Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 179 bits (455), Expect = 5e-50 Identities = 101/240 (42%), Positives = 147/240 (61%), Gaps = 5/240 (2%) Query: 1 MIELKNVNKYY--GTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEV 58 MI ++V+K Y G H L ++LSVK GE +IG SG+GKST IR +NGLE S+G+V Sbjct: 1 MITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQV 60 Query: 59 VVN--NLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETA 116 +V+ ++ + R+ M+FQHFNL TV QN+ P+KL + E + Sbjct: 61 IVDGDDVAALGVAGLRALRRRVGMIFQHFNLLSGKTVAQNVAF-PLKLAGRPAAEVKART 119 Query: 117 FKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLD 176 + L+ VGL A YPA LSGGQ+QRV IAR+L T +L DE TSALDPET +++LD Sbjct: 120 AELLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILD 179 Query: 177 VMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFL 236 ++ ++ + T+V++THEM + V DR+ ++ G +VEE E F +P ++ AR F+ Sbjct: 180 LIAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARRFV 239 Lambda K H 0.317 0.133 0.372 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: 148 Number of extensions: 9 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: 242 Length of database: 332 Length adjustment: 26 Effective length of query: 216 Effective length of database: 306 Effective search space: 66096 Effective search space used: 66096 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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