Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 152 bits (384), Expect = 9e-42 Identities = 92/246 (37%), Positives = 143/246 (58%), Gaps = 10/246 (4%) Query: 16 LEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLD 75 L + DLH G +LKGV L + +G +V L+G SGSGKTTLLR + LE G I + Sbjct: 6 LSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRI- 64 Query: 76 GESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHKD 135 GE + + + K++ ++ + G FQ + L+PH T +NV GL K++K+ Sbjct: 65 GEQMVFE--SAKKIE-----VSVEKRCLGFVFQSYALWPHRTVYENVAYGL-KLRKVPDG 116 Query: 136 EAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPEL 195 E ++ L +GL + + +P QLSGGQQQRVA+AR++ NP ++L DE S LD +L Sbjct: 117 EIRQRVQEVLANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKL 176 Query: 196 VGEVLSVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSP 254 E ++ L D ++ + VTH+ A ++DK+V + G IE+ G P+E++ P+S Sbjct: 177 REEARIWLRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSL 236 Query: 255 RLAEFL 260 +AEF+ Sbjct: 237 FVAEFM 242 Lambda K H 0.319 0.135 0.379 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: 209 Number of extensions: 8 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: 265 Length of database: 353 Length adjustment: 27 Effective length of query: 238 Effective length of database: 326 Effective search space: 77588 Effective search space used: 77588 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 Apr 09 2024. 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