Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate Echvi_4044 Echvi_4044 ABC-type transport system involved in resistance to organic solvents, ATPase component
Query= TCDB::P48243 (242 letters) >FitnessBrowser__Cola:Echvi_4044 Length = 249 Score = 155 bits (391), Expect = 9e-43 Identities = 80/238 (33%), Positives = 147/238 (61%), Gaps = 3/238 (1%) Query: 1 MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60 ++++ G++K FG+ L +DL++ +G+ VVVLG SG+GKS L + + L T +EGT+ + Sbjct: 5 VVEVRGLKKSFGELDVLMGVDLDLYKGENVVVLGKSGTGKSVLIKIMVGLLTQDEGTMNV 64 Query: 61 DGKVLPEEG-KGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIK-VRKMKKSEAEKLAM 118 GK + G K L LR +G FQ+ L+ +T+++N+ ++ V+ + ++E +K+ Sbjct: 65 LGKEVSNLGAKDLNELRLKIGFSFQASALYDSMTVRENLEFPLVRNVKGLSRTEKDKMVE 124 Query: 119 SLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLDV 178 +LE VG++ ++ P++LSGGQ++R+ IAR L + P+IML+DEPT+ LDP +++ ++ Sbjct: 125 EVLEAVGLSQTINQMPSELSGGQRKRIGIARTLILKPEIMLYDEPTAGLDPITCSDINNL 184 Query: 179 MASLAKE-GMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDF 235 + + + + + +TH++ AR DRV + DG + + + F P+ R K F Sbjct: 185 INEVRENYNTSSIIITHDLTCARDTGDRVAVLLDGQFGAEGKFEEVFKTPEDQRVKSF 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: 137 Number of extensions: 5 Number of successful extensions: 3 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: 249 Length adjustment: 24 Effective length of query: 218 Effective length of database: 225 Effective search space: 49050 Effective search space used: 49050 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 Apr 09 2024. 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