Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate BWI76_RS26345 BWI76_RS26345 branched-chain amino acid ABC transporter permease LivH
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Koxy:BWI76_RS26345 Length = 308 Score = 334 bits (857), Expect = 1e-96 Identities = 166/302 (54%), Positives = 226/302 (74%), Gaps = 3/302 (0%) Query: 3 YFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGI 62 YFLQQ+ NG++LG+ Y LIAIGYTMVYGIIGMINFAHGE+YMIG++V+ + A+ +GI Sbjct: 7 YFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGI 66 Query: 63 TWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQ 122 L + V +++ + YGW++ER+AYRP+RSS RL LISAIGMSIFLQNYV + + Sbjct: 67 DTSWLLVAAGFVGAIVIASAYGWSIERVAYRPVRSSKRLIALISAIGMSIFLQNYVSLTE 126 Query: 123 GARSKPLQPILPGNLTLMDG---AVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRA 179 G+R L + G T+ + +++ ++L V+T M T I + +GRA RA Sbjct: 127 GSRDVALPSLFNGQWTVGSSDNFSATITTMQLVIWVVTFIAMLALTLFIRYSRMGRACRA 186 Query: 180 CEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAA 239 C +D KMA LLG+N DRVI+LTFV+GAA+AAVAG+++ YGVI+ YIGF+AG+KAFTAA Sbjct: 187 CAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAA 246 Query: 240 VLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIE 299 VLGGIGS+PGAM+GG+++G+ EA S Y+ +E+KDV +F +L+LVL+ PTG+LGRPE+E Sbjct: 247 VLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEVE 306 Query: 300 KV 301 KV Sbjct: 307 KV 308 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: 388 Number of extensions: 7 Number of successful extensions: 2 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: 308 Length adjustment: 27 Effective length of query: 274 Effective length of database: 281 Effective search space: 76994 Effective search space used: 76994 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