Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate BWI76_RS20330 BWI76_RS20330 histidine/lysine/arginine/ornithine ABC transporter permease HisQ
Query= uniprot:B2TBJ7 (240 letters) >FitnessBrowser__Koxy:BWI76_RS20330 Length = 228 Score = 159 bits (401), Expect = 6e-44 Identities = 88/223 (39%), Positives = 132/223 (59%), Gaps = 1/223 (0%) Query: 13 GWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELL 72 G+ V+ AL+T+ L L+++ + + G A AKLS R L +I + YTT+ RGVP+L+ Sbjct: 4 GFSQVIFQGALVTLELALSSVVLAVLIGLAGAGAKLSNNRPLALIFEGYTTLIRGVPDLV 63 Query: 73 VIYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRG 132 ++ L ++G + SV G F + P V G + +G I GAY E +R A LAV G Sbjct: 64 LMLLIFYGLQIALNSVTDALGLAQF-DIDPMVAGIITLGFIYGAYFTETFRGAFLAVPTG 122 Query: 133 ELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQV 192 +EAA + G RRIL P ++R+ALPGIGN WQ+ LK +AL+S+ GL ++++ +Q+ Sbjct: 123 HIEAATAFGFSGGQTFRRILFPAMMRYALPGIGNNWQVILKATALVSLLGLEDVVKATQL 182 Query: 193 AAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAEAHVGRSFKR 235 A ST + F F +V G +YL+ T++SN V E KR Sbjct: 183 AGKSTWEPFYFAIVCGLIYLVFTTVSNGVLLMLERRYSVGVKR 225 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: 119 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: 228 Length adjustment: 23 Effective length of query: 217 Effective length of database: 205 Effective search space: 44485 Effective search space used: 44485 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 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