Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate GFF196 PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC
Query= TCDB::P48245 (273 letters) >FitnessBrowser__Phaeo:GFF196 Length = 432 Score = 103 bits (257), Expect = 6e-27 Identities = 65/206 (31%), Positives = 110/206 (53%), Gaps = 4/206 (1%) Query: 27 LPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIPVLILMIFAY 86 L G + V V L++ +G AL LGR S + +++W C V IE R +P++ L+ A Sbjct: 222 LGGFMLNMMLGVTCVSLSVPLGIALALGRQSNMPLIKWICVVFIEFVRGVPLITLLFVAS 281 Query: 87 QMFAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIALGMSSRQT 146 M + + ++ F VV +T+++ + IAE++R G+A+LPKGQ EAA +LG+ Q Sbjct: 282 VMLSYFFPPDATVDLFLRVVIMITLFSAAYIAEVIRGGLAALPKGQYEAADSLGLDYPQA 341 Query: 147 TWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVV---RSGI-QSASVNRNYLAA 202 I+LPQA+ +P +++ V KD+ L I ++V R I S N Y Sbjct: 342 MRLIILPQALKISIPGIVNVAVGLFKDTTLVSVISMFDLVGMIRGPILASTEWNGVYWEL 401 Query: 203 LFVVALIMIVLNFSLTALASRIERQL 228 L A + ++ + ++ + +ER+L Sbjct: 402 LGFAAFLFFIVCYGISQYSQWLERRL 427 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: 304 Number of extensions: 10 Number of successful extensions: 1 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: 432 Length adjustment: 29 Effective length of query: 244 Effective length of database: 403 Effective search space: 98332 Effective search space used: 98332 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: 49 (23.5 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