Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BWI76_RS05980 BWI76_RS05980 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__Koxy:BWI76_RS05980 Length = 260 Score = 198 bits (503), Expect = 1e-55 Identities = 119/259 (45%), Positives = 161/259 (62%), Gaps = 11/259 (4%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 +L+V+ ++M+FGGL AI+ SF +I LIGPNGAGKTT+FN IT YKPT G +T Sbjct: 7 ILEVQDVTMQFGGLRAIDSVSFHVDEAEIFGLIGPNGAGKTTMFNVITANYKPTSGSVTL 66 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133 KS L+ L R+ A +ARTFQNIRLF+ +TVLEN++V L AS Y++L Sbjct: 67 AGKS-----LKGLKPNRVVN-AGIARTFQNIRLFNSMTVLENVMVG----LDSASRYSLL 116 Query: 134 -GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPEL 192 + +G Y A A L+ + AD A +L YG QR++EIARA+ T P+L Sbjct: 117 EAALHIGRYFPAERAAKAKAMAILDDIGIAHFADVQATNLSYGNQRKVEIARALATSPKL 176 Query: 193 LCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKIS 252 L LDEPAAG+NP+E+ L L+ +R + S+LLIEHDM V ++ + V+VLEYG+ + Sbjct: 177 LLLDEPAAGMNPKETEELADLIFRMRNDYRLSVLLIEHDMPFVNKLCERVMVLEYGKPLF 236 Query: 253 DGTPDHVKNDPRVIAAYLG 271 G DP VI+AYLG Sbjct: 237 SGLMSEAIQDPDVISAYLG 255 Lambda K H 0.318 0.136 0.386 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: 211 Number of extensions: 7 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: 292 Length of database: 260 Length adjustment: 25 Effective length of query: 267 Effective length of database: 235 Effective search space: 62745 Effective search space used: 62745 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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