Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Ac3H11_3213 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
Query= TCDB::P73650 (240 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3213 Length = 236 Score = 176 bits (446), Expect = 4e-49 Identities = 98/236 (41%), Positives = 148/236 (62%), Gaps = 8/236 (3%) Query: 5 LVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIF 64 L V+++ GY +LQ ++ APG + ++GPNGAGK+TL K + GLL P G + Sbjct: 6 LTVQNLTTGYHG-FQVLQDLSLQAAPG-ITVIVGPNGAGKTTLLKALAGLL-PRTGTVAL 62 Query: 65 KGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRI---YT 121 G ++ + + V+RG+ V + +F +TV ENL++G +L P++T DR+ + Sbjct: 63 DGSDLPAMNATACVQRGLALVAEGRQLFPQMTVTENLELGGWLV--PSRTRADRLAQAFE 120 Query: 122 MFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKA 181 FP+L +R Q AGT+SGGE+QM+A+ RALM P LL+LDEPS L+P +V ++ A ++ Sbjct: 121 DFPRLKERATQLAGTMSGGEQQMVAVARALMSGPRLLMLDEPSLGLAPRMVDELLAIVQR 180 Query: 182 INATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLGAA 237 I A G +++VEQN ++AL +A RGYVLE GR G+ LL +V + YLG A Sbjct: 181 IAAQGVTVLMVEQNVRKALQIAQRGYVLERGRIVASGAASDLLQSDVVRQAYLGVA 236 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: 150 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: 240 Length of database: 236 Length adjustment: 23 Effective length of query: 217 Effective length of database: 213 Effective search space: 46221 Effective search space used: 46221 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