Psyllid ID: psy8227

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-----
Protein Sequence
MIARDEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHccccccccccccccccHHHHHHcccccHHHHHHcccccccEEcccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHccEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHccHHHHHHHHHEEEHHEccHHHHHHcccccHHHHHHccccHHHHHcccccccc
Coil and Loop (DISEMBL)
MIARDEVAQLWAYVRSHVHVqvgrmpesLAAKFTQHVGILCYCLWFLWTLVHSATmvhgtsnnnakiddfnNLAKYFRQARAclgcsqiktfdqfefdgcdncdeflhmknsrdnvynctssnfd
Flexible Loop (DISEMBL)
MIARDEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLhmknsrdnvynctssnfd
Low Complexity Region (SEG)
MIARDEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD
Disordered region (IsUnstruct)
******VAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVY********
Disordered Region (DISOPRED)
****DEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGILCYCLWFLWTLVHS******************NLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSN**
Disordered Region (DISEMBL)
MIARDEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD
Disordered Region (DISPRO)
MIARDEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNF*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MIARDEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	125	2.2.26 [Sep-21-2011]
Q9TVQ5	116	Transcription elongation	yes	N/A	0.448	0.482	0.625	7e-15
Q5RFH5	117	Transcription elongation	yes	N/A	0.448	0.478	0.589	9e-15
Q5HZ97	117	Transcription elongation	N/A	N/A	0.448	0.478	0.589	9e-15
Q4R941	117	Transcription elongation	N/A	N/A	0.448	0.478	0.589	1e-14
P63272	117	Transcription elongation	yes	N/A	0.448	0.478	0.589	1e-14
Q3SYX6	117	Transcription elongation	yes	N/A	0.448	0.478	0.589	1e-14
P63271	117	Transcription elongation	yes	N/A	0.448	0.478	0.589	1e-14
Q9Z199	117	Transcription elongation	yes	N/A	0.448	0.478	0.589	1e-14
Q6DGQ0	117	Transcription elongation	yes	N/A	0.448	0.478	0.571	2e-14
Q628A6	120	Transcription elongation	N/A	N/A	0.392	0.408	0.571	1e-11

>sp|Q9TVQ5|SPT4H_DROME Transcription elongation factor SPT4 OS=Drosophila melanogaster GN=spt4 PE=1 SV=1

 Score = 79.3 bits (194), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 35/56 (62%), Positives = 45/56 (80%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
           F+ + K  R  RACL CS +K+FDQFE DGC+NC+EFL MKN++DNVY+ TS+NFD
Sbjct: 3   FDAIPKDLRGLRACLVCSLVKSFDQFETDGCENCEEFLRMKNNKDNVYDHTSNNFD 58

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.
Drosophila melanogaster (taxid: 7227)

>sp|Q5RFH5|SPT4H_PONAB Transcription elongation factor SPT4 OS=Pongo abelii GN=SUPT4H1 PE=3 SV=1

 Score = 79.0 bits (193), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 41/56 (73%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              + K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct: 3   LETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

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.

Pongo abelii (taxid: 9601)

>sp|Q5HZ97|SPT4H_XENLA Transcription elongation factor SPT4 OS=Xenopus laevis GN=supt4h1 PE=3 SV=1

 Score = 78.6 bits (192), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 41/56 (73%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              + K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct: 3   LETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

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.

Xenopus laevis (taxid: 8355)

>sp|Q4R941|SPT4H_MACFA Transcription elongation factor SPT4 OS=Macaca fascicularis GN=SUPT4H1 PE=3 SV=1

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 41/56 (73%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              + K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct: 3   LETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

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.

Macaca fascicularis (taxid: 9541)

>sp|P63272|SPT4H_HUMAN Transcription elongation factor SPT4 OS=Homo sapiens GN=SUPT4H1 PE=1 SV=1

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 41/56 (73%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              + K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct: 3   LETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

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.

