Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate PfGW456L13_4639 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773 (244 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4639 Length = 254 Score = 222 bits (566), Expect = 5e-63 Identities = 122/249 (48%), Positives = 170/249 (68%), Gaps = 13/249 (5%) Query: 2 ISIKSINKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVVD 61 ++I+ ++K YGD +VL S + K G+VI + G SGSGKST ++C+N LE G + +D Sbjct: 4 LTIEGLHKSYGDHEVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQPNDGAMSLD 63 Query: 62 GTSIADPK----------TNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKE 111 G +I K L ++R+R+ MVFQHF L+ H+T+ EN+T+A +VLG ++ Sbjct: 64 GQNIRMIKDRHGMHVADANELQRIRTRLAMVFQHFNLWSHMTVLENITMAPRRVLGCDRK 123 Query: 112 EATKKGLQLLERVGLSAH-AHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPE 170 EA + + L++VGL+ A ++P LSGGQQQRVAIARALAM+P VMLFDEPTSALDPE Sbjct: 124 EAEDRARRYLDKVGLAPRVADQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALDPE 183 Query: 171 MVNEVLDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINAR 230 +V EVL V+ LA EG TM+ VTHEM FARKV+ +V+F+ QG + E+ EE G N + Sbjct: 184 LVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSSQVLFLHQGLVEEEGAPEEVLG--NPK 241 Query: 231 AERTQHFLN 239 +ER + FL+ Sbjct: 242 SERLKQFLS 250 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: 13 Number of successful extensions: 3 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: 254 Length adjustment: 24 Effective length of query: 220 Effective length of database: 230 Effective search space: 50600 Effective search space used: 50600 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