Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA
Query= reanno::pseudo5_N2C3_1:AO356_09895 (257 letters) >NCBI__GCF_000013785.1:WP_011911265.1 Length = 279 Score = 262 bits (669), Expect = 6e-75 Identities = 137/255 (53%), Positives = 180/255 (70%), Gaps = 1/255 (0%) Query: 2 AQATPALEIRNLHKRYGQLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPNQ 61 A A P + ++ KRYG+L VL+G+ L ++G+ ++I+G SGSGKST LR + LE + Sbjct: 20 APAQPMVRFASVTKRYGELTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLRVLMTLEGIDD 79 Query: 62 GQILVAGEELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPRR 121 G I V GE L +G LV A+ + + R+R ++G VFQ+FNL+PHM+ L N++EAP + Sbjct: 80 GLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQ 139 Query: 122 VLGQSKAEAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEPT 181 VLG SK EA E AE LLA VG+ DK +PA+LSGGQQQR AIAR LAM+PKV+LFDE T Sbjct: 140 VLGLSKREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVT 199 Query: 182 SALDPEMVQEVLSVIRALAE-EGRTMLLVTHEMGFARQVSSEVVFLHQGLVEEQGSPQQV 240 SALDPE+ EVLSVIR L E TML+VTH+MGFAR+ + V F HQG + EQGSP + Sbjct: 200 SALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDAL 259 Query: 241 FENPLSARCKQFMSS 255 F NP R ++F+S+ Sbjct: 260 FNNPQEDRTREFLSA 274 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: 181 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: 279 Length adjustment: 25 Effective length of query: 232 Effective length of database: 254 Effective search space: 58928 Effective search space used: 58928 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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