Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_068462410.1 APY04_RS10560 branched-chain amino acid transporter permease subunit LivH
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_001541235.1:WP_068462410.1 Length = 304 Score = 315 bits (808), Expect = 6e-91 Identities = 157/303 (51%), Positives = 226/303 (74%), Gaps = 2/303 (0%) Query: 7 YFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAAL-MMMG 65 YF+QQ+ NG+TLGS Y LIAIGYTMV+GIIGM+NFAHG+V+MI ++++ +++ L +G Sbjct: 3 YFVQQLINGLTLGSIYGLIAIGYTMVFGIIGMVNFAHGDVFMISAFIALILLILLTQFLG 62 Query: 66 IDTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLT 125 + + L + V + + + + W IER+AYRP+ S RL LISAIGM+IFL N+V +T Sbjct: 63 VTSIGLALLIVLVAGMFLTALWSWVIERIAYRPLAGSFRLAPLISAIGMAIFLLNFVQVT 122 Query: 126 EGSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACR 185 +G R+ A PS+ N + N S +I+ QA+I+IVT + +LA ++ +++GRA R Sbjct: 123 QGPRNKASPSILNNVMTIPMG-NGSVTISERQALIFIVTAILLLAFWAIVQKTKLGRAQR 181 Query: 186 ACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTA 245 AC +D +MA+LLGIN DR I+LTFVIG A+A+VAG++ +YGV++ GF G+KAFTA Sbjct: 182 ACEQDRRMAALLGINVDRTISLTFVIGGALASVAGLMFMSYYGVVSFSDGFTPGVKAFTA 241 Query: 246 AVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEV 305 AVLGGIGS+PGA+IGGL++G+ E + SAY S +YKDV +F++L +VL+ MP+G+LGRP+V Sbjct: 242 AVLGGIGSLPGAVIGGLLIGLIETMWSAYFSIDYKDVAAFSILAIVLIFMPSGLLGRPDV 301 Query: 306 EKV 308 EKV Sbjct: 302 EKV 304 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: 311 Number of extensions: 12 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: 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