Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate 3606891 Dshi_0321 ABC transporter related (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773 (244 letters) >FitnessBrowser__Dino:3606891 Length = 258 Score = 298 bits (764), Expect = 5e-86 Identities = 150/243 (61%), Positives = 184/243 (75%), Gaps = 2/243 (0%) Query: 2 ISIKSINKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVVD 61 I I +NKWYG F VL D + V +GE IV+CGPSGSGKSTLI+C+NALE Q G I VD Sbjct: 18 IEIDKMNKWYGQFHVLRDINLTVYRGERIVICGPSGSGKSTLIRCINALEEHQAGSITVD 77 Query: 62 GTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQLL 121 GT ++ N+ +RS VGM FQHF LFPHLTI EN T+A I V K+EA + L Sbjct: 78 GTLLSSDLKNIDTIRSEVGMCFQHFNLFPHLTILENCTLAPIWVRKTPKKEAEATAMHFL 137 Query: 122 ERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMVQ 181 E+V + A+K+PGQLSGGQQQRVAIAR+L M P +MLFDEPTSALDPEM+ EVLD M++ Sbjct: 138 EKVKIPDQANKYPGQLSGGQQQRVAIARSLCMRPRIMLFDEPTSALDPEMIKEVLDTMIE 197 Query: 182 LAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAERTQHFLNKI 241 LA EGMTM+CVTHEMGFAR+VA+RVIFMD G+I+E + EEFFG N +++RT+ FL++I Sbjct: 198 LAEEGMTMICVTHEMGFARQVANRVIFMDAGQIVEQNEPEEFFG--NPQSDRTKLFLSQI 255 Query: 242 LQH 244 L H Sbjct: 256 LGH 258 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: 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: 244 Length of database: 258 Length adjustment: 24 Effective length of query: 220 Effective length of database: 234 Effective search space: 51480 Effective search space used: 51480 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 17 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