Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF356 PS417_01815 peptide ABC transporter ATP-binding protein
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__WCS417:GFF356 Length = 244 Score = 261 bits (667), Expect = 1e-74 Identities = 133/229 (58%), Positives = 172/229 (75%), Gaps = 3/229 (1%) Query: 36 HVLRDI-NLT--VHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVDGIELTSDLKN 92 HV+R + N+T V +GE +V+ GPSGSGKST +RC+N LEE SG + +DG++L + Sbjct: 16 HVVRAVDNVTTQVAKGEVLVVIGPSGSGKSTFLRCLNGLEEFDSGSVSIDGLQLADPKTD 75 Query: 93 IDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYYLEKVKIPEQAQ 152 ++ R EVGMVFQHFNLFPH+T+LENL LA VRK K+E+E A+ LEKV I ++A Sbjct: 76 VNAYRREVGMVFQHFNLFPHMTVLENLCLAQKVVRKRSKKESEAKALALLEKVGIAQKAN 135 Query: 153 KYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTMIQLAEEGMTMLC 212 ++P +LSGGQQQRVAIAR+L M PK+MLFDEPTSALDPEM+ EVLD M LA EGMTM+C Sbjct: 136 EFPSRLSGGQQQRVAIARALAMDPKVMLFDEPTSALDPEMVGEVLDVMKTLALEGMTMVC 195 Query: 213 VTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFLSQIL 261 VTHEMGFA+ VA+RV+F G+++E P +FF P+ R + FL Q+L Sbjct: 196 VTHEMGFAREVADRVLFFDHGKLLEDAAPAEFFDAPKDPRAQAFLRQVL 244 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: 208 Number of extensions: 8 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: 263 Length of database: 244 Length adjustment: 24 Effective length of query: 239 Effective length of database: 220 Effective search space: 52580 Effective search space used: 52580 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