Homo sapiens (taxid: 9606)

>sp|Q3SYX6|SPT4H_BOVIN Transcription elongation factor SPT4 OS=Bos taurus GN=SUPT4H1 PE=3 SV=1

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 41/56 (73%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              + K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct: 3   LETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

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.

Bos taurus (taxid: 9913)

>sp|P63271|SPT41_MOUSE Transcription elongation factor SPT4 1 OS=Mus musculus GN=Supt4h1 PE=2 SV=1

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 41/56 (73%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              + K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct: 3   LETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

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.

Mus musculus (taxid: 10090)

>sp|Q9Z199|SPT42_MOUSE Transcription elongation factor SPT4 2 OS=Mus musculus GN=Supt4h2 PE=2 SV=1

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 41/56 (73%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              + K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct: 3   LETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

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.

Mus musculus (taxid: 10090)

>sp|Q6DGQ0|SPT4H_DANRE Transcription elongation factor SPT4 OS=Danio rerio GN=supt4h1 PE=3 SV=1

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 32/56 (57%), Positives = 40/56 (71%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              + K  R  RACL CS +KT DQFE+DGCDNC+ +L MK +R+ VY CTSS+FD
Sbjct: 3   LETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCESYLQMKGNREMVYECTSSSFD 58

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)

>sp|Q628A6|SPT4H_CAEBR Transcription elongation factor SPT4 OS=Caenorhabditis briggsae GN=spt-4 PE=3 SV=1

 Score = 68.6 bits (166), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 28/49 (57%), Positives = 36/49 (73%)

Query: 77  FRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
            R  RACL CS IK+ D F+ DGC+NCDE LH+K   + VY+CTS+N+D
Sbjct: 9   LRNLRACLLCSLIKSVDAFQTDGCENCDEVLHLKGDEEKVYDCTSANYD 57

May function as a component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates transcription elongation by RNA polymerase II. DSIF 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.

Caenorhabditis briggsae (taxid: 6238)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	125
427786237	118	Putative transcription elongation factor	0.448	0.474	0.714	4e-17
442747457	118	Putative transcription elongation factor	0.448	0.474	0.714	4e-17
241680460	118	transcription elongation factor SPT4, pu	0.448	0.474	0.714	5e-17
340711990	114	PREDICTED: transcription elongation fact	0.424	0.464	0.773	1e-16
350402496	114	PREDICTED: transcription elongation fact	0.424	0.464	0.773	2e-16
66513379	116	PREDICTED: transcription elongation fact	0.448	0.482	0.696	4e-16
307211608	116	Transcription elongation factor SPT4 [Ha	0.424	0.456	0.754	4e-16
193613262	116	PREDICTED: transcription elongation fact	0.448	0.482	0.696	4e-16
357626150	116	hypothetical protein KGM_12908 [Danaus p	0.448	0.482	0.696	4e-16
383861308	114	PREDICTED: transcription elongation fact	0.424	0.464	0.735	7e-16

>gi|427786237|gb|JAA58570.1| Putative transcription elongation factor spt4 [Rhipicephalus pulchellus]

 Score = 92.0 bits (227), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 40/56 (71%), Positives = 46/56 (82%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             ++ K  R  RACL CS IKTF+QFEFDGCDNCDE+LHMKN+RD VY+CTSSNFD
Sbjct: 5   LESIPKDLRNLRACLLCSMIKTFEQFEFDGCDNCDEYLHMKNNRDMVYDCTSSNFD 60

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|442747457|gb|JAA65888.1| Putative transcription elongation factor spt4 [Ixodes ricinus]

 Score = 92.0 bits (227), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 40/56 (71%), Positives = 46/56 (82%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             ++ K  R  RACL CS IKTF+QFEFDGCDNCDE+LHMKN+RD VY+CTSSNFD
Sbjct: 5   LESIPKDLRNLRACLLCSMIKTFEQFEFDGCDNCDEYLHMKNNRDMVYDCTSSNFD 60

