Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 6938989 Sama_3087 ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__SB2B:6938989 Length = 243 Score = 122 bits (306), Expect = 7e-33 Identities = 81/238 (34%), Positives = 125/238 (52%), Gaps = 7/238 (2%) Query: 9 QPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSV 68 Q L+ + + Y N + + V + VN G++V L+G NGAGK+T + G Q+ GS+ Sbjct: 3 QLTLKASNLAKSYKNRQVVKNVSLTVNTGQVVGLLGPNGAGKTTTFYMVVGLVQSDKGSI 62 Query: 69 VFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLEN----LQMGAGLDNLKHFAEDVE 124 D+T P H AR I P+ IF +++V +N LQM L N E +E Sbjct: 63 HINDDDLTLDPMHLRARKGIGYLPQEASIFRKLSVRDNIMAVLQMRKEL-NTDEREEALE 121 Query: 125 KIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFE 184 ++ F + G +LSGGE++ + I RAL A P+ +LLDEP G+ P+ V I + Sbjct: 122 QLLEEF-HITHIRDNLGMSLSGGERRRVEIARALAANPRFILLDEPFAGVDPISVIDIKK 180 Query: 185 AIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 I +L GL V + + N L + +AY++ +G + G+ E+L N +VRA YL Sbjct: 181 IIEQLKN-RGLGVLITDHNVRETLDVCEKAYIVSHGDLIAEGTPAEILDNQQVRAVYL 237 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: 135 Number of extensions: 5 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: 247 Length of database: 243 Length adjustment: 24 Effective length of query: 223 Effective length of database: 219 Effective search space: 48837 Effective search space used: 48837 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