Align ABC transporter related (characterized, see rationale)
to candidate SM_b21138 SM_b21138 amino acid ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__Smeli:SM_b21138 Length = 255 Score = 248 bits (632), Expect = 1e-70 Identities = 123/248 (49%), Positives = 181/248 (72%), Gaps = 1/248 (0%) Query: 9 LSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLA 68 L ++++HK +G VLKG+ QG+VISI+G+SGSGK+T LRC+N+LE G++++ Sbjct: 5 LEIRDLHKRYGTVEVLKGVDCSMRQGEVISIIGSSGSGKTTMLRCINMLEEFQGGTIAID 64 Query: 69 GEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSR 128 G+E+ + G G + R++ R R+ GM FQ FNL+ HMT N++ G ++V+K SR Sbjct: 65 GQEIGYETAG-GARRRKPEREIARQRALTGMAFQQFNLFPHMTAAANVMLGLVKVKKMSR 123 Query: 129 AESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPE 188 E+ AE L +VGL ++ HYP LSGGQQQRVAIARA+AM+PK+MLFDE TSALDPE Sbjct: 124 DEARVLAEKWLDRVGLLSRKDHYPGQLSGGQQQRVAIARAIAMNPKLMLFDEVTSALDPE 183 Query: 189 LVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSD 248 LV EVL+V++ LAE+G +ML+VTHEM FA VS+RV+F++QG++ +G P E+F++ +++ Sbjct: 184 LVNEVLQVIKGLAEDGMSMLIVTHEMRFAYEVSSRVIFMNQGRIGEEGHPREMFLKPRTE 243 Query: 249 RFRQFVSS 256 R +F+ + Sbjct: 244 RLAEFLKT 251 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: 187 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: 255 Length adjustment: 24 Effective length of query: 239 Effective length of database: 231 Effective search space: 55209 Effective search space used: 55209 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