Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_000942251.1 HK29_RS01475 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >NCBI__GCF_000382825.1:WP_000942251.1 Length = 254 Score = 239 bits (609), Expect = 5e-68 Identities = 126/245 (51%), Positives = 171/245 (69%), Gaps = 7/245 (2%) Query: 14 IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73 ++Q++ + K +G+ VL+D+NL V QG+ +V+ GPSGSGK+T +RCLN LE+ GR+ + Sbjct: 1 MLQVEHIAKTFGERQVLEDVNLQVNQGDVVVILGPSGSGKTTFLRCLNHLEKADSGRLTL 60 Query: 74 DGVELTNDL-----KQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEE 128 G T DL K I IR++ VFQH+NLF + T L+N + RK+PK +A + Sbjct: 61 AGK--TYDLAKLSKKDILEIRQKTAFVFQHYNLFANKTALENILEGLIVARKVPKEEALK 118 Query: 129 IAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEV 188 A LE+V + YP QLSGGQQQR+ IARA+ +KP+++L DEPTSALDPE+V +V Sbjct: 119 RAESALEKVGLLAYKDYYPSQLSGGQQQRIGIARAIAVKPEVILLDEPTSALDPELVGDV 178 Query: 189 LDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLF 248 LD + LA +G+TM+ VTHEMGFAR VAN VIFMD G IVE+ P+DFF PQ +RTK F Sbjct: 179 LDVLKQLAGEGVTMVVVTHEMGFARDVANHVIFMDGGRIVEENNPHDFFSRPQEERTKQF 238 Query: 249 LSQIL 253 L++IL Sbjct: 239 LARIL 243 Lambda K H 0.322 0.137 0.407 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: 199 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: 254 Length of database: 254 Length adjustment: 24 Effective length of query: 230 Effective length of database: 230 Effective search space: 52900 Effective search space used: 52900 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 (21.9 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