Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF558 Psest_0563 urea ABC transporter, ATP-binding protein UrtE
Query= TCDB::P73650 (240 letters) >FitnessBrowser__psRCH2:GFF558 Length = 232 Score = 148 bits (374), Expect = 8e-41 Identities = 84/215 (39%), Positives = 129/215 (60%), Gaps = 2/215 (0%) Query: 14 YVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLG 73 Y IL+G++F GE+ ++G NG GK+TL K + GL+ +G + ++G+ ITG Sbjct: 10 YYGGSHILRGLSFEAKVGEVTCLLGRNGVGKTTLLKCLMGLIPAKEGAVNWEGKPITGFK 69 Query: 74 SDQIVRRGMCYVPQVCNVFGSLTVAENLDMG-AFLHQGPTQTLKDRIYTMFPKLAQRRNQ 132 Q V G+ YVPQ +FG LTV ENL MG + + + + IY +FP L + +++ Sbjct: 70 PHQRVHAGIAYVPQGREIFGRLTVEENLLMGLSRFSAREAKEVPEFIYELFPVLKEMKHR 129 Query: 133 RAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATG-KAIIL 191 R G LSGG++Q LA+GRAL P LL+LDEP+ + P ++K++ A I+ + A G AI+L Sbjct: 130 RGGDLSGGQQQQLAIGRALASKPRLLILDEPTEGIQPSVIKEIGAVIRKLAARGDMAILL 189 Query: 192 VEQNAKQALMMADRGYVLENGRDKLEGSGQSLLND 226 VEQ A +AD+ V+ G +G G+++ D Sbjct: 190 VEQFYDFAAELADQYLVMSRGEIIQQGRGENMAAD 224 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: 129 Number of extensions: 6 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: 232 Length adjustment: 23 Effective length of query: 217 Effective length of database: 209 Effective search space: 45353 Effective search space used: 45353 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