Protein Info for Synpcc7942_1977 in Synechococcus elongatus PCC 7942

Name: ndhF1
Annotation: NAD(P)H-quinone oxidoreductase subunit F

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

1 50 100 150 200 250 300 350 400 450 500 550 600 665 transmembrane" amino acids 6 to 29 (24 residues), see Phobius details amino acids 41 to 62 (22 residues), see Phobius details amino acids 91 to 110 (20 residues), see Phobius details amino acids 122 to 141 (20 residues), see Phobius details amino acids 147 to 166 (20 residues), see Phobius details amino acids 179 to 200 (22 residues), see Phobius details amino acids 217 to 239 (23 residues), see Phobius details amino acids 260 to 281 (22 residues), see Phobius details amino acids 293 to 311 (19 residues), see Phobius details amino acids 323 to 344 (22 residues), see Phobius details amino acids 351 to 372 (22 residues), see Phobius details amino acids 391 to 412 (22 residues), see Phobius details amino acids 430 to 451 (22 residues), see Phobius details amino acids 496 to 516 (21 residues), see Phobius details amino acids 542 to 564 (23 residues), see Phobius details amino acids 646 to 664 (19 residues), see Phobius details TIGR01974: proton-translocating NADH-quinone oxidoreductase, chain L" amino acids 8 to 660 (653 residues), 639.6 bits, see alignment E=4e-196 PF00662: Proton_antipo_N" amino acids 75 to 125 (51 residues), 68.5 bits, see alignment 5.7e-23 PF00361: Proton_antipo_M" amino acids 141 to 434 (294 residues), 294.4 bits, see alignment E=1.4e-91 PF01010: Proton_antipo_C" amino acids 480 to 610 (131 residues), 38.5 bits, see alignment E=1.5e-13

Best Hits

Swiss-Prot: 74% identical to NU5C_SYNP2: NAD(P)H-quinone oxidoreductase chain 5 (ndhF) from Synechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6)

KEGG orthology group: K05577, NADH dehydrogenase I subunit 5 [EC: 1.6.5.3] (inferred from 100% identity to syc:syc2119_d)

MetaCyc: 100% identical to ferredoxin-plastoquinone oxidoreductase subunit F1 (Synechococcus elongatus PCC 7942 = FACHB-805)

Predicted SEED Role

"NADH dehydrogenase subunit 5, Involved in CO2 fixation" in subsystem CO2 uptake, carboxysome

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 1.6.5.3

Use Curated BLAST to search for 1.6.5.3

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Compare to protein structures

Predict protein localization: PSORTb (Gram-negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

See Q31LR2 at UniProt or InterPro

Protein Sequence (665 amino acids)

>Synpcc7942_1977 NAD(P)H-quinone oxidoreductase subunit F (Synechococcus elongatus PCC 7942)
MEFLYDYAWLIPVLPLLAATGVGLGLITVNQATNKLRQLNAALIMTALGGSATFAFGLLA
SQLSGHPTYTRMFDWASAGDFHLSMGYTIDPLTTVMLTVVTTVALLVMLYTDGYMAHDRG
YVRFYAYLSLFSSSMLGLVISPNLVQIYIFWELVGMCSYLLVGFWYDRKAAADACQKAFV
TNRVGDFGLLLGMLGLYWATGSFEFTEIGDRLQSLISSGALSAGLATLFGILVFLGPVAK
SAQFPLHVWLPDAMEGPTPISALIHAATMVAAGVFLIARMYPVFEQLPTVMDVIAWTGAF
TAFLGASIALTQNDIKKGLAYSTISQLGYMVMAMGVGAYSAGLFHLVTHAYFKAMLFLGS
GSVIHGMEAVVGHNPVLAQDMRLMGGLRKYMPVTAITFLIGNLAIAGIPPFAGFWSKDEI
LGATFAANPILWGVGFATAGLTAFYMFRIYFLTFEGSFRGEDATIQAKLLAEAGVTAGHG
HDEHHDHVPHESPWTMALPLAILAVPSALIGLLGMPWNNRFEAFVKAPGEAVHAGHFELQ
EFLTLGGASVAIALTGITIALLTYRLGRINPAAIAERFQPLYQFSRNKWYLDDLNDVLFV
QGSRRLARQVLEVDSKVVDGLVNLTGLVTLVTGESLKYFENGRAQFYALIVFGAVLGLVV
AFGVT