Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_085770499.1 B1812_RS04360 ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >NCBI__GCF_002117405.1:WP_085770499.1 Length = 266 Score = 160 bits (406), Expect = 2e-44 Identities = 93/241 (38%), Positives = 145/241 (60%), Gaps = 9/241 (3%) Query: 4 LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEI- 62 LL ++DV A Y + L+ ++ + GE+V ++G NG+GK+T+ LL +G+I Sbjct: 7 LLELRDVEASYNQAIVALRDVSLKVRRGEIVALLGANGSGKTTILNATSRLLAAERGQIT 66 Query: 63 ----IFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDR 118 +F G + + + ++ ++G+ V + VF SLTV ENL GA + + L+D Sbjct: 67 SGKILFDGRSTSKSSTAELAQKGLVQVLEGRRVFRSLTVEENLASGALARRSNRRELRDD 126 Query: 119 ---IYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDV 175 +Y +FP+L RR AG LSGGE+QM A+GRA+M P LL+LDEPS L+P++V+++ Sbjct: 127 LDYVYGVFPQLKHRRRSLAGLLSGGEQQMTAIGRAMMTHPRLLILDEPSMGLAPLVVEEI 186 Query: 176 FAQIKAIN-ATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYL 234 + + A+N G ++++ EQNA AL A RGYV+ENG LEG+ +L V + YL Sbjct: 187 YQVLGALNRMKGLSLLVAEQNAYVALRHAHRGYVVENGVVVLEGAAATLQEREDVKDFYL 246 Query: 235 G 235 G Sbjct: 247 G 247 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: 170 Number of extensions: 7 Number of successful extensions: 4 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: 266 Length adjustment: 24 Effective length of query: 216 Effective length of database: 242 Effective search space: 52272 Effective search space used: 52272 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 Apr 09 2024. 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