May regulate transcription elongation by RNA polymerase II. May enhance transcriptional pausing at sites proximal to the promoter, which may in turn facilitate the assembly of an elongation competent RNA polymerase II complex. Arabidopsis thaliana (taxid: 3702)
May regulate transcription elongation by RNA polymerase II. May enhance transcriptional pausing at sites proximal to the promoter, which may in turn facilitate the assembly of an elongation competent RNA polymerase II complex.
Score = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 45/108 (41%), Positives = 64/108 (59%), Gaps = 2/108 (1%)
Query: 4 APAQIPTSFGHELRACLRCRLVKTYDQFRESGCENC-PFFKMDEDHERVVDCTTPNFNGI 62
A +P H LRACL C LVKT DQF GC+NC + +M + E V DCT+ +F+GI
Sbjct: 2 ALETVPKDLRH-LRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGI 60
Query: 63 ISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQY 110
I++M P SW ++W R+ F PG Y ++V+ LP+ + + V Y
Sbjct: 61 IAMMSPGDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAY 108
Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates mRNA processing and transcription elongation by RNA polymerase II. DSIF positively regulates mRNA capping by stimulating the mRNA guanylyltransferase activity of RNGTT/CAP1A. DSIF also acts cooperatively with the negative elongation factor complex (NELF complex) to enhance transcriptional pausing at sites proximal to the promoter. Transcriptional pausing may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF and NELF promote pausing by inhibition of the transcription elongation factor TFIIS/S-II. TFIIS/S-II binds to RNA polymerase II at transcription pause sites and stimulates the weak intrinsic nuclease activity of the enzyme. Cleavage of blocked transcripts by RNA polymerase II promotes the resumption of transcription from the new 3' terminus and may allow repeated attempts at transcription through natural pause sites.
Score = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 45/108 (41%), Positives = 64/108 (59%), Gaps = 2/108 (1%)
Query: 4 APAQIPTSFGHELRACLRCRLVKTYDQFRESGCENC-PFFKMDEDHERVVDCTTPNFNGI 62
A +P H LRACL C LVKT DQF GC+NC + +M + E V DCT+ +F+GI
Sbjct: 2 ALETVPKDLRH-LRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGI 60
Query: 63 ISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQY 110
I++M P SW ++W R+ F PG Y ++V+ LP+ + + V Y
Sbjct: 61 IAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAY 108
Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates mRNA processing and transcription elongation by RNA polymerase II. DSIF positively regulates mRNA capping by stimulating the mRNA guanylyltransferase activity of RNGTT/CAP1A. DSIF also acts cooperatively with the negative elongation factor complex (NELF complex) to enhance transcriptional pausing at sites proximal to the promoter. Transcriptional pausing may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF and NELF promote pausing by inhibition of the transcription elongation factor TFIIS/S-II. TFIIS/S-II binds to RNA polymerase II at transcription pause sites and stimulates the weak intrinsic nuclease activity of the enzyme. Cleavage of blocked transcripts by RNA polymerase II promotes the resumption of transcription from the new 3' terminus and may allow repeated attempts at transcription through natural pause sites.
Score = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 45/108 (41%), Positives = 64/108 (59%), Gaps = 2/108 (1%)
Query: 4 APAQIPTSFGHELRACLRCRLVKTYDQFRESGCENC-PFFKMDEDHERVVDCTTPNFNGI 62
A +P H LRACL C LVKT DQF GC+NC + +M + E V DCT+ +F+GI
Sbjct: 2 ALETVPKDLRH-LRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGI 60
Query: 63 ISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQY 110
I++M P SW ++W R+ F PG Y ++V+ LP+ + + V Y
Sbjct: 61 IAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAY 108
Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates mRNA processing and transcription elongation by RNA polymerase II. DSIF positively regulates mRNA capping by stimulating the mRNA guanylyltransferase activity of RNGTT/CAP1A. DSIF also acts cooperatively with the negative elongation factor complex (NELF complex) to enhance transcriptional pausing at sites proximal to the promoter. Transcriptional pausing may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF and NELF promote pausing by inhibition of the transcription elongation factor TFIIS/S-II. TFIIS/S-II binds to RNA polymerase II at transcription pause sites and stimulates the weak intrinsic nuclease activity of the enzyme. Cleavage of blocked transcripts by RNA polymerase II promotes the resumption of transcription from the new 3' terminus and may allow repeated attempts at transcription through natural pause sites. DSIF can also positively regulate transcriptional elongation and is required for the efficient activation of transcriptional elongation by the HIV-1 nuclear transcriptional activator, Tat. DSIF acts to suppress transcriptional pausing in transcripts derived from the HIV-1 LTR and blocks premature release of HIV-1 transcripts at terminator sequences.
