Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate 8501186 DvMF_1920 ABC transporter related (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_00465 (263 letters) >FitnessBrowser__Miya:8501186 Length = 249 Score = 269 bits (687), Expect = 5e-77 Identities = 136/251 (54%), Positives = 183/251 (72%), Gaps = 10/251 (3%) Query: 12 PLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIV 71 P+++IR L K++G EVL+G+DL++ G VV +IG SGSGK+T LRC+N LEE G++V Sbjct: 7 PMIEIRNLHKRFGQNEVLRGIDLTVCPGEVVVIIGPSGSGKSTALRCINRLEEITSGKVV 66 Query: 72 LDGESIGYDDIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLP 131 +DG + YD P I R GM FQQFNLFPH++ L NVTLG ++V++ P Sbjct: 67 VDGHDL-YD---------PATDINYVRTEAGMVFQQFNLFPHMSVLHNVTLGPIRVRRTP 116 Query: 132 KDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDP 191 + EA L LE+VGL ++ +P QLSGGQ+QRVAIAR++AM P ++LFDE TSALDP Sbjct: 117 RAEADRLGLALLEKVGLADKATAYPDQLSGGQKQRVAIARSLAMQPKVLLFDEPTSALDP 176 Query: 192 ELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQS 251 ELVGEVL V++ LA +GMTM++VTHEM FA EV+D+++F++QGRI+E+GPP E F P++ Sbjct: 177 ELVGEVLEVMRALALEGMTMVIVTHEMGFAREVADRVIFIDQGRIQEEGPPDEFFSAPKN 236 Query: 252 PRLAEFLKNTR 262 PRL EFL R Sbjct: 237 PRLREFLGRVR 247 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: 222 Number of extensions: 5 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: 249 Length adjustment: 24 Effective length of query: 239 Effective length of database: 225 Effective search space: 53775 Effective search space used: 53775 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