Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_041670877.1 RSPH17029_RS18130 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >NCBI__GCF_000015985.1:WP_041670877.1 Length = 242 Score = 342 bits (876), Expect = 5e-99 Identities = 162/240 (67%), Positives = 201/240 (83%) Query: 14 IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73 +I+M V+KWYG F VL D++L+V++GER+V+CGPSGSGKST IRC+NRLE HQ G+I V Sbjct: 1 MIRMSHVSKWYGHFQVLHDVSLDVRKGERVVVCGPSGSGKSTLIRCINRLEVHQSGQIFV 60 Query: 74 DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133 G+E+T+++K I+ IRR +GMVFQ+FNLFPHLT+L+N TL PM R+M K AE++AMH+ Sbjct: 61 KGLEMTDNVKNIDTIRRHIGMVFQNFNLFPHLTVLENLTLGPMLTRQMKKSAAEDLAMHF 120 Query: 134 LERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMI 193 L +VRIPEQ+ KYP QLSGGQQQRVAIAR+LCM+P+IMLFDEPTSALDPEM+KEVLDTMI Sbjct: 121 LRKVRIPEQSGKYPLQLSGGQQQRVAIARSLCMEPEIMLFDEPTSALDPEMIKEVLDTMI 180 Query: 194 GLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQIL 253 LAE GMTM+ VTHEMGFARTVA+ V+FM G VE P +FF NP+ +RT+ FL QIL Sbjct: 181 ELAESGMTMIVVTHEMGFARTVADNVVFMADGRKVESGPPEEFFGNPREERTRAFLDQIL 240 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: 226 Number of extensions: 8 Number of successful extensions: 1 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: 242 Length adjustment: 24 Effective length of query: 230 Effective length of database: 218 Effective search space: 50140 Effective search space used: 50140 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: 46 (22.3 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