Score = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 45/108 (41%), Positives = 64/108 (59%), Gaps = 2/108 (1%)
Query: 4 APAQIPTSFGHELRACLRCRLVKTYDQFRESGCENC-PFFKMDEDHERVVDCTTPNFNGI 62
A +P H LRACL C LVKT DQF GC+NC + +M + E V DCT+ +F+GI
Sbjct: 2 ALETVPKDLRH-LRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGI 60
Query: 63 ISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQY 110
I++M P SW ++W R+ F PG Y ++V+ LP+ + + V Y
Sbjct: 61 IAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAY 108
Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates mRNA processing and transcription elongation by RNA polymerase II. DSIF positively regulates mRNA capping by stimulating the mRNA guanylyltransferase activity of RNGTT/CAP1A. DSIF also acts cooperatively with the negative elongation factor complex (NELF complex) to enhance transcriptional pausing at sites proximal to the promoter. Transcriptional pausing may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF and NELF promote pausing by inhibition of the transcription elongation factor TFIIS/S-II. TFIIS/S-II binds to RNA polymerase II at transcription pause sites and stimulates the weak intrinsic nuclease activity of the enzyme. Cleavage of blocked transcripts by RNA polymerase II promotes the resumption of transcription from the new 3' terminus and may allow repeated attempts at transcription through natural pause sites.
Score = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 45/108 (41%), Positives = 64/108 (59%), Gaps = 2/108 (1%)
Query: 4 APAQIPTSFGHELRACLRCRLVKTYDQFRESGCENC-PFFKMDEDHERVVDCTTPNFNGI 62
A +P H LRACL C LVKT DQF GC+NC + +M + E V DCT+ +F+GI
Sbjct: 2 ALETVPKDLRH-LRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGI 60
Query: 63 ISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQY 110
I++M P SW ++W R+ F PG Y ++V+ LP+ + + V Y
Sbjct: 61 IAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAY 108
Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates mRNA processing and transcription elongation by RNA polymerase II. DSIF positively regulates mRNA capping by stimulating the mRNA guanylyltransferase activity of RNGTT/CAP1A. DSIF also acts cooperatively with the negative elongation factor complex (NELF complex) to enhance transcriptional pausing at sites proximal to the promoter. Transcriptional pausing may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF and NELF promote pausing by inhibition of the transcription elongation factor TFIIS/S-II. TFIIS/S-II binds to RNA polymerase II at transcription pause sites and stimulates the weak intrinsic nuclease activity of the enzyme. Cleavage of blocked transcripts by RNA polymerase II promotes the resumption of transcription from the new 3' terminus and may allow repeated attempts at transcription through natural pause sites.
Score = 94.7 bits (234), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 44/91 (48%), Positives = 60/91 (65%), Gaps = 5/91 (5%)
Query: 16 LRACLRCRLVKTYDQFRESGCENCP-FFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAA 74
LRACL C LVK++DQF GCENC F +M + + V D T+ NF+GII++ PT SW A
Sbjct: 13 LRACLVCSLVKSFDQFETDGCENCEEFLRMKNNKDNVYDHTSNNFDGIIALTTPTDSWVA 72
Query: 75 RWLRIGRFVPGCYTLAVSEALPE----DLQN 101
+W R+ RF G Y ++VS LP+ D++N
Sbjct: 73 KWQRLSRFTRGIYAISVSGTLPQSTLRDMKN 103
Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates transcription elongation by RNA polymerase II. DSIF enhances transcriptional pausing at sites proximal to the promoter, which may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF may also promote transcriptional elongation within coding regions. DSIF is required for the transcriptional induction of heat shock response genes and regulation of genes which control anterior-posterior patterning during embryonic development.
