Align ABC transporter related (characterized, see rationale)
to candidate H281DRAFT_00221 H281DRAFT_00221 amino acid ABC transporter ATP-binding protein, PAAT family
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__Burk376:H281DRAFT_00221 Length = 259 Score = 313 bits (802), Expect = 2e-90 Identities = 157/253 (62%), Positives = 198/253 (78%), Gaps = 1/253 (0%) Query: 4 TAPVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDG 63 T L V +HK +GD+ VLKG++L A+ GDVIS++G+SGSGKST LRC+N LE P+ G Sbjct: 3 TTKQKLFVDELHKQYGDNEVLKGVTLKANAGDVISVIGSSGSGKSTMLRCINFLEQPNAG 62 Query: 64 SVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRV 123 + + GEE++ + +G L+ SD +Q+ RVR++L MVFQ+FNLWSHM VLEN++E P+ V Sbjct: 63 RIFVDGEEVRTQIAKNGALRVSDPKQLQRVRTKLSMVFQHFNLWSHMNVLENIVEAPVNV 122 Query: 124 QKRSRAESVEEAEALLAKVGLAEK-RGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPT 182 R E+ + A L KVGLA + YP+HLSGGQQQRVAIARALAMHP VMLFDEPT Sbjct: 123 LGLKRKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMHPDVMLFDEPT 182 Query: 183 SALDPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVF 242 SALDPELVGEVL+VM++LAEEGRTM+VVTHEM FAR+VSN VMFLHQG+VE +G PDEVF Sbjct: 183 SALDPELVGEVLKVMQTLAEEGRTMIVVTHEMAFARNVSNHVMFLHQGRVEEEGHPDEVF 242 Query: 243 VECKSDRFRQFVS 255 +S+R +QF+S Sbjct: 243 RNTRSERLKQFLS 255 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: 233 Number of extensions: 5 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: 259 Length adjustment: 25 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 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 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