Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_085773505.1 B1812_RS04375 branched-chain amino acid ABC transporter permease
Query= uniprot:D8IUY4 (309 letters) >NCBI__GCF_002117405.1:WP_085773505.1 Length = 299 Score = 159 bits (402), Expect = 8e-44 Identities = 94/306 (30%), Positives = 164/306 (53%), Gaps = 16/306 (5%) Query: 4 FIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPG 63 F++ +I GL+ G MY+L+A+G+ ++Y ++NFA G ++ A+ +SLL + Sbjct: 10 FVEVLIGGLLSGVMYSLVAMGFVLIYKTSGVLNFAQGSQILFAALTFVSLL----ERGYN 65 Query: 64 LPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAMMIW 123 LP + IA + +V+ LLIERI RPL N P + + +G+S +++ A + W Sbjct: 66 LPTTFAITIAAM------VVLGLLIERIVLRPLVNRPPITLFMATLGLSYVIEGAAQLAW 119 Query: 124 GRSPLPFPQVMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMRATAEN 183 G + P+ ++G +S ++ A+A L +V L T++G A RA AE+ Sbjct: 120 GAQVHGLDLGIDDRPLDVSGIFVSRFDLLAAAIAGLMVVMFSLFFRFTRIGLAFRAVAED 179 Query: 184 PRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAVLGG 243 P A +G+ +++ + + +A +AG++W A QF++ V LKA VLGG Sbjct: 180 PIAAMSVGLRLSRIWAMVWTASGLVALVAGLIWGARLG-VQFSLSLVV-LKALPVLVLGG 237 Query: 244 IGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGIMGE 303 +I G ++ G+L+G E L YIG+ + G + FA++ + L ++PSG+ G+ Sbjct: 238 FDSIAGVIVAGLLIGATEKLSEVYIGE----YFGGGIESWFAYVAALAFLLVQPSGLFGQ 293 Query: 304 RVADRA 309 R +RA Sbjct: 294 RPVERA 299 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: 231 Number of extensions: 10 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: 309 Length of database: 299 Length adjustment: 27 Effective length of query: 282 Effective length of database: 272 Effective search space: 76704 Effective search space used: 76704 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 Apr 09 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