Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_018124025.1 B149_RS0104755 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000375485.1:WP_018124025.1 Length = 299 Score = 310 bits (795), Expect = 2e-89 Identities = 162/305 (53%), Positives = 225/305 (73%), Gaps = 11/305 (3%) Query: 7 YFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGI 66 YFL+ F G+T GS YALIA+GYTMVYGII +INFAHGE+YMIG++ +I L G Sbjct: 3 YFLEIFFGGLTRGSIYALIALGYTMVYGIIELINFAHGEIYMIGAFTGLIIAGVLGAAGF 62 Query: 67 DTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTE 126 +LV A + A++ ++AYG++IE++AY+P+R ++RL LISAIGMSIFLQNYV L + Sbjct: 63 PVPAILVLA-LLAAVIYSAAYGFTIEKIAYKPLRGAQRLSPLISAIGMSIFLQNYVMLAQ 121 Query: 127 GSRDVALPSL---FNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRA 183 S + PSL F+ W+ GH I++ + VI +VT L + LT+FI+++R+G+A Sbjct: 122 TSDFLPFPSLIPEFHVPWI-GHI------ISSAELVIVLVTVLVCIGLTMFIKFTRLGKA 174 Query: 184 CRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAF 243 RA A++ KMA L+GIN D VI+ TFV+G+++AAV GVL+ G IN YIGF+AG+KAF Sbjct: 175 MRATAQNRKMAMLVGINVDTVISATFVVGSSLAAVGGVLIASHIGQINYYIGFIAGIKAF 234 Query: 244 TAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRP 303 TAAVLGGIGS+PGAM+G LILG EA ++ Y+S++Y+DV +FALL+L+L+ P GI+G+ Sbjct: 235 TAAVLGGIGSVPGAMLGALILGQTEAFATGYVSSDYEDVFAFALLVLILIFRPAGIMGKE 294 Query: 304 EVEKV 308 V+KV Sbjct: 295 PVQKV 299 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: 296 Number of extensions: 14 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: 308 Length of database: 299 Length adjustment: 27 Effective length of query: 281 Effective length of database: 272 Effective search space: 76432 Effective search space used: 76432 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 24 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