Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate AO356_10415 AO356_10415 glutamine ABC transporter permease
Query= TCDB::P48245 (273 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_10415 Length = 219 Score = 89.0 bits (219), Expect = 8e-23 Identities = 62/200 (31%), Positives = 107/200 (53%), Gaps = 12/200 (6%) Query: 33 TLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIPVLI---LMIFAYQMF 89 TL + S+ L+ V G G+ R ++ + V +E FRAIPVL+ L+ F +F Sbjct: 23 TLSISFLSIALSTVGGVLYGVLRTLGVKGVDVVLRVYLELFRAIPVLVWLYLLFFGLPIF 82 Query: 90 AQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIALGMSSRQTTWS 149 ++ PS F V L+++ S + E++R + SLP+GQ+EA +++G++ Q Sbjct: 83 FGLSL-PS----FWCAVLVLSLWGASEVGEVVRGALHSLPRGQREAGLSIGLNGLQLYGH 137 Query: 150 ILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSASVNRNYLAALFVVALI 209 +LLPQA+ M P I+ +K S+L IG ++V++ G Q + R Y + L AL Sbjct: 138 VLLPQALRRMTPPTINVYTRIIKTSSLAVLIGVVDVIKVGQQ--IIERTYESVLIYGALF 195 Query: 210 M--IVLNFSLTALASRIERQ 227 + + + L+A + +ER+ Sbjct: 196 LFFFFICYPLSAASRVLERR 215 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: 126 Number of extensions: 7 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: 219 Length adjustment: 24 Effective length of query: 249 Effective length of database: 195 Effective search space: 48555 Effective search space used: 48555 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: 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