Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate CA265_RS25230 CA265_RS25230 LPS export ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >FitnessBrowser__Pedo557:CA265_RS25230 Length = 246 Score = 124 bits (312), Expect = 1e-33 Identities = 67/221 (30%), Positives = 127/221 (57%), Gaps = 2/221 (0%) Query: 20 ILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVR 79 ++ ++F+++ GE+V ++GPNGAGK+T I GL+ P++G I + E+IT + + Sbjct: 17 VVNNVSFNVSQGEIVGLLGPNGAGKTTSFYMIVGLIKPNEGRIFLEDEDITEDPMYRRAQ 76 Query: 80 RGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPK--LAQRRNQRAGTL 137 +G+ Y+ Q +VF LTV +N+ + + +D++ + + L + R R L Sbjct: 77 KGIGYLAQEASVFRKLTVEDNILAILEMSNMSKEEQRDKLEELINEFSLHKVRKNRGDLL 136 Query: 138 SGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIILVEQNAK 197 SGGER+ + RAL +P+ +LLDEP A + PI V+++ + + + I++ + N + Sbjct: 137 SGGERRRTEIARALAANPNFILLDEPFAGVDPIAVEEIQSIVAKLKHKNIGILITDHNVQ 196 Query: 198 QALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLGAAY 238 + L + DR Y+L G+ +G + L + +V ++YLG+ + Sbjct: 197 ETLSITDRAYLLFEGKILEQGVPEVLAENEMVRKVYLGSNF 237 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: 139 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: 240 Length of database: 246 Length adjustment: 23 Effective length of query: 217 Effective length of database: 223 Effective search space: 48391 Effective search space used: 48391 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