 Number of extensions: 25 Number of successful extensions: 5 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: 299 Length adjustment: 27 Effective length of query: 274 Effective length of database: 272 Effective search space: 74528 Effective search space used: 74528 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