Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__MR1:200449 Length = 378 Score = 163 bits (413), Expect = 4e-45 Identities = 81/246 (32%), Positives = 147/246 (59%), Gaps = 6/246 (2%) Query: 16 QVSDEIAIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQ 75 + +++ ++I +++K + + D++LT+++GE + G SGSGKST++R + E Sbjct: 14 KTQEKVLLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPT 73 Query: 76 SGKIIVDGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAE 135 SG+I +DG D+ ++ + M+FQ + LFPH+T+ +N+ + K+PK E E Sbjct: 74 SGRIYLDG----EDITDLPPYERPINMMFQSYALFPHMTVAQNIAFG-LKQDKLPKAEIE 128 Query: 136 ETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKE 195 + L+ V + + ++ P QLSGGQ+QRVA+ARSL +PK++L DEP ALD ++ + Sbjct: 129 QRVQEMLKLVHMEQYGKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQ 188 Query: 196 VLDTMIQLAEE-GMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTK 254 + ++++ E G+T + VTH+ A +A R+ M+DG I + +P D + +P S Sbjct: 189 MQLEVVEILERVGVTCVMVTHDQEEAMTMAGRISIMSDGWIAQTGSPMDIYESPNSRMIA 248 Query: 255 QFLSQI 260 +F+ + Sbjct: 249 EFIGSV 254 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: 244 Number of extensions: 15 Number of successful extensions: 4 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: 378 Length adjustment: 27 Effective length of query: 236 Effective length of database: 351 Effective search space: 82836 Effective search space used: 82836 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: 48 (23.1 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