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 AO353_13345 AO353_13345 branched-chain amino acid transporter permease subunit LivH
Query= uniprot:A0A0D9B2B6 (307 letters) >FitnessBrowser__pseudo3_N2E3:AO353_13345 Length = 304 Score = 333 bits (853), Expect = 4e-96 Identities = 169/303 (55%), Positives = 225/303 (74%), Gaps = 5/303 (1%) Query: 7 FFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLD 66 F QQ++NGLT+GS Y LIAIGYTMVYGIIGMINFAHGEVYMI +Y+A I++A L+ G++ Sbjct: 5 FLQQVINGLTLGSVYGLIAIGYTMVYGIIGMINFAHGEVYMISAYLAAISLALLSYFGVE 64 Query: 67 SVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLSQD 126 S PLL+ + ++ VT YG+ IERIAY+PLR S RL PLISAIG+S+ LQN ++Q Sbjct: 65 SFPLLILGTLLFTVFVTGVYGWVIERIAYKPLRNSTRLAPLISAIGVSLILQNYAQIAQG 124 Query: 127 SKDKSIPNLIPGN--FAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACR 184 S+ + IP L+ G F IG G V I+Y +I + V + M LT I ++LGR CR Sbjct: 125 SRQQGIPTLLSGGLRFDIGTGF---VQITYTKIFILVAAFIGMALLTYIIKYTKLGRMCR 181 Query: 185 ACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTA 244 A +D KMA++LGINT+ +I+ F+IGAA+AA+A VL+++ YG + AGF++G+KAFTA Sbjct: 182 ATQQDRKMASILGINTDRVISYVFIIGAAMAALAGVLITVNYGTFDFYAGFVIGIKAFTA 241 Query: 245 AVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGRPEV 304 AVLGGIGS+PGAMLGG++LGV+E+ + + YKDV +F LLVL+L+FRP G+LGRP V Sbjct: 242 AVLGGIGSLPGAMLGGIILGVSESLFSGVINSDYKDVFSFSLLVLILIFRPQGLLGRPLV 301 Query: 305 EKV 307 KV Sbjct: 302 AKV 304 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: 356 Number of extensions: 10 Number of successful extensions: 2 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: 304 Length adjustment: 27 Effective length of query: 280 Effective length of database: 277 Effective search space: 77560 Effective search space used: 77560 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