Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_053938863.1 WG78_RS16125 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_2050 (263 letters) >NCBI__GCF_001294205.1:WP_053938863.1 Length = 246 Score = 235 bits (599), Expect = 8e-67 Identities = 123/242 (50%), Positives = 162/242 (66%), Gaps = 11/242 (4%) Query: 19 LRKQYG-PLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIMLDGESI 77 + K YG VLK + L +++G VV + G SGSGK+TL+R +N LE G+I Sbjct: 7 VNKWYGRDHHVLKNISLEVKQGEVVVVCGPSGSGKSTLIRTINQLEPVNDGEIW------ 60 Query: 78 GYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPKDEAVA 137 +DG +V HP I R R G FQ FNL+PHL+ LQN+TL +KV+K+ + +A Sbjct: 61 ----VDGVQVNHPRTNINRLREEVGFVFQHFNLYPHLSVLQNITLAPVKVRKMSQADADQ 116 Query: 138 LAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPELVGEV 197 + LERVGL +RD +P QLSGGQQQRVAIAR +AM P +MLFDE TSALDPE++GEV Sbjct: 117 RGMELLERVGLSNKRDAYPSQLSGGQQQRVAIARGLAMQPKVMLFDEPTSALDPEMIGEV 176 Query: 198 LNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSPRLAEF 257 L V++ LAE GMTM++VTHEM FA EV+D++VF++ G I EQ P + F PQ R +F Sbjct: 177 LKVMQNLAESGMTMMVVTHEMGFAREVADRVVFLDHGEILEQAAPAQFFNNPQCDRAQQF 236 Query: 258 LK 259 L+ Sbjct: 237 LR 238 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: 189 Number of extensions: 10 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: 246 Length adjustment: 24 Effective length of query: 239 Effective length of database: 222 Effective search space: 53058 Effective search space used: 53058 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 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