Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate 206399 DVU0967 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >MicrobesOnline__882:206399 Length = 337 Score = 151 bits (382), Expect = 1e-41 Identities = 79/211 (37%), Positives = 139/211 (65%), Gaps = 14/211 (6%) Query: 15 LLAGALVTVEITAASLLLGCVMGLLVGIGRL--NPKRRVVYALCTAYVAAIRGTPLLVQL 72 LL G +T+E++ ++++G V+G++ G+ R+ NP R L Y+ IRG+PLLVQ+ Sbjct: 127 LLEGLWITLEVSMLAIIIGIVLGVVTGLARISVNPALRW---LAITYIEIIRGSPLLVQV 183 Query: 73 FILFFGL--------PQFGI-LLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAA 123 F+ +F + + G+ +P GV+ L I++GAYV+E+VR IQS+ +GQMEAA Sbjct: 184 FLWYFVVGTLLNALFEKVGLSAIPPLWYGVMALAIFTGAYVAEIVRAGIQSVHRGQMEAA 243 Query: 124 RSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVS 183 RS+GMS +MR V+LPQA R++PPL +FI+L+K+S+L+ ++ + +L +++++ S Sbjct: 244 RSLGMSYAQSMRKVILPQAFRRIMPPLAGQFISLVKDSSLLGVIAVRELTKATREVVTTS 303 Query: 184 YRSLEVYLAIAVVYFILTGATTLVLRRIELR 214 + E+++ A++Y +LT +L ++ +E R Sbjct: 304 LQPFELWIVCALLYLVLTFTLSLCVQYLERR 334 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: 198 Number of extensions: 8 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: 222 Length of database: 337 Length adjustment: 25 Effective length of query: 197 Effective length of database: 312 Effective search space: 61464 Effective search space used: 61464 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: 47 (22.7 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