Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate Ac3H11_3327 Glutamine transport ATP-binding protein GlnQ (TC 3.A.1.3.2)
Query= TCDB::P73721 (252 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3327 Length = 249 Score = 251 bits (641), Expect = 1e-71 Identities = 133/248 (53%), Positives = 170/248 (68%), Gaps = 3/248 (1%) Query: 2 TSPTAPLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPIS 61 T P I D++ K+FGA QVL+ V+ +V IIG SG GKST LR +NRLEP Sbjct: 3 TGQATPFIVVDRVCKSFGAHQVLKDVSTTFNTGEVTVIIGASGSGKSTLLRAINRLEPHD 62 Query: 62 GGRLEVAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMA 121 G + + G + DQ L++ R VGMVFQ FNLF H++VL N+ LAPR++ P Sbjct: 63 SGTITIGGEPVGD---DQHLLQKQRSEVGMVFQQFNLFGHMSVLDNVTLAPRRIRHTPRT 119 Query: 122 EAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPEL 181 +A +AL L +VG+ A YP QLSGGQ+QRVAIAR L M+P+++LFDEPTSALDPE+ Sbjct: 120 QANAQALALLTRVGMQDHAHKYPWQLSGGQQQRVAIARALAMQPKVMLFDEPTSALDPEM 179 Query: 182 VGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDR 241 V EVL+VM++LA GMTM VVTHEM FAREVS+RV FF+QG I + P E F NP +DR Sbjct: 180 VQEVLDVMRELARGGMTMIVVTHEMGFAREVSDRVMFFDQGRIAHDAPPAEFFNNPANDR 239 Query: 242 LRAFLSRI 249 +RAF+ R+ Sbjct: 240 IRAFIGRM 247 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: 204 Number of extensions: 4 Number of successful extensions: 2 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: 249 Length adjustment: 24 Effective length of query: 228 Effective length of database: 225 Effective search space: 51300 Effective search space used: 51300 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: 46 (22.3 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