Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate Ac3H11_3327 Glutamine transport ATP-binding protein GlnQ (TC 3.A.1.3.2)
Query= TCDB::P0AAG3 (241 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3327 Length = 249 Score = 261 bits (666), Expect = 1e-74 Identities = 134/238 (56%), Positives = 170/238 (71%) Query: 2 ITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVD 61 I + V K +G QVL D ST GEV V+ G SGSGKSTL++ +N LEP G IT+ Sbjct: 10 IVVDRVCKSFGAHQVLKDVSTTFNTGEVTVIIGASGSGKSTLLRAINRLEPHDSGTITIG 69 Query: 62 GIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALKLL 121 G V D + L K RS VGMVFQ F LF H+S+++N+TLA ++ + A +AL LL Sbjct: 70 GEPVGDDQHLLQKQRSEVGMVFQQFNLFGHMSVLDNVTLAPRRIRHTPRTQANAQALALL 129 Query: 122 ERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVMVE 181 RVG+ HA+K+P QLSGGQQQRVAIARAL M P MLFDEPTSALDPEM+ EVLDVM E Sbjct: 130 TRVGMQDHAHKYPWQLSGGQQQRVAIARALAMQPKVMLFDEPTSALDPEMVQEVLDVMRE 189 Query: 182 LANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKDFLAKI 239 LA GMTM+VVTHEMGFAR+V++RV+F D+G+I D+P FF++P +DR + F+ ++ Sbjct: 190 LARGGMTMIVVTHEMGFAREVSDRVMFFDQGRIAHDAPPAEFFNNPANDRIRAFIGRM 247 Lambda K H 0.320 0.135 0.383 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: 185 Number of extensions: 6 Number of successful extensions: 1 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: 241 Length of database: 249 Length adjustment: 24 Effective length of query: 217 Effective length of database: 225 Effective search space: 48825 Effective search space used: 48825 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: 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