Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_011384270.1 AMB_RS09430 ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >NCBI__GCF_000009985.1:WP_011384270.1 Length = 262 Score = 145 bits (365), Expect = 1e-39 Identities = 85/210 (40%), Positives = 121/210 (57%), Gaps = 17/210 (8%) Query: 48 VNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREF 107 + DL L + G+ ++G SG+GKSTL+R L+ G + V+ +E Sbjct: 31 LQDLDLEVRHGDFIALVGQSGAGKSTLLRVIAGLVPAVLGQVYVEPP----------KEP 80 Query: 108 RRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPH 167 +I MVFQ LLP + VL NV YGL+ +S+ RAL ++ VGL + +++PH Sbjct: 81 DSRQIGMVFQDARLLPWRRVLANVEYGLEGLVKSRHERRRRALAALDLVGLTEFADRWPH 140 Query: 168 QLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITH 227 LSGG RQRVGLARALA ++LMDE F ALDP R +QDQLL + + +I+F+TH Sbjct: 141 HLSGGQRQRVGLARALAVRPALLLMDEPFGALDPATRHGLQDQLLSIWQATGTSIIFVTH 200 Query: 228 DLDEAVRIGNRIAILKDGKLIQVGTPREIL 257 D+DEA + +R+ +L G+P IL Sbjct: 201 DIDEATYLADRVIVLG-------GSPARIL 223 Lambda K H 0.321 0.138 0.387 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: 219 Number of extensions: 14 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: 276 Length of database: 262 Length adjustment: 25 Effective length of query: 251 Effective length of database: 237 Effective search space: 59487 Effective search space used: 59487 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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