Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate N515DRAFT_1687 N515DRAFT_1687 ABC-2 type transport system ATP-binding protein
Query= TCDB::P73650 (240 letters) >FitnessBrowser__Dyella79:N515DRAFT_1687 Length = 324 Score = 99.4 bits (246), Expect = 8e-26 Identities = 61/183 (33%), Positives = 103/183 (56%), Gaps = 9/183 (4%) Query: 37 IGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLT 96 +GPNG+GKST + + GLLTPS+GEI G ++ + +R+ + Y+ Q ++F L Sbjct: 43 LGPNGSGKSTTIRMLCGLLTPSEGEIDVLGLSVPR--EAEALRKRIGYMTQKFSLFDDLG 100 Query: 97 VAENLDMGAFLHQGPTQTLKDRIYTMFPK--LAQRRNQRAGTLSGGERQMLAMGRALMLD 154 V ENL A + P + RI + + R+ Q AGT+SGG++Q LA+ A++ D Sbjct: 101 VRENLQFMAAVQGVPKARTRQRIDELIEQYHFGDRQKQLAGTMSGGQKQRLALACAVIHD 160 Query: 155 PDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIILVEQNAKQA-----LMMADRGYVL 209 P+LL LDEP++A+ P +D + ++ + G +++ +A L + DRG ++ Sbjct: 161 PELLFLDEPTSAVDPESRRDFWEKLFELTDAGTTMLVSTHLMDEAERCHRLAVLDRGVLV 220 Query: 210 ENG 212 +G Sbjct: 221 ADG 223 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: 158 Number of extensions: 5 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: 324 Length adjustment: 25 Effective length of query: 215 Effective length of database: 299 Effective search space: 64285 Effective search space used: 64285 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: 47 (22.7 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