Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)
Query= reanno::pseudo5_N2C3_1:AO356_00465 (263 letters) >FitnessBrowser__MR1:200449 Length = 378 Score = 149 bits (377), Expect = 7e-41 Identities = 91/255 (35%), Positives = 140/255 (54%), Gaps = 16/255 (6%) Query: 5 STPSNTQPLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEE 64 +T + + LL I + K + + + V L++ +G + L+G SGSGK+TLLR + E Sbjct: 12 TTKTQEKVLLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFER 71 Query: 65 FQGGQIVLDGESIGYDDIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLGL 124 G+I LDGE I + + M FQ + LFPH+T QN+ GL Sbjct: 72 PTSGRIYLDGEDITD--------------LPPYERPINMMFQSYALFPHMTVAQNIAFGL 117 Query: 125 LKVKKLPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDE 184 K KLPK E ++ L+ V + + P QLSGGQ+QRVA+AR++A P L+L DE Sbjct: 118 -KQDKLPKAEIEQRVQEMLKLVHMEQYGKRKPHQLSGGQRQRVALARSLAKRPKLLLLDE 176 Query: 185 VTSALDPELVGEV-LNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPK 243 ALD +L ++ L V++ L G+T ++VTH+ A ++ +I M+ G I + G P Sbjct: 177 PMGALDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRISIMSDGWIAQTGSPM 236 Query: 244 ELFERPQSPRLAEFL 258 +++E P S +AEF+ Sbjct: 237 DIYESPNSRMIAEFI 251 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: 254 Number of extensions: 21 Number of successful extensions: 4 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: 378 Length adjustment: 27 Effective length of query: 236 Effective length of database: 351 Effective search space: 82836 Effective search space used: 82836 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: 48 (23.1 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