Align ABC transporter related (characterized, see rationale)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 229 bits (584), Expect = 4e-65 Identities = 118/247 (47%), Positives = 169/247 (68%), Gaps = 11/247 (4%) Query: 9 LSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLA 68 + + + K +G +H L+ +SLD +G+ I I G SGSGKST +RC+N LET D+G + + Sbjct: 2 IHMAGVGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIG 61 Query: 69 GEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSR 128 +E++ DRR + R+R+++GMVFQ+FNL+ H+T+LEN PM+V+ +R Sbjct: 62 EDEVR-----------PDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLAR 110 Query: 129 AESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPE 188 + A LL +V +A++ YPA LSGGQQQR AIARALAM P+++LFDEPTSALD E Sbjct: 111 DAAEALARELLERVRIADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAE 170 Query: 189 LVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSD 248 +V EVL +M++LA EG TML VTHEMGFAR V++R++F+ GQ+ G+P + F + Sbjct: 171 MVKEVLDIMKALATEGITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHE 230 Query: 249 RFRQFVS 255 R R F+S Sbjct: 231 RTRAFLS 237 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: 160 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: 241 Length adjustment: 24 Effective length of query: 239 Effective length of database: 217 Effective search space: 51863 Effective search space used: 51863 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: 46 (22.3 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