Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 206675 DVU1236 amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q52666 (263 letters) >MicrobesOnline__882:206675 Length = 247 Score = 290 bits (743), Expect = 2e-83 Identities = 145/247 (58%), Positives = 187/247 (75%) Query: 15 MQVSDEIAIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEH 74 M ++E I I + K++G+ L D++L V GE++VI GPSGSGKST++R INRLE Sbjct: 1 MTAANEPIISIRNVWKFFGELTALHDVSLDVQAGEKVVIIGPSGSGKSTLLRSINRLENV 60 Query: 75 QSGKIIVDGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREA 134 G IIVDG ++ ++ +I+ +R ++GMVFQ FNLFPH T+L+NLT+AP+ +RKVP+ EA Sbjct: 61 DKGSIIVDGKDIRAEDSDINVIRQDLGMVFQSFNLFPHKTVLQNLTMAPMRLRKVPRDEA 120 Query: 135 EETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIK 194 E A+ L+KV I ++A YP LSGGQQQRVAIAR+L M PKIMLFDEPTSALDPEMI Sbjct: 121 ESRALDLLKKVGISDKANVYPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMIG 180 Query: 195 EVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTK 254 EVLD M+ LA+EGMTM+CVTHEMGFA+ VA+R+IFM GQI+EQ P FF P+ R + Sbjct: 181 EVLDVMVTLAKEGMTMVCVTHEMGFAREVADRIIFMDHGQILEQGTPQHFFEAPEHPRLQ 240 Query: 255 QFLSQIL 261 +FL QIL Sbjct: 241 KFLQQIL 247 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: 222 Number of extensions: 7 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: 247 Length adjustment: 24 Effective length of query: 239 Effective length of database: 223 Effective search space: 53297 Effective search space used: 53297 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