Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate Ac3H11_3327 Glutamine transport ATP-binding protein GlnQ (TC 3.A.1.3.2)
Query= reanno::pseudo5_N2C3_1:AO356_00465 (263 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3327 Length = 249 Score = 229 bits (583), Expect = 6e-65 Identities = 120/253 (47%), Positives = 161/253 (63%), Gaps = 10/253 (3%) Query: 6 TPSNTQPLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEF 65 T P + + + K +G +VLK V + G V +IG+SGSGK+TLLR +N LE Sbjct: 2 TTGQATPFIVVDRVCKSFGAHQVLKDVSTTFNTGEVTVIIGASGSGKSTLLRAINRLEPH 61 Query: 66 QGGQIVLDGESIGYDDIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLGLL 125 G I + GE +G D + L+ + R+ GM FQQFNLF H++ L NVTL Sbjct: 62 DSGTITIGGEPVGDD----------QHLLQKQRSEVGMVFQQFNLFGHMSVLDNVTLAPR 111 Query: 126 KVKKLPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEV 185 +++ P+ +A A A L RVG+ + +P QLSGGQQQRVAIARA+AM P +MLFDE Sbjct: 112 RIRHTPRTQANAQALALLTRVGMQDHAHKYPWQLSGGQQQRVAIARALAMQPKVMLFDEP 171 Query: 186 TSALDPELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKEL 245 TSALDPE+V EVL+V++ LA GMTM++VTHEM FA EVSD+++F +QGRI PP E Sbjct: 172 TSALDPEMVQEVLDVMRELARGGMTMIVVTHEMGFAREVSDRVMFFDQGRIAHDAPPAEF 231 Query: 246 FERPQSPRLAEFL 258 F P + R+ F+ Sbjct: 232 FNNPANDRIRAFI 244 Lambda K H 0.320 0.138 0.392 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: 172 Number of extensions: 5 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: 263 Length of database: 249 Length adjustment: 24 Effective length of query: 239 Effective length of database: 225 Effective search space: 53775 Effective search space used: 53775 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: 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