Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate 3608728 Dshi_2120 ABC transporter related (RefSeq)
Query= TCDB::P48243 (242 letters) >FitnessBrowser__Dino:3608728 Length = 376 Score = 163 bits (413), Expect = 4e-45 Identities = 99/238 (41%), Positives = 139/238 (58%), Gaps = 6/238 (2%) Query: 1 MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60 ++K V K FG F A+ D EI RG+ + ++G SG GK+T R + LE EG I + Sbjct: 14 IVKFDNVVKRFGSFTAVKKADFEIGRGEFLAIMGSSGCGKTTTLRMLAGLEDPTEGAIYL 73 Query: 61 DGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLAMSL 120 DG E+ G A D MV+QS LFP LT+++NV A +K+R + K E + A Sbjct: 74 DG----EQVNGKATWDRDTPMVWQSLALFPFLTVQENVEFA-LKMRGIGKEERRQRADKW 128 Query: 121 LERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLDVMA 180 L+++ I AD+ QLSGGQ+QRVA+ARAL PKI+L DEP SALD + + V++ Sbjct: 129 LDKMQITEFADRNINQLSGGQKQRVALARALVTEPKILLLDEPLSALDAHLKVRMQSVLS 188 Query: 181 SLAKE-GMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDFLG 237 +L K+ G+T V VTH M A ADRV+ M+ G I + P+ + P + +FLG Sbjct: 189 NLQKDLGITFVYVTHSMSEAFSMADRVVIMSRGQIEQIGTPEEIYREPHNRFVAEFLG 246 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: 201 Number of extensions: 10 Number of successful extensions: 4 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: 376 Length adjustment: 27 Effective length of query: 215 Effective length of database: 349 Effective search space: 75035 Effective search space used: 75035 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: 48 (23.1 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