Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate Ac3H11_4984 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= ecocyc::LIVH-MONOMER (308 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4984 Length = 296 Score = 150 bits (378), Expect = 5e-41 Identities = 97/302 (32%), Positives = 159/302 (52%), Gaps = 14/302 (4%) Query: 7 YFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGI 66 Y + G+ G YAL A+ + MVY ++N A GE+ M+G+Y+ F A++ + + Sbjct: 9 YLFEISLTGIAGGGLYALAALAFVMVYKATRVVNIAIGELLMVGAYL-FFTFASMFALPL 67 Query: 67 DTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTE 126 WL + A +G ++ G IER RP+ + + +G++ L V + Sbjct: 68 ---WLAIPAAVLGTGLL----GALIERTMIRPLLGEPPISVFMVTVGLASVLVGLVEMIW 120 Query: 127 GSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRA 186 + LP Q ++ + F A AVI IV A+L + R+ R G A RA Sbjct: 121 TADQRRLPDFMPTQPIMV-GDAFLAPKVFWGAVIAIVFIAAVL---VVFRFWRGGVALRA 176 Query: 187 CAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAA 246 A D A +GIN RV +L +V A +AA++G+++G G+ + F G+ Sbjct: 177 TASDQAAAYSVGINVPRVFSLAWVASAMLAAISGIIVGSIGGISSSMGVF--GLSVLVVV 234 Query: 247 VLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEVE 306 ++GG+ S+ GA+IGG+++G+ EAL+ AYL EYK + +F +L+ VLLV P G+ G E+E Sbjct: 235 IVGGLDSVLGALIGGILIGLIEALAGAYLGGEYKLLATFIVLVAVLLVRPYGLFGTHEIE 294 Query: 307 KV 308 ++ Sbjct: 295 RL 296 Lambda K H 0.328 0.141 0.410 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: 244 Number of extensions: 12 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: 308 Length of database: 296 Length adjustment: 27 Effective length of query: 281 Effective length of database: 269 Effective search space: 75589 Effective search space used: 75589 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