Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate 200225 SO1042 amino acid ABC transporter, ATP-binding protein (NCBI ptt file)
Query= reanno::pseudo5_N2C3_1:AO356_09895 (257 letters) >FitnessBrowser__MR1:200225 Length = 241 Score = 256 bits (655), Expect = 2e-73 Identities = 132/247 (53%), Positives = 174/247 (70%), Gaps = 11/247 (4%) Query: 8 LEIRNLHKRYGQLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPNQGQILVA 67 + I NLHK YG VLKG++ R G+V+S++G SGSGKSTFLRCINLLENP QG I + Sbjct: 2 INITNLHKSYGDNAVLKGINEHIRQGEVVSVIGPSGSGKSTFLRCINLLENPTQGDIEIE 61 Query: 68 GEELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPRRVLGQSK 127 G+ + K A +++LR ++G VFQNFNL+PH +VL NI AP + ++ Sbjct: 62 GQSITAKDAC-----------VDKLRQKVGMVFQNFNLFPHKTVLQNITLAPVSLKLMTQ 110 Query: 128 AEAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEPTSALDPE 187 AEA A ALL +VG+ DK +AYP+ LSGGQ+QR AIAR LAM+P ++LFDEPTSALDPE Sbjct: 111 AEADNKALALLTQVGLQDKANAYPSSLSGGQKQRVAIARALAMEPDLMLFDEPTSALDPE 170 Query: 188 MVQEVLSVIRALAEEGRTMLLVTHEMGFARQVSSEVVFLHQGLVEEQGSPQQVFENPLSA 247 MV +VL V++ LA++G TM++VTHEMGFAR VS V+F+ G V E P+++F P A Sbjct: 171 MVGDVLDVMKDLAQKGMTMVIVTHEMGFARDVSDRVIFMDGGYVVESNIPEELFTRPKEA 230 Query: 248 RCKQFMS 254 R + F+S Sbjct: 231 RTQSFLS 237 Lambda K H 0.317 0.132 0.363 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: 183 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: 257 Length of database: 241 Length adjustment: 24 Effective length of query: 233 Effective length of database: 217 Effective search space: 50561 Effective search space used: 50561 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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