Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Dsui_0841 Dsui_0841 ABC-type branched-chain amino acid transport systems, ATPase component
Query= TCDB::P73650 (240 letters) >FitnessBrowser__PS:Dsui_0841 Length = 251 Score = 195 bits (496), Expect = 6e-55 Identities = 109/238 (45%), Positives = 154/238 (64%), Gaps = 9/238 (3%) Query: 4 LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEII 63 +L V D+ Y V L ++ I GE+VTVIGPNGAGK+TL + GLL P +GE+ Sbjct: 10 VLEVSDLCVAY-GKVEALHKVSLRIREGEIVTVIGPNGAGKTTLLSALMGLL-PYRGEVA 67 Query: 64 FKGENITG-LGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLH-----QGPTQTLKD 117 + N+ + ++ V +G+ VP+ +F ++V +NL +GAF + QT+++ Sbjct: 68 YVSHNLDAHVEVEERVGQGLTLVPEKRELFAEMSVEDNLLLGAFHRYRSGLRDHAQTMEE 127 Query: 118 RIYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFA 177 ++ +FP+L +RR Q AGTLSGGERQMLAMGRALM P LL+LDEPS L+P+++K++F Sbjct: 128 -VFALFPRLKERRTQAAGTLSGGERQMLAMGRALMAKPKLLMLDEPSLGLAPLIIKEIFR 186 Query: 178 QIKAINATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 + + TG +I+LVEQNA+ AL +AD GYVLE G LEG L +DP V E YLG Sbjct: 187 IVAELKQTGVSILLVEQNARAALQVADYGYVLETGEVSLEGPSHELADDPRVIETYLG 244 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: 173 Number of extensions: 9 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: 251 Length adjustment: 24 Effective length of query: 216 Effective length of database: 227 Effective search space: 49032 Effective search space used: 49032 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