Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_009563595.1 RSPH17029_RS17970 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000015985.1:WP_009563595.1 Length = 289 Score = 205 bits (522), Expect = 9e-58 Identities = 117/300 (39%), Positives = 184/300 (61%), Gaps = 15/300 (5%) Query: 8 FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGID 67 F+QQ+ NG+ LGSTYAL+A+G T+++G++ + NFAHGE YM+G+++++ ++ A M Sbjct: 5 FVQQLVNGLALGSTYALVALGLTLIFGVLLIPNFAHGEFYMLGAFLTYAMVLAGMNF--- 61 Query: 68 TGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEG 127 WL +A VGA+++ G ++R+A++PV + L +ISA+ SI LQ L G Sbjct: 62 --WLAMALA-VGAVILL---GCLVDRLAFKPVEQAPPLSMMISALAASIILQQSAMLIWG 115 Query: 128 SRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRAC 187 +P+ G V + F +T MQ ++ LA + + + SR+G A RA Sbjct: 116 GEARTIPAPVTG---VLRTPFFI--VTWMQLIVMASLLLAAAGVWLVLNRSRLGLAIRAV 170 Query: 188 AEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAAV 247 A++ A L+GI+ +V TF IGAA+ A+AG LLG + + P +G +KAF V Sbjct: 171 AQNRDAALLMGISMFQVRLATFAIGAALGAIAGALLGATFPIY-PTMGVNPVLKAFVVLV 229 Query: 248 LGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEVEK 307 LGGIGS+PGA+ GGL LG+ E + + Y+S+E D+ +FA+L+ VLL+ P G G+ +VE+ Sbjct: 230 LGGIGSLPGAVFGGLFLGVVEVMVAGYISSELSDIGAFAILVAVLLLRPQGFFGQAQVER 289 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: 239 Number of extensions: 15 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: 289 Length adjustment: 27 Effective length of query: 281 Effective length of database: 262 Effective search space: 73622 Effective search space used: 73622 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 Apr 10 2024. 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