Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_043743999.1 AMB_RS09135 branched-chain amino acid ABC transporter permease
Query= uniprot:D8IUY4 (309 letters) >NCBI__GCF_000009985.1:WP_043743999.1 Length = 304 Score = 251 bits (640), Expect = 2e-71 Identities = 138/309 (44%), Positives = 195/309 (63%), Gaps = 19/309 (6%) Query: 1 MDIFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQV 60 M+ F+QQ+INGL LG++Y L+ALGYTMVYGVL +INFAHG I MVGA + L V V Sbjct: 1 MEYFLQQLINGLTLGAIYGLVALGYTMVYGVLGMINFAHGTIYMVGAFISLITFLVATTV 60 Query: 61 APGLPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAM 120 G + LV+ +V A+ + + ER+AYRPLR+APRLAPLI+AIGVSI+LQ Sbjct: 61 L-GTSVPLALVLTLVAAMALTALWGWTAERVAYRPLRSAPRLAPLISAIGVSIMLQNFVA 119 Query: 121 MIWGRSPLPFPQV-------MPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKM 173 G P P V M S ++ +S Q++++AL + M ++ +T + Sbjct: 120 QAQGARAKPLPPVFRGGITLMDSGDFVVS---LSWMQMVIMALTLALMAVFTWVITRTAL 176 Query: 174 GRAMRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGL 233 GRA RA ++ ++A L+G+D ++VI TF IGAGLA +AG+M Y F +GF+ G+ Sbjct: 177 GRAQRACEQDMKMASLLGIDVDRVISTTFVIGAGLAGVAGMMVTLYYGVIDFYIGFLAGI 236 Query: 234 KAFSAAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVL 293 KAF+AAVLGGIG++ GAMLGG+L+GLIE+ + Y Y+D+ F +L+ VL Sbjct: 237 KAFTAAVLGGIGSLPGAMLGGLLIGLIEAFWSAY--------FSIEYKDVATFSILVAVL 288 Query: 294 TLRPSGIMG 302 RP+G++G Sbjct: 289 VFRPTGLLG 297 Lambda K H 0.328 0.144 0.416 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: 286 Number of extensions: 8 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: 309 Length of database: 304 Length adjustment: 27 Effective length of query: 282 Effective length of database: 277 Effective search space: 78114 Effective search space used: 78114 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