Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate H281DRAFT_02563 H281DRAFT_02563 amino acid ABC transporter membrane protein, PAAT family
Query= SwissProt::P0AER5 (224 letters) >FitnessBrowser__Burk376:H281DRAFT_02563 Length = 265 Score = 132 bits (333), Expect = 5e-36 Identities = 83/223 (37%), Positives = 129/223 (57%), Gaps = 9/223 (4%) Query: 5 DWSSIVPSLPYLLD-GLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVF 63 DW +V SLP L+ GLV TL ++V + +GI+ G LA+ +S + W + +V+VF Sbjct: 10 DWPLLVESLPTLIGTGLVNTLILSVVSTALGIVAGMALALCAVSHTRWLTWPVRVFVDVF 69 Query: 64 RSIPLVMVLLWFYLIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSI 123 R +P +V+L ++ G L L N L A+VA ++ +AY +EI R+GIQS+ Sbjct: 70 RGLPAALVIL---VVGQGLAPVGLSLFGPNPYPL--AIVALALVSSAYIAEIFRSGIQSV 124 Query: 124 SRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRT 183 RGQ SA ALGMT+W M+ +I+PQ R ++P L Q I + +D+SLVY L L R Sbjct: 125 GRGQMSACQALGMTYWSGMRHVIVPQGVRRILPALANQFISIVKDSSLVYFLGLLTSQRD 184 Query: 184 ASTIGER---DGTQVEMILFAGFVYFVISLSASLLVSYLKRRT 223 TIG+ + + ++ AG VY +I++ + +++L R T Sbjct: 185 LFTIGQNAAVNTANLSPLVAAGAVYLLITVPLTHTINHLDRWT 227 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: 167 Number of extensions: 12 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: 265 Length adjustment: 24 Effective length of query: 200 Effective length of database: 241 Effective search space: 48200 Effective search space used: 48200 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