Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate Ac3H11_102 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_102 Length = 293 Score = 156 bits (394), Expect = 6e-43 Identities = 106/291 (36%), Positives = 164/291 (56%), Gaps = 14/291 (4%) Query: 7 QLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWVP 66 Q+INGLS+G L+A+G T+++G++ +IN AHGE Y IGA++A + LA G + W Sbjct: 11 QMINGLSIGVAVVLMALGLTIIFGLLDVINMAHGEFYAIGAYLA-VALLATG-MSFWWA- 67 Query: 67 LALLVMLVASMLFTAVYGWTVER-IAYRPLRSSPR-LAPLISAIGMSIFLQNYVQILQGA 124 LV + L AV G+ ER + R S R L+ G+++ L++ ++I GA Sbjct: 68 ------LVLTPLLMAVLGFVTERGLIQRVFHSKDRHTLTLLLTFGVAVVLEDALKIAFGA 121 Query: 125 RSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQDK 184 L+ + G T M G +Y RL ++ AL+ L+ RTSLG RA D+ Sbjct: 122 NPLRLEAPISG-ATEMLGLFFPNY-RLFVMLFGGALIAAVWLLVFRTSLGAIVRAAAYDR 179 Query: 185 KMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGGI 244 M+ LGV V V + TF G ALA +AG+++ IY V +G + AF+ ++GG+ Sbjct: 180 NMSASLGVPVQLVYAGTFAFGVALAGIAGVLLAPIYSVFPT-MGKDFVLIAFSVVIIGGM 238 Query: 245 GSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGR 295 GS+ GA+L G+++ +++ S Y+ W D F I+VLVL++RP GL G+ Sbjct: 239 GSIKGALLAGLLLTQVQSISSLYISPVWSDPLLFGIMVLVLMWRPQGLFGK 289 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: 300 Number of extensions: 20 Number of successful extensions: 3 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