Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Pf6N2E2_1701 ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1701 Length = 258 Score = 172 bits (436), Expect = 6e-48 Identities = 97/242 (40%), Positives = 147/242 (60%), Gaps = 9/242 (3%) Query: 3 DLLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTP----- 57 +LL V+D+ Y + + G++ + G++V ++G NGAGKST K I GL+ Sbjct: 13 ELLAVQDIEVIYDGAILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRAQV 72 Query: 58 SQGEIIFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLK- 116 S+G I+F+G + G+ ++ + R+G+ +V + +VF LTV +NL G FL + + L+ Sbjct: 73 SRGRIVFQGRDTAGVAANLLARQGIVHVLEGRHVFAHLTVEDNLRSGGFLRKPTRRALEQ 132 Query: 117 --DRIYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKD 174 +RIY FP+L +R +AG SGGE+QMLA+GRALM P L+LLDEPS L+P+LV++ Sbjct: 133 DLERIYAWFPRLKTKRKTQAGLTSGGEQQMLAIGRALMTKPRLVLLDEPSMGLAPLLVEE 192 Query: 175 VFAQIKAINA-TGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELY 233 +FA + +NA G + ++ EQN AL A Y+LENGR EG +L + Y Sbjct: 193 IFAIVAQLNAQEGVSFLVAEQNINVALRHASYAYILENGRVVGEGDATALAAREDIQHFY 252 Query: 234 LG 235 LG Sbjct: 253 LG 254 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: 152 Number of extensions: 6 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: 258 Length adjustment: 24 Effective length of query: 216 Effective length of database: 234 Effective search space: 50544 Effective search space used: 50544 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