Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_012755251.1 RLEG_RS23810 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000023185.1:WP_012755251.1 Length = 304 Score = 115 bits (287), Expect = 2e-30 Identities = 87/305 (28%), Positives = 150/305 (49%), Gaps = 21/305 (6%) Query: 9 LQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGIDT 68 + + G+ LG YA+IA G + ++ ++ +IN AHG + + +Y +++ A GI Sbjct: 2 INTLLQGILLGGYYAVIACGLSFMFSVMRIINLAHGSLAVAAAYGLWLLAAKA---GIPP 58 Query: 69 GWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEGS 128 AG + + + +A GW ++R L+ +++ G+SI + N + G+ Sbjct: 59 -----FAGLLIVLPVMAAAGWLLQRFILERSARGGTLLPILTTFGLSIVIDNLLFEQFGA 113 Query: 129 --RDVA--LPSLFNGQWVV-GHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRA 183 R +A + +L W + GH + + ++ + L + L F+ +GRA Sbjct: 114 DTRSLAPFIGNLSYASWQLPGH-----IYVGKLAVLMMVTAILVLGGLQFFLSRFALGRA 168 Query: 184 CRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAF 243 RA AED A L+GI+ RV A+ I +AG LG +PY G + AF Sbjct: 169 IRATAEDPDTAGLVGIDARRVNAVATAITMVTVGIAGAFLGM-RATFSPYSGGPQLLFAF 227 Query: 244 TAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRP 303 AAV+GG GS+ G + GG++LG+A++L A L + + A+ +LVL V G P Sbjct: 228 EAAVIGGAGSLWGTLAGGIVLGLAQSL-GAQLHPQGFLIGGHAVFLLVLFVR-LSRFGMP 285 Query: 304 EVEKV 308 ++K+ Sbjct: 286 SLDKL 290 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: 228 Number of extensions: 13 Number of successful extensions: 5 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: 304 Length adjustment: 27 Effective length of query: 281 Effective length of database: 277 Effective search space: 77837 Effective search space used: 77837 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