Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate CCNA_00294 CCNA_00294 phosphate transport ATP-binding protein pstB
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Caulo:CCNA_00294 Length = 274 Score = 143 bits (361), Expect = 3e-39 Identities = 97/259 (37%), Positives = 142/259 (54%), Gaps = 16/259 (6%) Query: 2 TSPTAPLISFDQLQKN-----FGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNR 56 TS AP + +++ +G Q L V +I K V + IGPSGCGKSTFLRC+NR Sbjct: 15 TSTAAPATADPKIKARGVKVFYGDKQALFDVDLDIPAKSVTAFIGPSGCGKSTFLRCINR 74 Query: 57 L-EPISGGRLEVAGVDLSGAKIDQKHLRQ--LRVRVGMVFQHFNLFPHLTVLQNLLLAPR 113 + + I R+E + + GA ++ K + LR RVGMVFQ N FP T+ +N+ PR Sbjct: 75 MNDTIPSARVE-GSILIDGADVNAKSVDPVVLRSRVGMVFQKPNPFPK-TIFENVAYGPR 132 Query: 114 -KVLRIPMAEAKDRALTYLDKVGLGTKADNYPDQ----LSGGQKQRVAIARGLCMKPEIL 168 L AE + + L K GL + + Q LSGGQ+QR+ IAR + + PE++ Sbjct: 133 IHGLATGKAELEAIVESSLKKAGLWNEVADRLHQPGTGLSGGQQQRLVIARAIAVSPEVI 192 Query: 169 LFDEPTSALDPELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEG 228 L DEP SALDP ++ ++ +L + + +VTH M A VS R FF+ G + E G Sbjct: 193 LMDEPCSALDPIATAKIEELIDELRSQ-FCIVIVTHSMAQAARVSQRTAFFHLGKLVESG 251 Query: 229 DPNEVFRNPKSDRLRAFLS 247 E+F NP+ R + +++ Sbjct: 252 PTEEMFTNPRDSRTQDYIT 270 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: 177 Number of extensions: 8 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: 274 Length adjustment: 25 Effective length of query: 227 Effective length of database: 249 Effective search space: 56523 Effective search space used: 56523 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