Protein Info for PP_2148 in Pseudomonas putida KT2440

Annotation: transcription-repair coupling factor

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

1 100 200 300 400 500 600 700 800 900 1000 1149 signal peptide" amino acids 1 to 34 (34 residues), see Phobius details PF17757: UvrB_inter" amino acids 129 to 217 (89 residues), 95.6 bits, see alignment 5.3e-31 TIGR00580: transcription-repair coupling factor" amino acids 147 to 1080 (934 residues), 1094.9 bits, see alignment E=0 PF21132: MFD_D3" amino acids 376 to 450 (75 residues), 89.9 bits, see alignment 3e-29 PF02559: CarD_TRCF_RID" amino acids 479 to 534 (56 residues), 67.1 bits, see alignment 4.1e-22 PF04851: ResIII" amino acids 603 to 760 (158 residues), 42.8 bits, see alignment E=1.9e-14 PF00270: DEAD" amino acids 604 to 766 (163 residues), 94 bits, see alignment E=3.1e-30 PF00271: Helicase_C" amino acids 803 to 908 (106 residues), 66 bits, see alignment E=1.2e-21 PF03461: TRCF" amino acids 1008 to 1099 (92 residues), 99.7 bits, see alignment E=3.4e-32

Best Hits

KEGG orthology group: K03723, transcription-repair coupling factor (superfamily II helicase) [EC: 3.6.4.-] (inferred from 54% identity to aci:ACIAD1395)

Predicted SEED Role

"Transcription-repair coupling factor" in subsystem DNA-replication or Transcription factors bacterial

Isozymes

Compare fitness of predicted isozymes for: 3.6.4.-

Use Curated BLAST to search for 3.6.4.-

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

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

Search 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 Q88KZ1 at UniProt or InterPro

Protein Sequence (1149 amino acids)

>PP_2148 transcription-repair coupling factor (Pseudomonas putida KT2440)
MSVLRLPQMSATAGKQTWGNLPGAALSLAIAEAASSAGRFTLLLTADSQAADRLEQELRF
FAPDLPVLPFPDWETLPYDLFSPHQDIISQRIASLYRLPELSHGILVVPITTALHRLAPT
RFLLGSSLVLDVGQTIDVEQMRLRLEASGYRCVDTVYEHGEFAVRGALIDLFPMGSKLPY
RIDLFDNEIETLRTFDPETQRSIDKVDSVRLLPAREFPMQKEEVTRFKARFRERFDVDFR
RSAIFQDLASGIIPAGIEYYLPLFFEETSTLFDYLPTDTQVFSLPGVEQAAEHFWNDVRG
RYEDRRGDLSRPLLPPAELFLPVEDCFARLKQWPRVVVSSEELEPGVGRERFPARALPNL
AIEAKANQPLAELANFLDQFPGRVLFTAESAGRREVLLELLERLKLRPHTVEGWDDFITG
AERLAITIAPLDDGLLLDDPGLALIAESPLFGQRVMQRRRRDKRGETANDAVIKNLTELR
EGAPVVHIDHGVGRYLGLATLEIDGQAAEFLTLEYAENAKLYVPVANLHLIARYTGSDDA
LAPLHRLGSEAWQKAKRKAAEQVRDVAAELLDIYARRAARKGYAFADPSADYATFSAGFP
FEETPDQQAAIEAVRADMLAPKPMDRLVCGDVGFGKTEVAMRAAFIAVHSGRQVAVLVPT
TLLAQQHYNSFRDRFADWPVTVEVMSRFKSAKEVAAAAADLAEGKIDILIGTHKLLQDDV
RFKDLGLAIIDEEHRFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVAGMRDLSIIAT
PPARRLSVRTFVMEQNKSTVKEALLRELLRGGQVYYLHNDVKTIEKCAADLAELVPEARI
GIGHGQMRERELEQVMSDFYHKRFNVLVASTIIETGIDVPSANTIVIERADKFGLAQLHQ
LRGRVGRSHHQAYAYLLTPTRQKVSADAEKRLEAIANTQDLGAGFVLATNDLEIRGAGEL
LGEGQSGQIQAVGFTLYMEMLERAVKAIRKGTQPNLEQPLGGGPEINLRLPALIPEDYLP
DVHARLILYKRIASAADEEGLKDLQVEMIDRFGLLPEPTKNLMRLTSLKLHAEKLGIKKV
DAGPNGGKLEFEAETPVDPLTLIKLIQGQPKRYKFEGATQFRFLVPMERPDERFNTLEAL
FERLTPQPA