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 HSERO_RS08275 HSERO_RS08275 branched-chain amino acid transporter permease subunit LivH
Query= uniprot:A0A0D9B2B6 (307 letters) >FitnessBrowser__HerbieS:HSERO_RS08275 Length = 308 Score = 377 bits (968), Expect = e-109 Identities = 187/299 (62%), Positives = 235/299 (78%) Query: 9 QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLDSV 68 QQLVNGL++G+ YALIAIGYTMVYGIIGMINFAHGE+YMI SYV + + + + + Sbjct: 10 QQLVNGLSLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIASYVGLVTLTAIGVQSGYPL 69 Query: 69 PLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLSQDSK 128 PLL+ A I S++VT YG+++ER+AYRPLRG RL+PLISAIGMSIFLQN V + Q ++ Sbjct: 70 PLLLGGALIVSVLVTGLYGWTVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQIGQGAR 129 Query: 129 DKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACRACAE 188 D S+P LI G G V I Y ++V+ VTLV M+ LTLFI+RSR+GRACRACAE Sbjct: 130 DMSVPVLISGALEFQMGSDFTVTIPYSRMVIVGVTLVLMVALTLFIARSRMGRACRACAE 189 Query: 189 DIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTAAVLG 248 D+ MANLLGI+TN +I+ TFV+GA LAA+ VL+++ G +NP GF+ G+KAFTAAVLG Sbjct: 190 DMGMANLLGIDTNKVISFTFVLGAMLAAVGGVLIALTIGKLNPYIGFIAGIKAFTAAVLG 249 Query: 249 GIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGRPEVEKV 307 GIGSIPGAMLGG++LG+AE F A +YKDVV+FGLLVL+LLFRPTG+LG+P+VEKV Sbjct: 250 GIGSIPGAMLGGVLLGLAETFAAGYLPSEYKDVVSFGLLVLILLFRPTGLLGKPDVEKV 308 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: 393 Number of extensions: 9 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: 308 Length adjustment: 27 Effective length of query: 280 Effective length of database: 281 Effective search space: 78680 Effective search space used: 78680 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