Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS34800 RR42_RS34800 leucine/isoleucine/valine transporter ATP-binding subunit
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__Cup4G11:RR42_RS34800 Length = 235 Score = 207 bits (528), Expect = 1e-58 Identities = 106/236 (44%), Positives = 158/236 (66%), Gaps = 3/236 (1%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +LQ+ V YG+ RAL + ++ GE+V L+GANGAGKS++ M + G + GS+ F Sbjct: 1 MLQLERVSLSYGSFRALDNITLNAAAGELVVLLGANGAGKSSIFMALSGIHRTSGGSMRF 60 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKH--FAEDVEKIFT 128 +GR++ M +I + + PEGR++FP M+V +NL +GA + +E +F Sbjct: 61 DGRELAGMKPSQIVQAGLVHCPEGRKLFPAMSVQKNLTLGAYVHRRDSAGIKRSLEDVFE 120 Query: 129 LFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRK 188 +FP L+++ G+LSGG+QQM+++GRALM RP+ LLLDEPSLGLAPL+VK +FE I++ Sbjct: 121 MFPILRQKKDDPAGSLSGGQQQMVALGRALMGRPRTLLLDEPSLGLAPLVVKQMFEVIQR 180 Query: 189 LNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLEG 244 +N A G TV L EQNA+AAL ++HRAYV+ +G++ M G LL + +R AY+ G Sbjct: 181 INRA-GTTVLLAEQNAYAALGIAHRAYVIESGRIVMQGDRDALLKDEGIRRAYIGG 235 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: 192 Number of extensions: 7 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: 235 Length adjustment: 23 Effective length of query: 224 Effective length of database: 212 Effective search space: 47488 Effective search space used: 47488 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