Source: Ixodes ricinus

Species: Ixodes ricinus

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241680460|ref|XP_002400900.1| transcription elongation factor SPT4, putative [Ixodes scapularis] gi|215504294|gb|EEC13788.1| transcription elongation factor SPT4, putative [Ixodes scapularis]

 Score = 91.7 bits (226), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 40/56 (71%), Positives = 46/56 (82%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             ++ K  R  RACL CS IKTF+QFEFDGCDNCDE+LHMKN+RD VY+CTSSNFD
Sbjct: 5   LESIPKDLRNLRACLLCSMIKTFEQFEFDGCDNCDEYLHMKNNRDMVYDCTSSNFD 60

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340711990|ref|XP_003394548.1| PREDICTED: transcription elongation factor SPT4-like isoform 1 [Bombus terrestris] gi|340711992|ref|XP_003394549.1| PREDICTED: transcription elongation factor SPT4-like isoform 2 [Bombus terrestris]

 Score = 90.1 bits (222), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/53 (77%), Positives = 46/53 (86%)

Query: 73  LAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
           +AK  R  RACL CS IKTFDQFEFDGCDNCDEFL MKN++DNV++CTSSNFD
Sbjct: 4   VAKDLRNLRACLVCSLIKTFDQFEFDGCDNCDEFLRMKNNKDNVFDCTSSNFD 56

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350402496|ref|XP_003486507.1| PREDICTED: transcription elongation factor SPT4-like [Bombus impatiens]

 Score = 89.7 bits (221), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/53 (77%), Positives = 46/53 (86%)

Query: 73  LAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
           +AK  R  RACL CS IKTFDQFEFDGCDNCDEFL MKN++DNV++CTSSNFD
Sbjct: 4   VAKDLRGLRACLVCSLIKTFDQFEFDGCDNCDEFLRMKNNKDNVFDCTSSNFD 56

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66513379|ref|XP_624457.1| PREDICTED: transcription elongation factor SPT4 isoform 2 [Apis mellifera] gi|380030199|ref|XP_003698741.1| PREDICTED: transcription elongation factor SPT4-like [Apis florea]

 Score = 89.0 bits (219), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 39/56 (69%), Positives = 45/56 (80%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              + K  R  RACL CS +KTFDQFEFDGCDNCDEFL MKN++DNV++CTSSNFD
Sbjct: 3   METVPKELRGLRACLVCSLVKTFDQFEFDGCDNCDEFLRMKNNKDNVFDCTSSNFD 58

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307211608|gb|EFN87657.1| Transcription elongation factor SPT4 [Harpegnathos saltator]

 Score = 89.0 bits (219), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 40/53 (75%), Positives = 45/53 (84%)

Query: 73  LAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
           + K  R  RACL CS IKTFDQFEFDGCDNCDEFL MKN++DNV++CTSSNFD
Sbjct: 6   VPKDLRGLRACLVCSLIKTFDQFEFDGCDNCDEFLRMKNNKDNVFDCTSSNFD 58

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193613262|ref|XP_001952282.1| PREDICTED: transcription elongation factor SPT4-like [Acyrthosiphon pisum]

 Score = 89.0 bits (219), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 39/56 (69%), Positives = 47/56 (83%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
            +++ K  R ARACL CS IK+FDQFE DGCDNCDEFL +KN+RD+VY+CTSSNFD
Sbjct: 3   LDSIPKDMRSARACLVCSLIKSFDQFEIDGCDNCDEFLRLKNNRDHVYDCTSSNFD 58

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357626150|gb|EHJ76345.1| hypothetical protein KGM_12908 [Danaus plexippus]

 Score = 88.6 bits (218), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 39/56 (69%), Positives = 46/56 (82%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
            + + K  R  RACL CS IKTFDQFE+DGCDNCDEFL MKN++DNVY+CTS+NFD
Sbjct: 3   LDTVPKDLRGLRACLVCSLIKTFDQFEYDGCDNCDEFLRMKNNKDNVYDCTSNNFD 58

