Align ABC transporter related (characterized, see rationale)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA
Query= uniprot:B2TBJ9 (263 letters) >NCBI__GCF_000013785.1:WP_011911265.1 Length = 279 Score = 258 bits (658), Expect = 1e-73 Identities = 138/259 (53%), Positives = 182/259 (70%), Gaps = 3/259 (1%) Query: 1 MNATAPVALSVK--NIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLE 58 M A AP V+ ++ K +G+ VL+G+ LD +G+ ++I+G SGSGKST LR L LE Sbjct: 16 MAAAAPAQPMVRFASVTKRYGELTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLRVLMTLE 75 Query: 59 TPDDGSVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIE 118 DDG + + GE L G G+L P++ R + RVR ++GMVFQ+FNL+ HM L+N++E Sbjct: 76 GIDDGLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVME 135 Query: 119 GPMRVQKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLF 178 P++V S+ E+ E AE LLA VGL +K H+PA LSGGQQQRVAIARALAM PKVMLF Sbjct: 136 APVQVLGLSKREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLF 195 Query: 179 DEPTSALDPELVGEVLRVMRSLAE-EGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGT 237 DE TSALDPEL GEVL V+R L E TML+VTH+MGFAR ++RV F HQG++ G+ Sbjct: 196 DEVTSALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGS 255 Query: 238 PDEVFVECKSDRFRQFVSS 256 PD +F + DR R+F+S+ Sbjct: 256 PDALFNNPQEDRTREFLSA 274 Lambda K H 0.318 0.133 0.377 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: 228 Number of extensions: 9 Number of successful extensions: 2 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: 279 Length adjustment: 25 Effective length of query: 238 Effective length of database: 254 Effective search space: 60452 Effective search space used: 60452 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 (21.7 bits) S2: 47 (22.7 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