Align ABC transporter related (characterized, see rationale)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >NCBI__GCF_000017185.1:WP_011974043.1 Length = 238 Score = 149 bits (375), Expect = 7e-41 Identities = 90/229 (39%), Positives = 140/229 (61%), Gaps = 16/229 (6%) Query: 9 LSVKNIHKSFGDHH----VLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGS 64 + KNI K +G VL+GI+L +G+ ++I+G SG GKST L L LL+ P+ G Sbjct: 18 IEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKGM 77 Query: 65 VSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQ 124 V + G++ M D R V R R G +FQ FNL + +T LEN +E P+ + Sbjct: 78 VYIKGKKTTMFSEND--------RAVFR-RKISGFIFQQFNLINTLTALEN-VELPLVLD 127 Query: 125 KRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSA 184 ++++ +++A+ LL + L + +YP LSGGQQQRVAIARAL+ +PK++ DEPT Sbjct: 128 EKNKNYRIKKAKKLLKIINLGHRENYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTGN 187 Query: 185 LDPELVGEVLRVMRSLAE-EGRTMLVVTHEMGFARHVSNRVMFLHQGQV 232 LD + EV+ +++ L E EG T+++VTHE FA++ S R++ + G++ Sbjct: 188 LDSKNSREVMDILKELNEKEGITVIMVTHEPEFAKYAS-RIINMKDGEI 235 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: 141 Number of extensions: 10 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: 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 (21.7 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