Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 17516 b3455 leucine/isoleucine/valine transporter subunit (NCBI)
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__Keio:17516 Length = 255 Score = 127 bits (318), Expect = 3e-34 Identities = 79/250 (31%), Positives = 136/250 (54%), Gaps = 16/250 (6%) Query: 9 QPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSV 68 QPLL VNG+ +G + A+ V++ + EIVSLIG NGAGK+T+ + G + G++ Sbjct: 3 QPLLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTI 62 Query: 69 VFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMG----------AGLDNLKH 118 + + + +P +IAR+ + ++ + R+F MTV+ENL + +GL Sbjct: 63 LLRDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPS 122 Query: 119 F----AEDVEKIFTLFPR--LKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSL 172 F +E +++ T R L E ++ L+ G+Q+ L I R ++ +P++L+LDEP+ Sbjct: 123 FRRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAA 182 Query: 173 GLAPLIVKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELL 232 GL P K + E I +L T+ L+E + + +S R YV+ G +G+ +++ Sbjct: 183 GLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIR 242 Query: 233 ANPEVRAAYL 242 NP+V AYL Sbjct: 243 NNPDVIRAYL 252 Lambda K H 0.320 0.137 0.387 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: 165 Number of extensions: 9 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: 247 Length of database: 255 Length adjustment: 24 Effective length of query: 223 Effective length of database: 231 Effective search space: 51513 Effective search space used: 51513 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 (21.8 bits) S2: 46 (22.3 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