Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate WP_156477079.1 CAter10_RS07860 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773 (244 letters) >NCBI__GCF_001584165.1:WP_156477079.1 Length = 255 Score = 230 bits (586), Expect = 2e-65 Identities = 133/248 (53%), Positives = 167/248 (67%), Gaps = 10/248 (4%) Query: 1 MISIKSINKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 60 MISI+++ K +GD VL D S E+ KG V+ + GPSGSGKSTL++C+N L G + V Sbjct: 1 MISIRNLKKCFGDNVVLKDISLEISKGSVVAMIGPSGSGKSTLLRCINLLTIPDAGTVNV 60 Query: 61 DGTSIA-DPK-TNLPK------LRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEE 112 G SIA D K T LPK RS+ GMVFQHF LFPH+T+ +N+ + VL K++ Sbjct: 61 GGQSIAFDGKHTKLPKAKDLAHFRSKTGMVFQHFNLFPHMTVRQNVMEGMVTVLKIPKQD 120 Query: 113 ATKKGLQLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMV 172 A LL+RVGLS A +PG LSGGQ+QRVAIARALAM P VMLFDE TSALDPE+V Sbjct: 121 ARITADALLQRVGLSDRADAYPGMLSGGQKQRVAIARALAMKPDVMLFDEATSALDPELV 180 Query: 173 NEVLDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAE 232 EVL V+ LA +GMTM+ VTHE+ FAR+VAD+VIFM G ++E C D N E Sbjct: 181 GEVLSVIRSLAADGMTMILVTHEIAFAREVADQVIFMRDGVVVE-CGPPSVVID-NPEKE 238 Query: 233 RTQHFLNK 240 T+ FL++ Sbjct: 239 ATRSFLSR 246 Lambda K H 0.321 0.136 0.394 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: 192 Number of extensions: 10 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: 244 Length of database: 255 Length adjustment: 24 Effective length of query: 220 Effective length of database: 231 Effective search space: 50820 Effective search space used: 50820 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 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