Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF3277 PS417_16775 branched-chain amino acid ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >FitnessBrowser__WCS417:GFF3277 Length = 255 Score = 166 bits (421), Expect = 3e-46 Identities = 97/241 (40%), Positives = 145/241 (60%), Gaps = 9/241 (3%) Query: 4 LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTP-----S 58 LL V D+ Y + + G++ S+ G V ++G NGAGKST K I GL+ S Sbjct: 13 LLSVNDIEVIYDGAILAVAGVSLSVPKGATVALLGANGAGKSTTLKAISGLVRAERAEVS 72 Query: 59 QGEIIFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLK-- 116 +G I + G ++ G+ Q VR+GM +V + +VFG L+V +NL G F+ + Q ++ Sbjct: 73 RGTIEYAGTDLAGIDPSQRVRQGMVHVLEGRHVFGQLSVEDNLRSGGFVRRLSRQEMEHD 132 Query: 117 -DRIYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDV 175 +R+Y FP+L +R+ RAG SGGE+QM+A+GRALM P L+LLDEPS L+P++V+++ Sbjct: 133 LERLYAWFPRLKTKRHTRAGLTSGGEQQMVAIGRALMTRPTLVLLDEPSMGLAPMIVQEI 192 Query: 176 FAQIKAINATGK-AIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYL 234 F I +N + + ++ EQN AL A GYVL+ GR L GS LL + ++YL Sbjct: 193 FEIIGQLNREQQVSFLIAEQNINVALNYASHGYVLDTGRVALSGSAAELLARGDLHDIYL 252 Query: 235 G 235 G Sbjct: 253 G 253 Lambda K H 0.320 0.139 0.393 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: 144 Number of extensions: 8 Number of successful extensions: 4 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: 240 Length of database: 255 Length adjustment: 24 Effective length of query: 216 Effective length of database: 231 Effective search space: 49896 Effective search space used: 49896 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