Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate 206400 DVU0968 amino acid ABC transporter, ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09895 (257 letters) >MicrobesOnline__882:206400 Length = 246 Score = 232 bits (591), Expect = 6e-66 Identities = 128/252 (50%), Positives = 172/252 (68%), Gaps = 17/252 (6%) Query: 8 LEIRNLHKRY---GQLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPNQGQI 64 + RN++K + +L L+ VSL G+V+ I+G SGSGKSTFLRC+N LE + G+I Sbjct: 4 ISARNVNKYFYVPEELHALRDVSLDVAPGEVVVIIGPSGSGKSTFLRCLNRLEYADSGEI 63 Query: 65 LVAGEELKLKAAKNGELVAADGK-QINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPRRVL 123 L+ G ++ D K +IN +R+E+G VFQ+FNL+PH+SVL+N+ A V Sbjct: 64 LIEGRDI------------LDPKCEINEVRAEVGMVFQSFNLFPHLSVLENVALAQMTVR 111 Query: 124 GQSKAEAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEPTSA 183 +S+AE+ + LL KVGIADK YP +LSGGQQQR AIAR+LAM PK++LFDEPTSA Sbjct: 112 KRSRAESEKKGMELLTKVGIADKHAVYPDQLSGGQQQRVAIARSLAMDPKIMLFDEPTSA 171 Query: 184 LDPEMVQEVLSVIRALAEEGRTMLLVTHEMGFARQVSSEVVFLHQGLVEEQGSPQQVFEN 243 LDPEMV EVL V+R LA EG TM++VTHEMGFAR+V+ VVF+ G + E +P+ +F Sbjct: 172 LDPEMVGEVLDVMRNLAREGMTMVVVTHEMGFAREVADRVVFMDHGAILEIATPKDLFTT 231 Query: 244 PLS-ARCKQFMS 254 + R K F+S Sbjct: 232 GATHDRTKLFLS 243 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: 179 Number of extensions: 7 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: 246 Length adjustment: 24 Effective length of query: 233 Effective length of database: 222 Effective search space: 51726 Effective search space used: 51726 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