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383861308|ref|XP_003706128.1| PREDICTED: transcription elongation factor SPT4-like [Megachile rotundata]

 Score = 87.8 bits (216), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 39/53 (73%), Positives = 45/53 (84%)

Query: 73  LAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
           + K  R  RACL CS +KTFDQFEFDGCDNCDEFL MKN++DNV++CTSSNFD
Sbjct: 4   VPKDLRGLRACLVCSLVKTFDQFEFDGCDNCDEFLRMKNNKDNVFDCTSSNFD 56

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	125
FB|FBgn0028683	116	spt4 "spt4" [Drosophila melano	0.448	0.482	0.625	7.7e-16
UNIPROTKB|Q3SYX6	117	SUPT4H1 "Transcription elongat	0.408	0.435	0.647	5.4e-15
UNIPROTKB|E2RAN9	117	SUPT4H1 "Uncharacterized prote	0.408	0.435	0.647	5.4e-15
UNIPROTKB|J3QR04	59	SUPT4H1 "Transcription elongat	0.408	0.864	0.647	5.4e-15
UNIPROTKB|P63272	117	SUPT4H1 "Transcription elongat	0.408	0.435	0.647	5.4e-15
UNIPROTKB|F2Z535	96	LOC100515097 "Uncharacterized	0.408	0.531	0.647	5.4e-15
UNIPROTKB|K7GKT6	117	LOC100515097 "Uncharacterized	0.408	0.435	0.647	5.4e-15
UNIPROTKB|Q4R941	117	SUPT4H1 "Transcription elongat	0.408	0.435	0.647	5.4e-15
UNIPROTKB|Q5HZ97	117	supt4h1 "Transcription elongat	0.408	0.435	0.647	5.4e-15
UNIPROTKB|Q5RFH5	117	SUPT4H1 "Transcription elongat	0.408	0.435	0.647	5.4e-15

FB|FBgn0028683 spt4 "spt4" [Drosophila melanogaster (taxid:7227)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 35/56 (62%), Positives = 45/56 (80%)

Query:    70 FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             F+ + K  R  RACL CS +K+FDQFE DGC+NC+EFL MKN++DNVY+ TS+NFD
Sbjct:     3 FDAIPKDLRGLRACLVCSLVKSFDQFETDGCENCEEFLRMKNNKDNVYDHTSNNFD 58

GO:0016582 "non-covalent chromatin modification" evidence=ISS

GO:0005634 "nucleus" evidence=ISS;IDA

GO:0003682 "chromatin binding" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032786 "positive regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0008023 "transcription elongation factor complex" evidence=IDA

UNIPROTKB|Q3SYX6 SUPT4H1 "Transcription elongation factor SPT4" [Bos taurus (taxid:9913)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 33/51 (64%), Positives = 40/51 (78%)

Query:    75 KYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct:     8 KDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

GO:0032044 "DSIF complex" evidence=ISS

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0034244 "negative regulation of transcription elongation from RNA polymerase II promoter" evidence=IEA

GO:0032786 "positive regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E2RAN9 SUPT4H1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 33/51 (64%), Positives = 40/51 (78%)

Query:    75 KYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct:     8 KDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0034244 "negative regulation of transcription elongation from RNA polymerase II promoter" evidence=IEA

GO:0032786 "positive regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0032044 "DSIF complex" evidence=IEA

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|J3QR04 SUPT4H1 "Transcription elongation factor SPT4" [Homo sapiens (taxid:9606)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 33/51 (64%), Positives = 40/51 (78%)

Query:    75 KYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct:     8 KDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

GO:0034244 "negative regulation of transcription elongation from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|P63272 SUPT4H1 "Transcription elongation factor SPT4" [Homo sapiens (taxid:9606)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 33/51 (64%), Positives = 40/51 (78%)

Query:    75 KYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct:     8 KDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

GO:0008270 "zinc ion binding" evidence=IEA

GO:0034244 "negative regulation of transcription elongation from RNA polymerase II promoter" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0032785 "negative regulation of DNA-dependent transcription, elongation" evidence=IDA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=IDA;TAS

