Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate RR42_RS29660 RR42_RS29660 amino acid transporter
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__Cup4G11:RR42_RS29660 Length = 264 Score = 243 bits (620), Expect = 3e-69 Identities = 127/248 (51%), Positives = 174/248 (70%), Gaps = 12/248 (4%) Query: 23 IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82 + + ++K +G VL+ ++LT +G+ I I G SGSGKST +RCIN LE +SG+I +D Sbjct: 13 LAVQDIHKSFGDNEVLKGVSLTAKKGDVISIIGASGSGKSTFLRCINYLERPKSGQIFLD 72 Query: 83 GIEL------TSDL-----KNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPK 131 G E+ T DL K + ++R+++ MVFQHFNL+ H+ +LEN+ AP V + + Sbjct: 73 GEEIRTKKDKTGDLVVVEPKQLQRMRTKLSMVFQHFNLWAHMNVLENIIEAPTHVLGLSR 132 Query: 132 REAEETAMYYLEKVKIPEQAQK-YPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDP 190 +EAEE A YLEKV +P + +K YP LSGGQQQRVAIAR+L M P +MLFDEPTSALDP Sbjct: 133 KEAEERAREYLEKVGLPPRVEKQYPSHLSGGQQQRVAIARALAMNPDVMLFDEPTSALDP 192 Query: 191 EMIKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQS 250 E++ EVL M +LAEEG TM+ VTHEMGFA+ V+N V+F+ G+ EQ P + ++P+S Sbjct: 193 ELVGEVLKVMQKLAEEGRTMIVVTHEMGFARNVSNHVMFLHQGRTEEQGPPEEVLNSPRS 252 Query: 251 ERTKQFLS 258 ER +QFLS Sbjct: 253 ERLRQFLS 260 Lambda K H 0.320 0.134 0.391 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: 193 Number of extensions: 6 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: 263 Length of database: 264 Length adjustment: 25 Effective length of query: 238 Effective length of database: 239 Effective search space: 56882 Effective search space used: 56882 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: 47 (22.7 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