Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate HSERO_RS17565 HSERO_RS17565 glutamate/aspartate ABC transporter permease GltJ
Query= SwissProt::P0AER3 (246 letters) >FitnessBrowser__HerbieS:HSERO_RS17565 Length = 241 Score = 286 bits (732), Expect = 3e-82 Identities = 144/248 (58%), Positives = 184/248 (74%), Gaps = 9/248 (3%) Query: 1 MSIDWNWGIFLQQAPFGNTTYLGWIWSGFQVTIALSICAWIIAFLVGSFFGILRTVPNRF 60 M+ W W +FLQ AP TYL W+ SG VT+AL + AWI+A ++G+F GILRT+PNR Sbjct: 1 MAYQWQWSVFLQ-APSTGQTYLDWLLSGLGVTVALGLSAWILALVLGTFLGILRTLPNRA 59 Query: 61 LSGLGTLYVELFRNVPLIVQFFTWYLVIPELLPEKIGMWFKA--ELDPNIQFFLSSMLCL 118 LSG YVELFRNVPL+VQ F WY +PELLP W A L P Q F+ +MLCL Sbjct: 60 LSGFAACYVELFRNVPLLVQIFIWYFAMPELLP-----WGDAVKALPPMTQQFVMAMLCL 114 Query: 119 GLFTAARVCEQVRAAIQSLPRGQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSEMMN 178 G+FTAARVCEQVR+ I+SLPRGQK A LA+GLTL Q Y +VLLP A R+++PP+TSE +N Sbjct: 115 GMFTAARVCEQVRSGIESLPRGQKGAGLALGLTLGQTYLFVLLPMAMRIVLPPLTSEFLN 174 Query: 179 LVKNSAIASTIGLVDMAAQAGKLLDYSAHAWESFTAITLAYVLINAFIMLVMTLVERKVR 238 + KNSA+ASTIGL+++AAQ +L+DY+A +E+F A+TLAY+LIN +M +M ++ERK Sbjct: 175 IFKNSAVASTIGLLELAAQGRQLVDYTAQPYEAFIAVTLAYMLINICVMSLMRILERKTS 234 Query: 239 LPGNMGGK 246 LPG M GK Sbjct: 235 LPG-MAGK 241 Lambda K H 0.328 0.140 0.443 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: 256 Number of extensions: 5 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: 246 Length of database: 241 Length adjustment: 23 Effective length of query: 223 Effective length of database: 218 Effective search space: 48614 Effective search space used: 48614 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: 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