Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate SM_b20784 SM_b20784 branched-chain amino acid ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >FitnessBrowser__Smeli:SM_b20784 Length = 238 Score = 143 bits (361), Expect = 3e-39 Identities = 89/232 (38%), Positives = 129/232 (55%), Gaps = 5/232 (2%) Query: 5 LVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIF 64 L V ++ AGY +L+GI+FS+ G + V+G NG GK+TL T+ G +G I Sbjct: 6 LEVDNLSAGY-GPTRVLEGISFSVPAGARLAVLGRNGMGKTTLLATLAGQTRRYEGRIRI 64 Query: 65 KGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFP 124 N+T L S +G+ +VPQ VF SLTV ENL +G +G +T Y MFP Sbjct: 65 GDANVTALPSASRALKGLGFVPQARCVFPSLTVEENLFVGL---KGRPKTALSEAYEMFP 121 Query: 125 KLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINA 184 +L +RR LSGGE+QML+ R+++ P +LLLDEP L+P++ +++ + Sbjct: 122 RLYERRRNLGSQLSGGEQQMLSTARSILGRPSVLLLDEPLEGLAPVICEELMKAFAELAK 181 Query: 185 T-GKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 T G I+LVEQ + AL ADR +LE GR G+ ++L + E LG Sbjct: 182 TGGMTILLVEQRIQSALDFADRVIILERGRLAWSGTPEALAKEHATVERLLG 233 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: 130 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: 238 Length adjustment: 23 Effective length of query: 217 Effective length of database: 215 Effective search space: 46655 Effective search space used: 46655 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