Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate PfGW456L13_120 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
Query= TCDB::P73650 (240 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_120 Length = 238 Score = 185 bits (470), Expect = 6e-52 Identities = 106/229 (46%), Positives = 146/229 (63%), Gaps = 6/229 (2%) Query: 9 DVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGEN 68 DVF G + L+G++ I GE V++IG NGAGKSTL +IFG + G+I+++G + Sbjct: 12 DVFYG---PIQALKGVSLHINEGETVSLIGSNGAGKSTLLMSIFGQPRAADGQILYQGVD 68 Query: 69 ITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKD--RIYTMFPKL 126 IT S I G+ P+ VF +TV ENL MG + G +D R++ +FP+L Sbjct: 69 ITHKSSHYIASNGIAQSPEGRRVFPDMTVEENLLMGT-IPIGDKYAKEDMQRMFELFPRL 127 Query: 127 AQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATG 186 +RR QRA T+SGGE+QMLA+ RALM P LLLLDEPS L+PI+VK +FA ++ + TG Sbjct: 128 EERRTQRAMTMSGGEQQMLAIARALMSRPKLLLLDEPSLGLAPIVVKQIFATLRELAKTG 187 Query: 187 KAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 I LVEQNA AL ++DR YV+ NG ++ G+G+ LL + V YLG Sbjct: 188 MTIFLVEQNANHALRLSDRAYVMVNGEIRMTGTGKELLVNEDVRSAYLG 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: 155 Number of extensions: 9 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: 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