Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate PP_1300 PP_1300 putative amino acid ABC transporter - ATP-binding subunit
Query= reanno::pseudo5_N2C3_1:AO356_00465 (263 letters) >FitnessBrowser__Putida:PP_1300 Length = 254 Score = 244 bits (622), Expect = 2e-69 Identities = 127/255 (49%), Positives = 174/255 (68%), Gaps = 10/255 (3%) Query: 4 ISTPSNTQPLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLE 63 I P+ + ++ ++G+ K YG VLK ++L++++G + L G SGSGK+T +RC+N LE Sbjct: 5 IKQPAGPEGIIQMQGVNKWYGQFHVLKDINLNVRQGERIVLCGPSGSGKSTTIRCLNRLE 64 Query: 64 EFQGGQIVLDGESIGYDDIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLG 123 E Q G+IV+DG + D K I R GM FQ FNLFPHL+ L+N TL Sbjct: 65 EHQQGRIVVDGVELTND----------LKQIEAIRREVGMVFQHFNLFPHLSILENCTLA 114 Query: 124 LLKVKKLPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFD 183 + V+K+P+ +A +A +LERV + E+ +PGQLSGGQQQRVAIARA+ M P +MLFD Sbjct: 115 PMWVRKMPRRKAEEIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFD 174 Query: 184 EVTSALDPELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPK 243 E TSALDPE+V EVL+ + GLAEDGMTML VTHEM FA V+++++FM++G I EQ P Sbjct: 175 EPTSALDPEMVKEVLDTMVGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPD 234 Query: 244 ELFERPQSPRLAEFL 258 + F+RP+S R FL Sbjct: 235 DFFDRPRSDRTKLFL 249 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: 193 Number of extensions: 6 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: 254 Length adjustment: 24 Effective length of query: 239 Effective length of database: 230 Effective search space: 54970 Effective search space used: 54970 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