Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate WP_013554635.1 NITSA_RS08635 amino acid ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >NCBI__GCF_000186245.1:WP_013554635.1 Length = 384 Score = 76.3 bits (186), Expect = 8e-19 Identities = 40/131 (30%), Positives = 78/131 (59%), Gaps = 1/131 (0%) Query: 87 PAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSSGLAMRTVVLPQAVVRM 146 P F+ + L IY+ +++E +R I+++ KGQ EAA S+G+S +R V+LPQAV Sbjct: 250 PEFLALLFALSIYTATFIAEAIRSGIEAVPKGQKEAATSLGLSPLQQLRLVILPQAVRIA 309 Query: 147 IPPLGNEFIALIKNSALVSLLTIHDLMH-EGQKIISVSYRSLEVYLAIAVVYFILTGATT 205 IP + N+++ LIKNS+L + + +L+ ++ + ++LE+ L + Y +++ + Sbjct: 310 IPSIINQYLNLIKNSSLAAAIGYPELVTIFAGTSLNQTGQALEILLITMLTYLLISLIVS 369 Query: 206 LVLRRIELRLR 216 L+L +++ Sbjct: 370 LILNWFNAKMK 380 Score = 37.4 bits (85), Expect = 4e-07 Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 1/74 (1%) Query: 3 LDFSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAA 62 + F+P + G L T+ ++ ++ ++GLL+GI RL+P ++ + AY+ Sbjct: 63 IPFTPASTHLKVFEVGLLNTLIVSFWGIVFSSLIGLLIGIWRLSPNW-LINRIAAAYIET 121 Query: 63 IRGTPLLVQLFILF 76 R P+L+Q+ + Sbjct: 122 FRNIPVLLQILFWY 135 Lambda K H 0.328 0.143 0.412 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: 201 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 222 Length of database: 384 Length adjustment: 26 Effective length of query: 196 Effective length of database: 358 Effective search space: 70168 Effective search space used: 70168 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 (21.8 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