Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate WP_076948807.1 C1M55_RS07375 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09895 (257 letters) >NCBI__GCF_002893965.1:WP_076948807.1 Length = 261 Score = 250 bits (639), Expect = 2e-71 Identities = 128/248 (51%), Positives = 171/248 (68%), Gaps = 1/248 (0%) Query: 7 ALEIRNLHKRYGQLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPNQGQILV 66 A+E R +HK +G LEVL GV L R G+V ILG SGSGKST LR +N LE ++G + + Sbjct: 12 AVEARGIHKSFGTLEVLAGVDLLVRKGEVTVILGPSGSGKSTLLRTLNHLEKVDRGTVRI 71 Query: 67 AGEELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPRRVLGQS 126 GE + + K L ++I + RS IGFVFQNFNL+PH++ L+N++EAP + Sbjct: 72 DGELIGYRR-KGNRLHELRDREILKQRSHIGFVFQNFNLFPHLTALENVVEAPLSAQKRD 130 Query: 127 KAEAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEPTSALDP 186 + E A ALL +VG+ +K YP +LSGGQQQR AIAR LA++P VILFDEPTSALDP Sbjct: 131 RDEVYREARALLERVGVGEKADEYPRQLSGGQQQRVAIARALALRPAVILFDEPTSALDP 190 Query: 187 EMVQEVLSVIRALAEEGRTMLLVTHEMGFARQVSSEVVFLHQGLVEEQGSPQQVFENPLS 246 E+V EVL V+ LA +G T+++VTHE+GFAR+V+ VF+ G++ EQG P QV +NP+ Sbjct: 191 ELVGEVLEVLAQLARDGATLVIVTHEVGFAREVADTAVFMDGGVIVEQGPPSQVIDNPVH 250 Query: 247 ARCKQFMS 254 R K F+S Sbjct: 251 ERTKAFLS 258 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: 187 Number of extensions: 6 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: 261 Length adjustment: 24 Effective length of query: 233 Effective length of database: 237 Effective search space: 55221 Effective search space used: 55221 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 Sep 24 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