Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_089136028.1 CES79_RS00805 amino acid ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >NCBI__GCF_002217945.1:WP_089136028.1 Length = 246 Score = 100 bits (248), Expect = 3e-26 Identities = 69/220 (31%), Positives = 116/220 (52%), Gaps = 13/220 (5%) Query: 14 YVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLG 73 Y D L IN +I GE V +IGP+G+GKSTL +T+ GL +G++I G+++ Sbjct: 12 YYGDFHALHDINLTIDAGETVVLIGPSGSGKSTLIRTVNGLERIQEGQLIVNGQDLANRK 71 Query: 74 SD-QIVRRGMCYVPQVCNVFGSLTVAENLDMG-AFLHQGPTQTLKDRIYTMFPK--LAQR 129 +D +R+ + V Q N++ + T+ EN+ + + + P + K M + LA + Sbjct: 72 TDMNRIRKNVGMVFQHFNLYANKTILENIMLAPRLVLKRPEEENKKIAMDMLDRVGLADQ 131 Query: 130 RNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAI 189 + LSGG++Q +A+ R+L + P LL DEP++AL P ++ DV +K I Sbjct: 132 APKMPAQLSGGQQQRIAIARSLAMRPKALLFDEPTSALDPEMIDDVLNVMKDIARDSSMT 191 Query: 190 ILV--------EQNAKQALMMADRGYVLENGRDKLEGSGQ 221 +LV + A + + MAD G++LE+ + GQ Sbjct: 192 MLVVTHEMGFAREVANRVVFMAD-GHILEDDSKEKFFDGQ 230 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: 115 Number of extensions: 4 Number of successful extensions: 1 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 24 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