Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__psRCH2:GFF16 Length = 278 Score = 221 bits (564), Expect = 1e-62 Identities = 118/250 (47%), Positives = 166/250 (66%), Gaps = 12/250 (4%) Query: 23 IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82 ++ + + K YG+ VL ++L + GE++ I GPSGSGKST++R + LE G I VD Sbjct: 25 VRFAGVTKRYGELTVLDGLDLQIEEGEKVAIIGPSGSGKSTLLRVLMTLEGIDEGVIEVD 84 Query: 83 GIELT-----------SDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPK 131 G LT ++ +++ +VR +VGMVFQ FNLFPH+ L+N+ AP+ V + K Sbjct: 85 GEPLTHMPDASGQLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQVLGLSK 144 Query: 132 REAEETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPE 191 EA A L V + ++ + +P QLSGGQQQRVAIAR+L M+PK+MLFDE TSALDPE Sbjct: 145 AEARGRAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVTSALDPE 204 Query: 192 MIKEVLDTMIQLAE-EGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQS 250 + EVL+ + +L E +TML VTH+MGFA+ A+RV F G+I EQ +P + F+NPQ Sbjct: 205 LCGEVLNVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDELFNNPQE 264 Query: 251 ERTKQFLSQI 260 ERT++FLS + Sbjct: 265 ERTREFLSAV 274 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: 226 Number of extensions: 10 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: 278 Length adjustment: 25 Effective length of query: 238 Effective length of database: 253 Effective search space: 60214 Effective search space used: 60214 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