Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate GFF3101 Psest_3160 ABC-type polar amino acid transport system, ATPase component
Query= reanno::pseudo5_N2C3_1:AO356_00465 (263 letters) >FitnessBrowser__psRCH2:GFF3101 Length = 255 Score = 238 bits (608), Expect = 7e-68 Identities = 126/247 (51%), Positives = 168/247 (68%), Gaps = 10/247 (4%) Query: 12 PLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIV 71 P++ ++G+ K +G VLK ++LS+++G + L G SGSGK+T +RC+N LEE Q G+IV Sbjct: 14 PVIQMQGVHKWFGQFHVLKDINLSVRQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIV 73 Query: 72 LDGESIGYDDIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLP 131 ++G + D K I R+ GM FQ FNLFPHLT LQN TL + V+KLP Sbjct: 74 INGVELTSD----------LKQIEAIRSEVGMVFQHFNLFPHLTVLQNCTLAPMWVRKLP 123 Query: 132 KDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDP 191 + +A +A +LERV + E+ + FPGQLSGGQQQRVAIARA+ M P +MLFDE TSALDP Sbjct: 124 RRQAEEIAMHYLERVRIPEQANKFPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDP 183 Query: 192 ELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQS 251 E+V EVL+ + LAE GMTML VTHEM FA V+D+++FM++G I EQ P+ F P + Sbjct: 184 EMVKEVLDTMVSLAESGMTMLCVTHEMGFARTVADRVIFMDKGEIVEQAEPEMFFTNPVN 243 Query: 252 PRLAEFL 258 R FL Sbjct: 244 DRTKLFL 250 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: 7 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: 255 Length adjustment: 24 Effective length of query: 239 Effective length of database: 231 Effective search space: 55209 Effective search space used: 55209 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