Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate Synpcc7942_0249 Synpcc7942_0249 ATPase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2050 (263 letters) >FitnessBrowser__SynE:Synpcc7942_0249 Length = 261 Score = 239 bits (610), Expect = 4e-68 Identities = 129/252 (51%), Positives = 170/252 (67%), Gaps = 11/252 (4%) Query: 8 SNTQPLLDIRGLRKQYG-PLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQ 66 S + ++ G+ K YG + L GV L++QRG VV ++G SGSGK+T LR +N LE Q Sbjct: 16 SAPETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQ 75 Query: 67 GGQIMLDGESIGYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLK 126 G+I I+G R+ H + IA R GM FQQFNLFPHLT LQN+ L ++ Sbjct: 76 RGEIW----------IEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQ 125 Query: 127 VKKLPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVT 186 V++ P +A A A + LERV + E+ D +PGQLSGGQQQRVAIARA+AM P ++LFDE T Sbjct: 126 VRRWPVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPT 185 Query: 187 SALDPELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELF 246 SALDPE+V EVL+V++ LA +GMTML+ THE+ FA EV+D++V M G+I E+ PP F Sbjct: 186 SALDPEMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFF 245 Query: 247 ERPQSPRLAEFL 258 PQS R +FL Sbjct: 246 TAPQSDRAKQFL 257 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: 184 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: 263 Length of database: 261 Length adjustment: 25 Effective length of query: 238 Effective length of database: 236 Effective search space: 56168 Effective search space used: 56168 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