Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate HSERO_RS17565 HSERO_RS17565 glutamate/aspartate ABC transporter permease GltJ
Query= TCDB::P48245 (273 letters) >FitnessBrowser__HerbieS:HSERO_RS17565 Length = 241 Score = 112 bits (280), Expect = 8e-30 Identities = 74/229 (32%), Positives = 118/229 (51%), Gaps = 15/229 (6%) Query: 12 KWTPFINS----QTWTTYILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCA 67 +W+ F+ + QT+ ++L GL T+ + + ILALV+GT LG+ R R L F A Sbjct: 6 QWSVFLQAPSTGQTYLDWLLSGLGVTVALGLSAWILALVLGTFLGILRTLPNRALSGFAA 65 Query: 68 VIIETFRAIPVLILMIFAYQMFAQYNIVPSSQLA---------FAAVVFGLTMYNGSVIA 118 +E FR +P+L+ + Y FA ++P F + L M+ + + Sbjct: 66 CYVELFRNVPLLVQIFIWY--FAMPELLPWGDAVKALPPMTQQFVMAMLCLGMFTAARVC 123 Query: 119 EILRSGIASLPKGQKEAAIALGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGY 178 E +RSGI SLP+GQK A +ALG++ QT +LLP A+ +LP L S+ + K+SA+ Sbjct: 124 EQVRSGIESLPRGQKGAGLALGLTLGQTYLFVLLPMAMRIVLPPLTSEFLNIFKNSAVAS 183 Query: 179 QIGYIEVVRSGIQSASVNRNYLAALFVVALIMIVLNFSLTALASRIERQ 227 IG +E+ G Q A V L +++N + +L +ER+ Sbjct: 184 TIGLLELAAQGRQLVDYTAQPYEAFIAVTLAYMLINICVMSLMRILERK 232 Lambda K H 0.323 0.136 0.395 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: 181 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: 273 Length of database: 241 Length adjustment: 24 Effective length of query: 249 Effective length of database: 217 Effective search space: 54033 Effective search space used: 54033 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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