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 AZOBR_RS03565 AZOBR_RS03565 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A0D9B2B6 (307 letters) >FitnessBrowser__azobra:AZOBR_RS03565 Length = 304 Score = 236 bits (603), Expect = 4e-67 Identities = 123/294 (41%), Positives = 181/294 (61%) Query: 7 FFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLD 66 F QQL+N TV Y L+A+GYT+VYGI+G IN A GE+ MIG+ + + A L M GL Sbjct: 4 FLQQLINAATVACVYGLLALGYTLVYGILGQINLAMGELTMIGAMLTAMGAAALGMAGLG 63 Query: 67 SVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLSQD 126 S+PL + F + T+ G++++R+ +R LR ++ PLI+A+G+SI Q + L Sbjct: 64 SLPLAVLGVFATVMAFTAVQGWTMDRLVFRRLRRTHNHTPLIAAVGLSIAYQEGMRLLHG 123 Query: 127 SKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACRAC 186 ++D + + GA V Q V+ ++T L + R+ GRA RAC Sbjct: 124 ARDWWPAQFLADRHELLSDGAFTVTALTSQAVILLMTGGLYALLWAIMQRTAYGRAHRAC 183 Query: 187 AEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTAAV 246 A+D+ A L+G++ + +A TF +G ALAA A ++++ YG +N G+LVG KA AAV Sbjct: 184 ADDVGAAELVGVDVDRTVATTFAVGGALAAAAGAVIALYYGGVNFYTGYLVGFKALAAAV 243 Query: 247 LGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILG 300 +GGIGS+PGAMLGG +LG+ E F + F YKD+VAFGLL L L++RP G++G Sbjct: 244 VGGIGSVPGAMLGGALLGLVETFWSAYFAIAYKDIVAFGLLTLFLIYRPDGLMG 297 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: 296 Number of extensions: 15 Number of successful extensions: 3 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