Align ABC transporter related (characterized, see rationale)
to candidate WP_091519694.1 BM253_RS04260 phosphate ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >NCBI__GCF_900115115.1:WP_091519694.1 Length = 248 Score = 129 bits (325), Expect = 5e-35 Identities = 88/255 (34%), Positives = 145/255 (56%), Gaps = 19/255 (7%) Query: 9 LSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLET--PD---DG 63 LS +N++ SFG+ HVLK IS+ + ++ +++G SG GKST LR N + PD +G Sbjct: 5 LSAENLNISFGEKHVLKNISVSFAEHEITALIGPSGCGKSTLLRSFNRMHDLFPDAKING 64 Query: 64 SVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRV 123 S+ L EEL + R V +R ++GMVFQ N + ++ EN+ G Sbjct: 65 SLHL--EELDLYDR---------HVPVTEIRKRIGMVFQKANPFPK-SIYENIAYGLKIN 112 Query: 124 QKRSRAESVEEAEALLAKVGLAEKRGHYPA-HLSGGQQQRVAIARALAMHPKVMLFDEPT 182 E V++A + PA LSGGQQQR+ IARA+A+ P+V+L DEP Sbjct: 113 NLPCNKEVVQKALEEAYLWDEVKNDLKMPATRLSGGQQQRLCIARAVALRPEVILMDEPC 172 Query: 183 SALDPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVF 242 SALDP ++ +++ L ++ T+++VTH M A+ ++++ +F++ G+V+ +GT DE+F Sbjct: 173 SALDPVSTLKIEELIKHLKKK-YTIVIVTHNMQQAQRIADKTVFMYLGEVKEEGTTDEIF 231 Query: 243 VECKSDRFRQFVSSH 257 K++ ++S + Sbjct: 232 NHPKNEMTANYISGY 246 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: 140 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: 248 Length adjustment: 24 Effective length of query: 239 Effective length of database: 224 Effective search space: 53536 Effective search space used: 53536 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 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