Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_013093620.1 BC1002_RS29450 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000092885.1:WP_013093620.1 Length = 244 Score = 231 bits (588), Expect = 1e-65 Identities = 121/241 (50%), Positives = 171/241 (70%), Gaps = 8/241 (3%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 +L VK L YG ++ + G+ +V +G +V+LIGSNGAGKTTTM+AI+G + +DG I Sbjct: 1 MLSVKNLHAGYGKVKVLHGISIDVPKGSVVTLIGSNGAGKTTTMRAISGMIRPSDGEITM 60 Query: 69 -LGKSIKGKGAWD---LVKEGLVMVPEGRGVFARMTITENLQMGAYIR----KDKAGILA 120 +G S K A D + + GL PEGR VFA M++ +NL +GA+ R + + + A Sbjct: 61 GVGASAKRIDALDSHRIARLGLAHSPEGRRVFATMSVHDNLILGAFPRLTWARPRGDVNA 120 Query: 121 DIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDK 180 D+E+ +FPRL+ER+ QLAGT+SGGEQQMLAM RA+M P+++LLDEPSMGL+PI+V++ Sbjct: 121 DLERAIELFPRLKERRHQLAGTLSGGEQQMLAMARAIMLNPELVLLDEPSMGLAPILVEE 180 Query: 181 IFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYL 240 +F ++ ++ GVT++LVEQ A+ AL +AD GYV+E+G I GP QL NDP V+AAYL Sbjct: 181 VFRIIENLKGQGVTMLLVEQFAAAALNVADYGYVLENGRIAAHGPALQLRNDPSVKAAYL 240 Query: 241 G 241 G Sbjct: 241 G 241 Lambda K H 0.317 0.136 0.373 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: 186 Number of extensions: 6 Number of successful extensions: 3 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: 242 Length of database: 244 Length adjustment: 23 Effective length of query: 219 Effective length of database: 221 Effective search space: 48399 Effective search space used: 48399 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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