Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_012760292.1 RLEG_RS30575 ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >NCBI__GCF_000023185.1:WP_012760292.1 Length = 239 Score = 161 bits (408), Expect = 9e-45 Identities = 91/236 (38%), Positives = 140/236 (59%), Gaps = 2/236 (0%) Query: 4 LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEII 63 LL + + A Y L G++ + GE V +IG NGAGK+TL ++I G+LT + I+ Sbjct: 3 LLETRGLTASY-GGFQALFGVDIVVGAGETVAIIGANGAGKTTLMRSISGVLTNAASSIL 61 Query: 64 FKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMF 123 ++ E I L + I+ RG+ VP+ +F SL+V ENL +G + + + I+ +F Sbjct: 62 YRDEPIGALSAPDILARGIAMVPEGRKLFPSLSVEENLLVGNYGRKVDGPWTLESIFALF 121 Query: 124 PKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAIN 183 P L +RR+ A LSGG++QM+A+GR LM +P +LL DE S L+P++V+D++A I Sbjct: 122 PILKERRDNPATALSGGQQQMVAIGRGLMSNPAMLLCDEISLGLAPVVVRDIYAAFPRIR 181 Query: 184 ATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLGAAYH 239 TG +I++VEQ+ QAL +ADR Y + GR L G L D + + Y G +H Sbjct: 182 ETGASIVIVEQDIAQALKVADRVYCMMEGRVTLSGRAADLSRDD-IHKAYFGTDHH 236 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: 144 Number of extensions: 5 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: 239 Length adjustment: 23 Effective length of query: 217 Effective length of database: 216 Effective search space: 46872 Effective search space used: 46872 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