Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate 5210884 Shew_3310 ABC transporter-related protein (RefSeq)
Query= uniprot:A0A159ZWL6 (233 letters) >FitnessBrowser__PV4:5210884 Length = 243 Score = 129 bits (323), Expect = 7e-35 Identities = 76/238 (31%), Positives = 133/238 (55%), Gaps = 10/238 (4%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 +L+ EN++ Y + V++ V+ G+IV L+G NGAGK+T + G Q+ G I + Sbjct: 5 ILKAENLAKSYKSRAVVQDVSLTVKTGQIVGLLGPNGAGKTTTFYMVVGLVQSDKGRI-F 63 Query: 61 MGEELVGQDSSHIM-RKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDY-----QEQMD 114 + ++ + D H+ RK I +P+ +F +L+V +N+ + D +E+++ Sbjct: 64 IDDDDLTLDPMHLRARKGIGYLPQEASIFRKLSVRDNIM--AVLQTRSDLNNDGREEELE 121 Query: 115 KVLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFD 174 +L F R G +SGGE++ + I RAL + PK +LLDEP G+ PI + I Sbjct: 122 HLLEEFHITHIR-DSHGMALSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIKK 180 Query: 175 IIEQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232 IIEQL+ G+ V + + N + L + ++AY++ +G ++ +GT +L + +VR YLG Sbjct: 181 IIEQLKNRGLGVLITDHNVRETLDVCEKAYIVSHGNLIAEGTPAEILDNQQVRAVYLG 238 Lambda K H 0.320 0.137 0.381 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: 127 Number of extensions: 7 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: 233 Length of database: 243 Length adjustment: 23 Effective length of query: 210 Effective length of database: 220 Effective search space: 46200 Effective search space used: 46200 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