Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate 16031 b1917 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= reanno::pseudo5_N2C3_1:AO356_00465 (263 letters) >FitnessBrowser__Keio:16031 Length = 250 Score = 233 bits (595), Expect = 2e-66 Identities = 127/247 (51%), Positives = 170/247 (68%), Gaps = 6/247 (2%) Query: 14 LDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIVLD 73 ++++ L K++ VL G+DL ++ G VV +IG SGSGKTTLLR +N+LE+ + G I Sbjct: 4 IEVKNLVKKFHGQTVLHGIDLEVKPGEVVAIIGPSGSGKTTLLRSINLLEQPEAGTI--- 60 Query: 74 GESIGYDDIDGKRVRHPEK-LIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPK 132 ++G ID R +K LI + R G FQ FNLFPH T L+N+ G + VK PK Sbjct: 61 --TVGDITIDTARSLSQQKSLIRQLRQHVGFVFQNFNLFPHRTVLENIIEGPVIVKGEPK 118 Query: 133 DEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 192 +EA A A + L +VGL + +P +LSGGQQQRVAIARA+AM P ++LFDE TSALDPE Sbjct: 119 EEATARARELLAKVGLAGKETSYPRRLSGGQQQRVAIARALAMRPEVILFDEPTSALDPE 178 Query: 193 LVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSP 252 LVGEVLN I+ LA++ TM++VTHEM FA +V+D+ +FM+QGRI EQG K LF P+ P Sbjct: 179 LVGEVLNTIRQLAQEKRTMVIVTHEMSFARDVADRAIFMDQGRIVEQGAAKALFADPEQP 238 Query: 253 RLAEFLK 259 R +FL+ Sbjct: 239 RTRQFLE 245 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: 176 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: 250 Length adjustment: 24 Effective length of query: 239 Effective length of database: 226 Effective search space: 54014 Effective search space used: 54014 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