Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_043743902.1 AMB_RS08455 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000009985.1:WP_043743902.1 Length = 291 Score = 169 bits (427), Expect = 9e-47 Identities = 101/306 (33%), Positives = 169/306 (55%), Gaps = 18/306 (5%) Query: 5 FLYFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMM 64 F FLQ +F+G+T G+ YAL +G+ ++Y +INFA GE MIG + ++AA + + Sbjct: 2 FAAFLQYLFSGLTSGAIYALAGLGFAIIYNASHVINFAQGEFIMIGGMATATMVAAGVPI 61 Query: 65 GIDTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSL 124 + + A+ VG ++E+ A P RN+ + +I IG SIF++ L Sbjct: 62 YLAIPLAMAASMLVGV---------AMEKFAIEPARNADVVTIIIITIGASIFMRGAAQL 112 Query: 125 TEGSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWI--VTFLAMLALTIFIRYSRMGR 182 +LP+ F+G+ + T M +W+ ++ +A+ L F + G+ Sbjct: 113 IWDKEFHSLPA-FSGETPIA-----VMGATLMPQSLWVFGISAVAIALLWYFFNRTMFGK 166 Query: 183 ACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKA 242 A + + A L+G+ RV+ +F + A + AV G+++ N G M G+K Sbjct: 167 AMLGTSHNRLAAQLVGVAVKRVLLASFALSALLGAVGGIVVTPIT-FTNYEAGIMLGLKG 225 Query: 243 FTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGR 302 F+AAVLGG+G+ GA+IGGLI+GIAEA++S YLS+ YKD ++F +++ VL MP+G+ G+ Sbjct: 226 FSAAVLGGLGNGTGAIIGGLIVGIAEAMASGYLSSAYKDAIAFIIILFVLFFMPSGLFGK 285 Query: 303 PEVEKV 308 ++V Sbjct: 286 RGTDRV 291 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: 242 Number of extensions: 15 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: 291 Length adjustment: 27 Effective length of query: 281 Effective length of database: 264 Effective search space: 74184 Effective search space used: 74184 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