Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 203044 SO3960 ABC transporter, ATP-binding protein (NCBI ptt file)
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__MR1:203044 Length = 243 Score = 119 bits (298), Expect = 6e-32 Identities = 79/239 (33%), Positives = 125/239 (52%), Gaps = 9/239 (3%) Query: 9 QPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSV 68 Q L+ + Y + + + V + V G++V L+G NGAGK+T + G ++ G + Sbjct: 3 QITLKAQNLAKSYKSRQVVKDVSLTVKTGQVVGLLGPNGAGKTTTFYMVVGLVKSDKGHI 62 Query: 69 VFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFT 128 + D+T P H AR I P+ IF ++TV +N+ A L K D ++ Sbjct: 63 FIDDDDLTADPMHLRARKGIGYLPQEASIFRKLTVHDNIM--AVLQTRKELNSD-QREEA 119 Query: 129 LFPRLKERHA-----QRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIF 183 L L+E H +G +LSGGE++ + I RAL A PK +LLDEP G+ P+ V I Sbjct: 120 LEQLLEEFHITHIRDSQGMSLSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIK 179 Query: 184 EAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 + I +L ++ GL V + + N L + AY++ +G + G+ E+L N +VRA YL Sbjct: 180 KIIEQL-KSRGLGVLITDHNVRETLDVCEHAYIVSHGSLIAEGTPAEILDNQQVRAVYL 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: 136 Number of extensions: 6 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