Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_068003610.1 PsAD2_RS05610 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_00465 (263 letters) >NCBI__GCF_001623255.1:WP_068003610.1 Length = 243 Score = 213 bits (543), Expect = 2e-60 Identities = 109/247 (44%), Positives = 159/247 (64%), Gaps = 7/247 (2%) Query: 13 LLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIVL 72 ++ IRGL K Y + VL G+DL +++G + +IG SG+GK+TLLRC+N LE + G+ +L Sbjct: 1 MIQIRGLTKIYNGVPVLNGIDLDIKKGERIAIIGPSGTGKSTLLRCLNFLETPEKGEYIL 60 Query: 73 DGESIGYDDIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPK 132 DG+ I +++ R T FQ + LF + TA N+ GL+ V+ + K Sbjct: 61 DGKMIDVQKAKAAQIKEM-------RLRTAFIFQNYALFANKTARDNIAEGLITVRGVAK 113 Query: 133 DEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 192 + A+ A+ L+ +GL ++ D +P LSGGQQQRV I RA+A + LML DE TSALDPE Sbjct: 114 ERALERADHILQDIGLADKADAYPASLSGGQQQRVGIGRAMASDAELMLVDEPTSALDPE 173 Query: 193 LVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSP 252 V EVL ++ +A+ TML+VTHEM FA E++D+++FM GRI EQGPP+++F P+ P Sbjct: 174 WVDEVLQLLTRVAQAHQTMLIVTHEMAFAKEIADRVLFMEGGRIVEQGPPEKIFTNPEDP 233 Query: 253 RLAEFLK 259 R FL+ Sbjct: 234 RTRSFLR 240 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: 169 Number of extensions: 7 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: 243 Length adjustment: 24 Effective length of query: 239 Effective length of database: 219 Effective search space: 52341 Effective search space used: 52341 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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