Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate 8501185 DvMF_1919 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >FitnessBrowser__Miya:8501185 Length = 223 Score = 179 bits (455), Expect = 3e-50 Identities = 95/220 (43%), Positives = 146/220 (66%), Gaps = 4/220 (1%) Query: 1 MELDF--SPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTA 58 M LDF S +W VP LL G +T+ IT L +G ++G G+ + + ++ AL Sbjct: 1 MALDFKASVMWESVPLLLGGVHLTIIITLGGLAIGFLLGTATGLAK-TARGKLPRALADI 59 Query: 59 YVAAIRGTPLLVQLFILFFGLP-QFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDK 117 YV AIRGTPL+VQ+ L+FG+P G+ +P G+I + + SGAY++E+VRGA++SID Sbjct: 60 YVEAIRGTPLIVQVMFLYFGVPLATGMRIPPVTAGIIAIAVNSGAYIAEIVRGAVESIDV 119 Query: 118 GQMEAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQ 177 GQ EA RSIG++ + VV PQA RMIPPLGN+FI +K+++L+ ++ + +L +GQ Sbjct: 120 GQTEAGRSIGLTRMQTLLYVVWPQAFRRMIPPLGNQFIISLKDTSLLVVIGVGELTRQGQ 179 Query: 178 KIISVSYRSLEVYLAIAVVYFILTGATTLVLRRIELRLRA 217 +II+V++R+ EV+L +AV+Y ++T + LR E +L A Sbjct: 180 EIIAVNFRAFEVWLTVAVMYLVMTLSIARALRVYERKLNA 219 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: 139 Number of extensions: 6 Number of successful extensions: 3 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: 223 Length adjustment: 22 Effective length of query: 200 Effective length of database: 201 Effective search space: 40200 Effective search space used: 40200 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: 45 (21.9 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