Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_012103084.1 CKL_RS13420 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQH9 (318 letters) >NCBI__GCF_000016505.1:WP_012103084.1 Length = 324 Score = 275 bits (703), Expect = 1e-78 Identities = 147/309 (47%), Positives = 210/309 (67%), Gaps = 4/309 (1%) Query: 8 NILWLLL-LLAGYSLISVLVSVGVLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGH 66 NIL++L +L + LI L+S+ +++ + VQIL IGINIILAV LN+IVG++GQ +LGH Sbjct: 6 NILFILAAVLIVFGLIQTLISLEMIDEYIVQILIIIGINIILAVSLNMIVGYTGQLALGH 65 Query: 67 AGFMAIGAYAAAIIGSKSPTYGAFFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLG 126 AGFM+IG Y AAI+ K FF ++ G L++ +++GIPTLRLKGDYLA+ TLG Sbjct: 66 AGFMSIGGYTAAILTLKLDA--PFFLVLIAGGLMAAFFGVIIGIPTLRLKGDYLAITTLG 123 Query: 127 VSEIIRIFIINGGSLTNGAAGILGIPNFTTWQMVYFFVVITTIATLNFLRSPIGRSTLSV 186 EIIRI I+N +L GA G+ GIP T++ MV+F ++ I N +S GR+ LS+ Sbjct: 124 FGEIIRIAIVNSNTL-GGAEGLAGIPKKTSFAMVFFITILIIIIAYNIKKSSYGRAMLSI 182 Query: 187 REDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSINVLIIV 246 REDE+A+ S+G+NTTK K+IAFV + A IAG L A + + PK + ++ S +++ V Sbjct: 183 REDELASSSIGINTTKYKMIAFVTASFFAGIAGVLYAHYFMFLDPKSFDYLKSFDIVTYV 242 Query: 247 VFGGLGSITGAIVSAIVLGILNMLLQDVASVRMIIYALALVLVMIFRPGGLLGTWELSLS 306 VFGG+GSI+G I+S +L L +L+ VA RM+IY+ ALV +MIFRP G+ G E+S Sbjct: 243 VFGGMGSISGCILSTAILTSLPEILRPVADYRMVIYSAALVALMIFRPEGVFGMKEISFK 302 Query: 307 RFFKKSKKE 315 + +KK+ Sbjct: 303 KIVSSAKKK 311 Lambda K H 0.327 0.143 0.403 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: 254 Number of extensions: 14 Number of successful extensions: 5 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: 318 Length of database: 324 Length adjustment: 28 Effective length of query: 290 Effective length of database: 296 Effective search space: 85840 Effective search space used: 85840 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 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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