Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate AZOBR_RS03565 AZOBR_RS03565 branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__azobra:AZOBR_RS03565 Length = 304 Score = 267 bits (682), Expect = 3e-76 Identities = 138/298 (46%), Positives = 197/298 (66%), Gaps = 9/298 (3%) Query: 3 YFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGI 62 +FLQQLIN ++ +YGL+A+GYT+VYGI+G IN A GE+ MIGA + + A+G G+ Sbjct: 3 FFLQQLINAATVACVYGLLALGYTLVYGILGQINLAMGELTMIGAMLTAMGAAALGMAGL 62 Query: 63 TWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQ 122 +PLA+L + M FTAV GWT++R+ +R LR + PLI+A+G+SI Q +++L Sbjct: 63 GSLPLAVLGVFATVMAFTAVQGWTMDRLVFRRLRRTHNHTPLIAAVGLSIAYQEGMRLLH 122 Query: 123 GARSK-PLQPILPGNLTLMDGAVSVSYVRLATIVITI-----ALMYGFTQLITRTSLGRA 176 GAR P Q + + L DGA +V+ + +++ + AL++ Q RT+ GRA Sbjct: 123 GARDWWPAQFLADRHELLSDGAFTVTALTSQAVILLMTGGLYALLWAIMQ---RTAYGRA 179 Query: 177 QRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAF 236 RAC D A L+GV+VDR ++ TF +G ALAA AG ++ L YG ++FY G+L G KA Sbjct: 180 HRACADDVGAAELVGVDVDRTVATTFAVGGALAAAAGAVIALYYGGVNFYTGYLVGFKAL 239 Query: 237 TAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLG 294 AAV+GGIGS+PGAMLGG ++GL+E FWS Y +KD+ F +L L LI+RP GL+G Sbjct: 240 AAAVVGGIGSVPGAMLGGALLGLVETFWSAYFAIAYKDIVAFGLLTLFLIYRPDGLMG 297 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: 372 Number of extensions: 20 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: 304 Length adjustment: 27 Effective length of query: 274 Effective length of database: 277 Effective search space: 75898 Effective search space used: 75898 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