Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_16275 (244 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 199 bits (506), Expect = 6e-56 Identities = 115/242 (47%), Positives = 155/242 (64%), Gaps = 7/242 (2%) Query: 1 MISIKNVNKWY--GDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDV 58 MI+ ++V+K Y G L+ S VK GEV V G SG+GKSTLI+ +N LE G V Sbjct: 1 MITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQV 60 Query: 59 VVDGTSIAD-PKTDLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKG 117 +VDG +A L LR RVGM+FQHF L T+ +N+ +K+ GR E + Sbjct: 61 IVDGDDVAALGVAGLRALRRRVGMIFQHFNLLSGKTVAQNVAFP-LKLAGRPAAEVKART 119 Query: 118 LQLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLD 177 +LLERVGLSAHA K+P QLSGGQ+QRV IARALA +P V+L DE TSALDPE ++LD Sbjct: 120 AELLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILD 179 Query: 178 VMVQLANE-GMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARSDRAQH 236 ++ L E G+T++ +THEM R+V DRV +D G+++E+ EE F ++ SD A+ Sbjct: 180 LIAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVF--LHPASDTARR 237 Query: 237 FL 238 F+ Sbjct: 238 FV 239 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: 214 Number of extensions: 12 Number of successful extensions: 4 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: 332 Length adjustment: 26 Effective length of query: 218 Effective length of database: 306 Effective search space: 66708 Effective search space used: 66708 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 (21.8 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