Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_011842387.1 RSPH17029_RS17510 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_2050 (263 letters) >NCBI__GCF_000015985.1:WP_011842387.1 Length = 266 Score = 251 bits (641), Expect = 1e-71 Identities = 134/252 (53%), Positives = 178/252 (70%), Gaps = 4/252 (1%) Query: 8 SNTQPLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQG 67 ++ PLL +R +RK +G EVLKGV L + +G VV++IG+SGSGK+T LR +N++E Q Sbjct: 2 TDATPLLRLREIRKSFGTFEVLKGVSLDVAQGEVVSIIGASGSGKSTFLRSINVMEMPQA 61 Query: 68 GQIMLDGESIGYDDIDGKRVRHPEKV-IARHRAMTGMAFQQFNLFPHLTALQNVTLGLLK 126 G +D +D G HP KV + + RA GM FQ +NL+PH+T LQNV + Sbjct: 62 GT--MDFGDFHFDFRKGA-ASHPTKVQLQKLRAEIGMVFQSYNLWPHMTVLQNVIHAPMT 118 Query: 127 VKKLPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVT 186 +++ P+ +AV AE L R+GL E+RD +P +LSGGQQQRVAIARA+AM P LMLFDEVT Sbjct: 119 LRRTPRAQAVEEAEALLARIGLYEKRDSYPARLSGGQQQRVAIARALAMKPRLMLFDEVT 178 Query: 187 SALDPELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELF 246 SALDPELV EVL ++ LA DGMTMLLVTHE+ FA +VS +++F +QG + EQGPP + Sbjct: 179 SALDPELVHEVLVLMASLAADGMTMLLVTHEIAFARDVSSRVLFFDQGVMAEQGPPDRVL 238 Query: 247 ERPQSPRLAEFL 258 P+SPRL +FL Sbjct: 239 RNPESPRLRQFL 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: 204 Number of extensions: 4 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: 266 Length adjustment: 25 Effective length of query: 238 Effective length of database: 241 Effective search space: 57358 Effective search space used: 57358 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 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