Align ABC transporter related (characterized, see rationale)
to candidate WP_337833398.1 BUB04_RS10875 amino acid ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >NCBI__GCF_900129305.1:WP_337833398.1 Length = 257 Score = 248 bits (633), Expect = 9e-71 Identities = 132/248 (53%), Positives = 171/248 (68%), Gaps = 6/248 (2%) Query: 9 LSVKNIHKSFG-DHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSL 67 + V N+HK FG D HVL+GI L+ +G+V+ ILG SGSGKST LRC+N LE P G++ + Sbjct: 8 VEVSNLHKVFGEDLHVLRGIDLEVKKGEVVVILGPSGSGKSTLLRCINFLEEPTAGTIRV 67 Query: 68 AGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRS 127 + G GK ++ +R ++GM FQ+FNL+ HMT LEN+IEGP+ V +S Sbjct: 68 GDITI-----GAGKKTKEHNAKILEIRRRVGMCFQSFNLFPHMTALENIIEGPVTVLGQS 122 Query: 128 RAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDP 187 + E++ AE LLA VGL +KR YP+ LSGGQQQRVAIAR+LAM P VMLFDEPTSALDP Sbjct: 123 KKEAIPYAEELLAWVGLTDKRDEYPSRLSGGQQQRVAIARSLAMKPDVMLFDEPTSALDP 182 Query: 188 ELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKS 247 ELV EV+ VM LA EG T++ VTHEM FAR V++RV+ + G G P+E+F K Sbjct: 183 ELVKEVVDVMERLAAEGMTIIAVTHEMHFARDVADRVLIMDGGVWVESGPPEEIFTNPKE 242 Query: 248 DRFRQFVS 255 R RQF++ Sbjct: 243 ARSRQFLA 250 Lambda K H 0.318 0.133 0.377 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: 171 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: 257 Length adjustment: 24 Effective length of query: 239 Effective length of database: 233 Effective search space: 55687 Effective search space used: 55687 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 (21.7 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