Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 5210884 Shew_3310 ABC transporter-related protein (RefSeq)
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__PV4:5210884 Length = 243 Score = 119 bits (298), Expect = 6e-32 Identities = 79/242 (32%), Positives = 124/242 (51%), Gaps = 19/242 (7%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +L+ + Y + + V + V G+IV L+G NGAGK+T + G Q+ G + Sbjct: 5 ILKAENLAKSYKSRAVVQDVSLTVKTGQIVGLLGPNGAGKTTTFYMVVGLVQSDKGRIFI 64 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLEN----LQMGAGLDN------LKHFA 120 + D+T P H AR I P+ IF +++V +N LQ + L+N L+H Sbjct: 65 DDDDLTLDPMHLRARKGIGYLPQEASIFRKLSVRDNIMAVLQTRSDLNNDGREEELEHLL 124 Query: 121 EDVEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVK 180 E+ +++ H G LSGGE++ + I RAL A PK +LLDEP G+ P+ V Sbjct: 125 EEFH-----ITHIRDSH---GMALSGGERRRVEIARALAANPKFILLDEPFAGVDPISVI 176 Query: 181 GIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAA 240 I + I +L GL V + + N L + +AY++ +G + G+ E+L N +VRA Sbjct: 177 DIKKIIEQLKN-RGLGVLITDHNVRETLDVCEKAYIVSHGNLIAEGTPAEILDNQQVRAV 235 Query: 241 YL 242 YL Sbjct: 236 YL 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: 140 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