Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 183 bits (464), Expect = 4e-51 Identities = 109/242 (45%), Positives = 144/242 (59%), Gaps = 6/242 (2%) Query: 8 LISFDQLQKNF--GALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRL 65 +I+F + K + G L GV+ + +V +IG SG GKST +R +N LE S G++ Sbjct: 1 MITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQV 60 Query: 66 EVAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKD 125 V G D+ A + LR LR RVGM+FQHFNL TV QN+ P K+ P AE K Sbjct: 61 IVDGDDV--AALGVAGLRALRRRVGMIFQHFNLLSGKTVAQNVAF-PLKLAGRPAAEVKA 117 Query: 126 RALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEV 185 R L++VGL A YP QLSGGQKQRV IAR L P++LL DE TSALDPE ++ Sbjct: 118 RTAELLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQI 177 Query: 186 LNVMKQLAEE-GMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRA 244 L+++ L E G+T+ ++THEM R V +RV + G + EEG EVF +P SD R Sbjct: 178 LDLIAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARR 237 Query: 245 FL 246 F+ Sbjct: 238 FV 239 Lambda K H 0.321 0.139 0.397 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: 209 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: 252 Length of database: 332 Length adjustment: 26 Effective length of query: 226 Effective length of database: 306 Effective search space: 69156 Effective search space used: 69156 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: 48 (23.1 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