Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease
Query= uniprot:B2TBJ7 (240 letters) >NCBI__GCF_900115975.1:WP_092487756.1 Length = 234 Score = 137 bits (346), Expect = 1e-37 Identities = 75/218 (34%), Positives = 126/218 (57%), Gaps = 9/218 (4%) Query: 17 VLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELLVIYL 76 ++ A +T+ +T+ ++A+G + G + ++LSR + LR + Y FRG P L+ I++ Sbjct: 11 LIFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFI 70 Query: 77 FYFG--------GSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLA 128 YFG S +V S G A+ F +P F+ +A + SGAY AE++R+ V + Sbjct: 71 VYFGIPKLLMDLQSFMVDSYGMTPVADSFA-LPRFLAAVIACSLNSGAYVAEIFRAGVQS 129 Query: 129 VSRGELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLR 188 + RG++EAARS+GM R +++PQ + +P +GN + LKD++L+SV G AEL R Sbjct: 130 IERGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTR 189 Query: 189 TSQVAAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAE 226 Q+ T++ F ++ G +YLIMT +R+ + E Sbjct: 190 NGQLIIARTYESFAIWLTVGFIYLIMTFTLSRIVDYLE 227 Lambda K H 0.327 0.141 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: 104 Number of extensions: 3 Number of successful extensions: 2 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: 240 Length of database: 234 Length adjustment: 23 Effective length of query: 217 Effective length of database: 211 Effective search space: 45787 Effective search space used: 45787 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: 46 (22.3 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