Align ABC transporter related (characterized, see rationale)
to candidate H281DRAFT_05297 H281DRAFT_05297 amino acid ABC transporter ATP-binding protein, PAAT family
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__Burk376:H281DRAFT_05297 Length = 287 Score = 261 bits (668), Expect = 9e-75 Identities = 135/252 (53%), Positives = 177/252 (70%), Gaps = 1/252 (0%) Query: 9 LSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLA 68 + V+++ K FG+ VL+G+ L+ + +V+ I+G SGSGKST LRCL LET D G V + Sbjct: 23 IQVRDLRKRFGEVEVLRGVDLEIARSEVVCIIGPSGSGKSTLLRCLAALETYDHGDVRIE 82 Query: 69 GEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSR 128 GE L R +GK + + +++RVR +GMVFQ FNLW HMT L N++E +RV+ Sbjct: 83 GELLGYSER-NGKRVRATQGEINRVRRNVGMVFQQFNLWPHMTALGNVMEALLRVRHLPH 141 Query: 129 AESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPE 188 A++ A A+L VGL+ K YPA LSGGQQQRVAIARALAM P +MLFDEPTSALDPE Sbjct: 142 ADARRRANAMLETVGLSNKGDAYPAKLSGGQQQRVAIARALAMEPHIMLFDEPTSALDPE 201 Query: 189 LVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSD 248 LVGEVL+VM+ LA +G TM VVTHEMGFA V+++VMF+ QG++ G P EVF + Sbjct: 202 LVGEVLQVMKQLARDGMTMAVVTHEMGFAAQVADKVMFIDQGRIAVQGQPREVFHDAGQP 261 Query: 249 RFRQFVSSHQDR 260 R RQF+ ++ DR Sbjct: 262 RLRQFLQNYFDR 273 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: 224 Number of extensions: 4 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: 287 Length adjustment: 25 Effective length of query: 238 Effective length of database: 262 Effective search space: 62356 Effective search space used: 62356 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