Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_0627 Dsui_0627 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__PS:Dsui_0627 Length = 267 Score = 203 bits (516), Expect = 4e-57 Identities = 120/270 (44%), Positives = 161/270 (59%), Gaps = 12/270 (4%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 LL+ ++ FGG+ A+ S + G+I LIGPNGAGKTT FNC+TG Y P G I F Sbjct: 7 LLEASDVAKHFGGVKALRGVSLTIREGEIYGLIGPNGAGKTTFFNCLTGLYVPNGGRIVF 66 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133 +G + L+ ++ +ARTFQNIRLF+ +T LEN++V +H + + Sbjct: 67 ---AGAE--LDTSAPHKVAARG-IARTFQNIRLFAHMTALENVMVGRHQRTRAG----VF 116 Query: 134 GLIGVGPYKREAAEAIEL-ARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPEL 192 G I P R AI+ A L + DRA D A L YG QRRLEIARA+ T P+L Sbjct: 117 GAIFRTPGTRAEEAAIQRRAEELLHYVGIADRAHDLAKHLSYGDQRRLEIARALATEPKL 176 Query: 193 LCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKIS 252 L LDEPAAG+N E+ L L++ IR + G ++LLIEHD+ +VM + D V VL+YG+KI Sbjct: 177 LALDEPAAGMNASETGELRTLIEGIRKD-GITVLLIEHDVKLVMGLCDRVAVLDYGEKIC 235 Query: 253 DGTPDHVKNDPRVIAAYLGVEDEEVEEVIA 282 + P V+ DPRVI AYLG E + +A Sbjct: 236 EDVPAVVQKDPRVITAYLGAEAQPAGSEVA 265 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: 204 Number of extensions: 11 Number of successful extensions: 4 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: 267 Length adjustment: 26 Effective length of query: 266 Effective length of database: 241 Effective search space: 64106 Effective search space used: 64106 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