Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate PP_1068 PP_1068 glutamate / aspartate ABC transporter - ATP binding subunit
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__Putida:PP_1068 Length = 256 Score = 279 bits (713), Expect = 5e-80 Identities = 141/242 (58%), Positives = 176/242 (72%), Gaps = 2/242 (0%) Query: 14 IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73 +I ++ VNKWYG F VL D + VK+GE +V+CGPSGSGKST I+C+N LE Q+G IVV Sbjct: 13 MISIKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 72 Query: 74 DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133 DG + + + +R VGMVFQHF LFPHLTI +N T+A V + +A + + Sbjct: 73 DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQRKVLGRSEAEATKKGLAL 132 Query: 134 LERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMI 193 L+RV + A K+PGQLSGGQQQRVAIARAL M P +MLFDEPTSALDPEMV EVLD M+ Sbjct: 133 LDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSEVLDVMV 192 Query: 194 GLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFF--DNPQNDRTKLFLSQ 251 LA++GMTM+CVTHEMGFAR VANRVIFMDKG I+E +FF + ++ RT+ LS+ Sbjct: 193 QLAQEGMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFFGDQSARDQRTQHLLSK 252 Query: 252 IL 253 IL Sbjct: 253 IL 254 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: 203 Number of extensions: 3 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: 256 Length adjustment: 24 Effective length of query: 230 Effective length of database: 232 Effective search space: 53360 Effective search space used: 53360 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 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