Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein
Query= TCDB::Q52666 (263 letters) >NCBI__GCF_000017185.1:WP_011974043.1 Length = 238 Score = 143 bits (360), Expect = 4e-39 Identities = 89/204 (43%), Positives = 123/204 (60%), Gaps = 5/204 (2%) Query: 37 VLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVDGIELTSDLKNIDKV 96 VLR INL + GE + I GPSG GKST++ + L+ G + + G + T +N V Sbjct: 36 VLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKGMVYIKGKKTTMFSENDRAV 95 Query: 97 --RSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYYLEKVKIPEQAQKY 154 R G +FQ FNL LT LEN+ L P+ + + K + A L+ + + + Y Sbjct: 96 FRRKISGFIFQQFNLINTLTALENVEL-PLVLDEKNKNYRIKKAKKLLKIINLGHRENYY 154 Query: 155 PGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTMIQLAE-EGMTMLCV 213 P QLSGGQQQRVAIAR+L PKI+ DEPT LD + +EV+D + +L E EG+T++ V Sbjct: 155 PNQLSGGQQQRVAIARALSNNPKIIFADEPTGNLDSKNSREVMDILKELNEKEGITVIMV 214 Query: 214 THEMGFAQAVANRVIFMADGQIVE 237 THE FA+ A+R+I M DG+IVE Sbjct: 215 THEPEFAK-YASRIINMKDGEIVE 237 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: 164 Number of extensions: 6 Number of successful extensions: 5 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: 238 Length adjustment: 24 Effective length of query: 239 Effective length of database: 214 Effective search space: 51146 Effective search space used: 51146 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