Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_086511522.1 BZY95_RS19340 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_002151265.1:WP_086511522.1 Length = 264 Score = 144 bits (364), Expect = 2e-39 Identities = 91/272 (33%), Positives = 141/272 (51%), Gaps = 20/272 (7%) Query: 7 NTMSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKP 66 + + + LL+ + L+ +FGGL+A+ND F ++G+I A++GPNGAGK+T+ N ++G + P Sbjct: 8 DVLLETPLLETKGLTRRFGGLVAVNDVDFTLRQGEIHAILGPNGAGKSTLINLLSGEFPP 67 Query: 67 TMGMITFNQK--SGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKL 124 + G I F + G++ R + R+ Q +F LT L+N +A L Sbjct: 68 SEGEILFQGQPIQGRK--------ARQIARMGIGRSHQKTNIFPRLTCLQNCQLAARIHL 119 Query: 125 MKASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIAR 184 G+ G + A E E A LE L+ RA PA + YG QR+L+IA Sbjct: 120 G--------GVFGSWRSRHRAREVDERALEVLETCQLVHRAHTPASAMSYGEQRQLQIAM 171 Query: 185 AMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVV 244 + T P+L+ LDEP AG+ E+A + LLK + ++LIEHDM V ++D + V Sbjct: 172 VLATAPKLMLLDEPMAGMGREETAQVTELLKGL--SDRYPLVLIEHDMDSVFRLADRITV 229 Query: 245 LEYGQKISDGTPDHVKNDPRVIAAYLGVEDEE 276 + G + G ++ RV YLG EE Sbjct: 230 MVDGCVLETGPTAQIRASERVRDVYLGRHHEE 261 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: 158 Number of extensions: 10 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: 264 Length adjustment: 25 Effective length of query: 267 Effective length of database: 239 Effective search space: 63813 Effective search space used: 63813 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 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