Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate GFF3113 HP15_3056 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Marino:GFF3113 Length = 307 Score = 350 bits (897), Expect = e-101 Identities = 170/302 (56%), Positives = 230/302 (76%), Gaps = 3/302 (0%) Query: 3 YFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGI 62 YF QQLINGL++G+ Y LIAIGYTMVYGIIGMINFAHGEIYMIGA+ ALI + +LGI Sbjct: 6 YFSQQLINGLTIGSTYALIAIGYTMVYGIIGMINFAHGEIYMIGAYTALIAITGLAALGI 65 Query: 63 TWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQ 122 W+PL L+V L+ +M+ ++ GW VER+AYRP+R RL PLISAIGMSIFLQNYV + Q Sbjct: 66 AWLPLILIVALLCAMIVSSSMGWAVERVAYRPVRGRHRLIPLISAIGMSIFLQNYVHLAQ 125 Query: 123 GARSKPLQPILPGNLTLMDG---AVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRA 179 G+R+ ++ G G +S+SY+++ + T+ M + I+R+ GRA RA Sbjct: 126 GSRNIGFPALIDGGFNFGSGDGFQMSLSYMQITIFITTLICMTALSLFISRSRTGRACRA 185 Query: 180 CEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAA 239 QD MA LLG++ +R+IS TFV+GAALAAVAG+++ + YG +D GF+AG+KAFTAA Sbjct: 186 VSQDLGMANLLGIDTNRIISATFVIGAALAAVAGLLLGMYYGSVDPLFGFIAGLKAFTAA 245 Query: 240 VLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIE 299 VLGGIGS+PGAMLGG+++G+ E+ SGY+ E+KDV +F++L+L+L+F+PTGLLG+PE+E Sbjct: 246 VLGGIGSIPGAMLGGLILGVAESMTSGYLSGEYKDVISFSLLILILLFKPTGLLGKPEVE 305 Query: 300 KV 301 K+ Sbjct: 306 KI 307 Score = 26.9 bits (58), Expect = 6e-04 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 1/73 (1%) Query: 186 MAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAV-LGGI 244 M LL + + LT AL A+ MV I G+I+F G + + A+TA + + G+ Sbjct: 1 MQDLLYFSQQLINGLTIGSTYALIAIGYTMVYGIIGMINFAHGEIYMIGAYTALIAITGL 60 Query: 245 GSLPGAMLGGVVI 257 +L A L ++I Sbjct: 61 AALGIAWLPLILI 73 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: 381 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 301 Length of database: 307 Length adjustment: 27 Effective length of query: 274 Effective length of database: 280 Effective search space: 76720 Effective search space used: 76720 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