Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate 8502445 DvMF_3151 ABC transporter related (RefSeq)
Query= TCDB::P48243 (242 letters) >FitnessBrowser__Miya:8502445 Length = 242 Score = 300 bits (767), Expect = 2e-86 Identities = 145/240 (60%), Positives = 190/240 (79%) Query: 1 MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60 MI+ V K++G+FH L I ++ +G+V+V+ GPSGSGKS+ R +NRLE I++G I + Sbjct: 3 MIEFHDVHKWYGEFHVLKGITQKVEKGEVLVICGPSGSGKSSFIRCLNRLEPIQKGQILL 62 Query: 61 DGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLAMSL 120 +GK + ++G + LR +VG+VFQ FNL+PHL++ NVTLAP KVRKM K++AE +AM L Sbjct: 63 EGKSIHDKGVDVNELRTEVGIVFQQFNLYPHLSVLHNVTLAPTKVRKMPKAKAESIAMEL 122 Query: 121 LERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLDVMA 180 LERVGI +QA KYP +LSGGQQQRVAIARALAM PK+MLFDEPTSALDPEM+NEVL+ M Sbjct: 123 LERVGIHDQARKYPVELSGGQQQRVAIARALAMQPKVMLFDEPTSALDPEMINEVLNAMK 182 Query: 181 SLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDFLGKIL 240 LA+ GMTM+CVTHEMGFAR+ ADRV+FM G ++E+ PD FF++PK +R + FL +IL Sbjct: 183 DLARAGMTMLCVTHEMGFAREVADRVVFMDGGKVIEEAPPDVFFSSPKHERTQAFLREIL 242 Lambda K H 0.319 0.135 0.379 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: 208 Number of extensions: 4 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: 242 Length of database: 242 Length adjustment: 23 Effective length of query: 219 Effective length of database: 219 Effective search space: 47961 Effective search space used: 47961 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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