Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate AO353_24420 AO353_24420 amino acid ABC transporter permease
Query= SwissProt::P0AER5 (224 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24420 Length = 222 Score = 124 bits (312), Expect = 1e-33 Identities = 70/221 (31%), Positives = 117/221 (52%), Gaps = 7/221 (3%) Query: 2 YEFDWSSIVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVN 61 Y+FD I L LL GLV+TL++TV A +IG+ G ++A++ +S + W ++ Sbjct: 3 YQFDLFFITSGLWPLLKGLVVTLQLTVAANIIGLTLGFVIALLVMSPNPILRWPFTLFIE 62 Query: 62 VFRSIPLVMVLLWFYLIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQ 121 FR P ++ ++WF+ +P + L ++A + AA+ +E RA IQ Sbjct: 63 FFRCTPALVQIVWFFYCIPIIFDVYIDA-------LTMGILAIGLNLAAFNAEAYRAAIQ 115 Query: 122 SISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFF 181 + Q A +ALG++ +Q ++LPQAFR+ +P+L+ GI FQ T+LV +++L D Sbjct: 116 GVQSNQYDATVALGLSPFQRTVYVVLPQAFRSALPVLVANGIGAFQQTALVAIVALQDLM 175 Query: 182 RTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222 + +E+ +YF IS S LV Y++RR Sbjct: 176 YMGKILATDTYRPIEVFTVIALIYFAISFPISQLVEYIERR 216 Lambda K H 0.330 0.140 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: 128 Number of extensions: 6 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: 224 Length of database: 222 Length adjustment: 22 Effective length of query: 202 Effective length of database: 200 Effective search space: 40400 Effective search space used: 40400 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 (21.9 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