Score = 94.4 bits (233), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 45/108 (41%), Positives = 64/108 (59%), Gaps = 2/108 (1%)
Query: 4 APAQIPTSFGHELRACLRCRLVKTYDQFRESGCENC-PFFKMDEDHERVVDCTTPNFNGI 62
A +P H LRACL C LVKT DQF GC+NC + +M + E V DCT+ +F+GI
Sbjct: 2 ALETVPKDLRH-LRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGI 60
Query: 63 ISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQY 110
+++M P SW ++W RI F PG Y ++V+ LP+ + + V Y
Sbjct: 61 VAMMSPDDSWVSKWQRITNFKPGVYAVSVTGRLPQGIVRELKSRGVVY 108
May function as a component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates transcription elongation by RNA polymerase II. Probably enhances transcriptional pausing at sites proximal to the promoter, which may in turn facilitate the assembly of an elongation competent RNA polymerase II complex.
Score = 94.0 bits (232), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 43/90 (47%), Positives = 58/90 (64%), Gaps = 2/90 (2%)
Query: 8 IPTSFGHELRACLRCRLVKTYDQFRESGCENC-PFFKMDEDHERVVDCTTPNFNGIISVM 66
+P H LRACL C LVKT DQF GC+NC + +M + E V +CT+ +F+G+I++M
Sbjct: 6 VPKDLRH-LRACLLCSLVKTIDQFEYDGCDNCESYLQMKGNREMVYECTSSSFDGVIAMM 64
Query: 67 DPTRSWAARWLRIGRFVPGCYTLAVSEALP 96
P SW A+W RIG F PG Y + V+ LP
Sbjct: 65 SPEDSWVAKWQRIGNFKPGVYAVTVTGRLP 94
May function as a component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates transcription elongation by RNA polymerase II. Probably enhances transcriptional pausing at sites proximal to the promoter, which may facilitate the assembly of an elongation competent RNA polymerase II complex. Also acts to stimulate transcriptional elongation at low nucleotide concentrations. Regulation of transcriptional elongation by this protein is required for the expression of genes which control neuronal development.
Danio rerio (taxid: 7955)
Close Homologs in the Non-Redundant Database Detected by BLAST
>gi|224109936|ref|XP_002315361.1| predicted protein [Populus trichocarpa] gi|118489920|gb|ABK96757.1| unknown [Populus trichocarpa x Populus deltoides] gi|222864401|gb|EEF01532.1| predicted protein [Populus trichocarpa]
Score = 155 bits (393), Expect = 1e-50
Identities = 53/98 (54%), Positives = 65/98 (66%), Gaps = 1/98 (1%)
Query: 14 HELRACLRCRLVKTYDQFRESGCENC-PFFKMDEDHERVVDCTTPNFNGIISVMDPTRSW 72
LRACL C L+KT DQF GC NC + M +HERV DCT+PNF GII++MDP +SW
Sbjct: 1 RGLRACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFEGIIALMDPEKSW 60
Query: 73 AARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQY 110
ARW RI +FVPG Y ++VS LPED+ E + Y
Sbjct: 61 VARWQRIDKFVPGIYAISVSGRLPEDIVEELESRGIIY 98
Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 complex. Spt4 homolog is not found in bacteria. Length = 98
Score = 131 bits (331), Expect = 1e-41
Identities = 43/77 (55%), Positives = 55/77 (71%)
Query: 16 LRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAAR 75
LRACL C LVKT DQF + GC NC F M D ERV +CT+ NF G+++++DP +SW A+
Sbjct: 1 LRACLLCSLVKTEDQFEDDGCPNCEFLHMKGDRERVSECTSENFEGLVAILDPEKSWVAK 60
Query: 76 WLRIGRFVPGCYTLAVS 92
W R+G+FVPG Y L V
Sbjct: 61 WQRLGKFVPGKYALKVR 77
This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery. Length = 77
Score = 98.1 bits (244), Expect = 6e-28
Identities = 41/96 (42%), Positives = 54/96 (56%)
Query: 17 RACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARW 76
RACL C +VKT + FR+ GC NCP M V +CT+P F G+++++ PT SW A+W
Sbjct: 10 RACLGCGIVKTLNGFRKDGCPNCPMLNMKGGVTNVEECTSPKFEGVVAMLQPTNSWVAKW 69
Query: 77 LRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQYVP 112
RI F G Y + V AL ED+ E Y P
Sbjct: 70 QRIDEFRKGLYAMVVEGALSEDVVEDLEQHGRIYYP 105
Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
>PF06093 Spt4: Spt4/RpoE2 zinc finger; InterPro: IPR022800 This entry consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 []
Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles []. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in []. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery. ; PDB: 2EXU_A 3H7H_A 3LPE_F 3P8B_A 1RYQ_A 3QQC_E.
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines
The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
>PRK00076 recR recombination protein RecR; Reviewed
