Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate Ac3H11_4180 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4180 Length = 367 Score = 228 bits (581), Expect = 2e-64 Identities = 126/305 (41%), Positives = 187/305 (61%), Gaps = 14/305 (4%) Query: 9 IRKRY-GEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIGERSV 67 ++K Y GE ++ +D+ ++ GEFL LLG SG GK+T L ++AG P+ GDIL+ + + Sbjct: 14 VQKTYDGEQLVVRALDLDIQRGEFLSLLGPSGSGKTTTLMMLAGFESPTAGDILLDGKQI 73 Query: 68 LGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQIENLL 127 P R+ MVFQ+YAL+P+L+V N+ + L +R+VP+AE + V+ ++++ + Sbjct: 74 TRTPPHKRNFGMVFQNYALFPHLTVGENVAYPLTVRKVPKAEQAERVKKALDMVRLTGMA 133 Query: 128 DRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQMLRTTV 187 DR P++LSGGQ+QRVA+ RALV NPQ+ L DEPL LD +LR M+ ELK LH+ L T Sbjct: 134 DRLPARLSGGQQQRVALARALVFNPQLVLMDEPLGALDKQLREHMQIELKELHRQLGVTF 193 Query: 188 VYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNILDAEMT 247 VYVTHDQ EA+T++ R+AV +G I+QLA + +Y+ P+ +VAGFVG D+ + Sbjct: 194 VYVTHDQGEALTMSDRVAVFNEGVIQQLADVESLYETPSNRFVAGFVG-------DSTVL 246 Query: 248 ANGLKIEGCEEVLPLPAAF------NGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASVE 301 + L+ G + + +P F A G RV+ +RPE + L SE R A Sbjct: 247 SGTLQGAGADAAIQMPGGFLLPGVNVNQAPVGARVQACVRPERVVLLPQSEYPRPNAIPA 306 Query: 302 VVELT 306 V T Sbjct: 307 TVART 311 Lambda K H 0.320 0.136 0.385 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: 318 Number of extensions: 11 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: 360 Length of database: 367 Length adjustment: 29 Effective length of query: 331 Effective length of database: 338 Effective search space: 111878 Effective search space used: 111878 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: 49 (23.5 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