Align Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale)
to candidate 8501893 DvMF_2608 inner-membrane translocator (RefSeq)
Query= uniprot:A0A0D9B2B6 (307 letters) >FitnessBrowser__Miya:8501893 Length = 302 Score = 302 bits (774), Expect = 6e-87 Identities = 158/305 (51%), Positives = 220/305 (72%), Gaps = 4/305 (1%) Query: 3 DIYHFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAM 62 D +F++ GLT GS YALIA+GYTMVYGII +INFAHGEVYM+G++ A I L + Sbjct: 2 DWQYFWELFFGGLTRGSIYALIALGYTMVYGIIELINFAHGEVYMMGAFTALIVAGALGI 61 Query: 63 MGLDSVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVL 122 G ++ +L+ AA +A ++ ++YG ++E+IAY+PLR + RL PLISAIGMSIFLQN V+ Sbjct: 62 YGFPALAILIIAAVVA-VIYCAAYGLTLEKIAYKPLRDAPRLSPLISAIGMSIFLQNYVI 120 Query: 123 LSQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRA 182 L+Q S PNL+P + P AH ++ ++++ V + ++M LTLFI +R+G+A Sbjct: 121 LAQTSDFMPFPNLVPQPDFLEPI-AH--IMGASEVLIIVTSAISMAALTLFIKYTRMGKA 177 Query: 183 CRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAF 242 RA A++ KMA LLGI+ + +I+LTFVIG++LAA+ VL++ G +N GF+ G+KAF Sbjct: 178 MRATAQNRKMAMLLGIDADKVISLTFVIGSSLAAVGGVLIASHVGQVNFAIGFIAGIKAF 237 Query: 243 TAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGRP 302 TAAVLGGIGSIPGAMLGGLVLG E+F Y+D +AF LLVL+L+FRP+GILG+ Sbjct: 238 TAAVLGGIGSIPGAMLGGLVLGWCESFATGYISSDYEDALAFALLVLILIFRPSGILGKA 297 Query: 303 EVEKV 307 + +KV Sbjct: 298 KTQKV 302 Lambda K H 0.327 0.144 0.411 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: 315 Number of extensions: 13 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: 307 Length of database: 302 Length adjustment: 27 Effective length of query: 280 Effective length of database: 275 Effective search space: 77000 Effective search space used: 77000 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 (21.7 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