Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_068171602.1 HTA01S_RS12260 branched-chain amino acid ABC transporter permease
Query= uniprot:D8IUY4 (309 letters) >NCBI__GCF_001592305.1:WP_068171602.1 Length = 306 Score = 133 bits (334), Expect = 6e-36 Identities = 86/276 (31%), Positives = 141/276 (51%), Gaps = 38/276 (13%) Query: 6 QQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPGLP 65 + +I GL+LG YA++A G ++++GV+ +IN AHGD+ +VGA G+ L ++P L Sbjct: 3 EALIQGLLLGGFYAILAAGLSLMFGVMRIINLAHGDLAIVGAF-GVIALTERFGLSPWL- 60 Query: 66 GIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQT-------- 117 A++ +PV ++ + ++R + A L PL+ G+ +LQ Sbjct: 61 -------ALLLVLPVMALIGIGLQRWLFARTLRAGILLPLLVTFGLGAVLQNTLYGAFGS 113 Query: 118 --------LAMMIWGRSPLPFPQVMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVE 169 L + W LP G ++ ++ +AV + L L++ Sbjct: 114 EARSLGSALGDLAWASWELP------------GGIVVGQLPVITFVIAVAVLGALQLLLS 161 Query: 170 KTKMGRAMRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGF 229 T +GRA+RA A +P A L GVDA +V AI LA +AG + A + + G Sbjct: 162 HTALGRAIRAAASDPEAAALCGVDARRVHRAAAAIAVALAGLAGALLAMQATVEPYG-GP 220 Query: 230 VPGLKAFSAAVLGGIGNIYGAMLGGILLGLIESLGA 265 ++AF A V+GGIG+++G +LGG+LLG+ +SLGA Sbjct: 221 TLLIQAFEAVVIGGIGSLWGTLLGGVLLGVAQSLGA 256 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: 248 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: 309 Length of database: 306 Length adjustment: 27 Effective length of query: 282 Effective length of database: 279 Effective search space: 78678 Effective search space used: 78678 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 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