Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_007692556.1 C447_RS07635 ABC transporter ATP-binding protein
Query= TCDB::Q52666 (263 letters) >NCBI__GCF_000336675.1:WP_007692556.1 Length = 362 Score = 141 bits (356), Expect = 2e-38 Identities = 75/238 (31%), Positives = 135/238 (56%), Gaps = 6/238 (2%) Query: 21 IAIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKII 80 + +++S ++K +G + D++LT+ GE +++ GPSG GK+T +R I LE+ SG+I Sbjct: 1 MTVELSNISKRFGSIVAVDDVSLTIENGEFLILVGPSGCGKTTTLRMIAGLEKPSSGRIY 60 Query: 81 VDGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMY 140 DG D+ + + VFQ++ L+PH+T +N++ A + + +P E + Sbjct: 61 FDG----DDVTQFSPQQRHIAFVFQNYALYPHMTTRKNMSFA-LEDQDIPSDEVAQRVTS 115 Query: 141 YLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTM 200 +K+ I +Q + PG+LSGGQQQRVA+ RS+ P + L DEP S LD ++ + + Sbjct: 116 TADKLGITDQLDQRPGELSGGQQQRVALGRSIVRNPSVFLLDEPLSNLDAKLRTNMRAEL 175 Query: 201 IQLAEE-GMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFL 257 +L ++ TM+ VTH+ A + +R+ M +G I + P++ ++ P + F+ Sbjct: 176 QELHQDLETTMVYVTHDQEEAMTMGDRIAVMDEGTIQQVAPPNEAYNQPANRFVAGFI 233 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: 215 Number of extensions: 9 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: 362 Length adjustment: 27 Effective length of query: 236 Effective length of database: 335 Effective search space: 79060 Effective search space used: 79060 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 24 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