GO:0046982 "protein heterodimerization activity" evidence=IPI

GO:0032786 "positive regulation of DNA-dependent transcription, elongation" evidence=IDA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0032044 "DSIF complex" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=TAS

GO:0006338 "chromatin remodeling" evidence=TAS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0050434 "positive regulation of viral transcription" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F2Z535 LOC100515097 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 33/51 (64%), Positives = 40/51 (78%)

Query:    75 KYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct:     5 KDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 55

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0034244 "negative regulation of transcription elongation from RNA polymerase II promoter" evidence=IEA

GO:0032786 "positive regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0032044 "DSIF complex" evidence=IEA

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|K7GKT6 LOC100515097 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 33/51 (64%), Positives = 40/51 (78%)

Query:    75 KYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct:     8 KDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

GO:0032786 "positive regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q4R941 SUPT4H1 "Transcription elongation factor SPT4" [Macaca fascicularis (taxid:9541)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 33/51 (64%), Positives = 40/51 (78%)

Query:    75 KYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct:     8 KDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

GO:0032044 "DSIF complex" evidence=ISS

UNIPROTKB|Q5HZ97 supt4h1 "Transcription elongation factor SPT4" [Xenopus laevis (taxid:8355)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 33/51 (64%), Positives = 40/51 (78%)

Query:    75 KYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct:     8 KDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

GO:0032044 "DSIF complex" evidence=ISS

UNIPROTKB|Q5RFH5 SUPT4H1 "Transcription elongation factor SPT4" [Pongo abelii (taxid:9601)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 33/51 (64%), Positives = 40/51 (78%)

Query:    75 KYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
             K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct:     8 KDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58

GO:0032044 "DSIF complex" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9TVQ5	SPT4H_DROME	No assigned EC number	0.625	0.448	0.4827	yes	N/A
Q3SYX6	SPT4H_BOVIN	No assigned EC number	0.5892	0.448	0.4786	yes	N/A
Q9Z199	SPT42_MOUSE	No assigned EC number	0.5892	0.448	0.4786	yes	N/A
P63272	SPT4H_HUMAN	No assigned EC number	0.5892	0.448	0.4786	yes	N/A
P63271	SPT41_MOUSE	No assigned EC number	0.5892	0.448	0.4786	yes	N/A
Q5RFH5	SPT4H_PONAB	No assigned EC number	0.5892	0.448	0.4786	yes	N/A
Q6DGQ0	SPT4H_DANRE	No assigned EC number	0.5714	0.448	0.4786	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	125
cd07973	98	cd07973, Spt4, Transcription elongation factor Spt	9e-24
pfam06093	77	pfam06093, Spt4, Spt4/RpoE2 zinc finger	3e-18
COG5204	112	COG5204, SPT4, Transcription elongation factor SPT	1e-09

>gnl|CDD|153422 cd07973, Spt4, Transcription elongation factor Spt4

 Score = 87.3 bits (217), Expect = 9e-24
 Identities = 29/48 (60%), Positives = 35/48 (72%)

Query: 78  RQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
           R  RACL CS IKT DQFE DGC NC+ +L MK + + VY+CTS NF+
Sbjct: 1   RGLRACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFE 48

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

>gnl|CDD|203389 pfam06093, Spt4, Spt4/RpoE2 zinc finger

 Score = 72.7 bits (179), Expect = 3e-18
 Identities = 30/45 (66%), Positives = 33/45 (73%), Gaps = 1/45 (2%)

Query: 81  RACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
           RACL CS +KT DQFE DGC NC EFLHMK  R+ V  CTS NF+
Sbjct: 2   RACLLCSLVKTEDQFEDDGCPNC-EFLHMKGDRERVSECTSENFE 45

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

>gnl|CDD|227530 COG5204, SPT4, Transcription elongation factor SPT4 [Transcription]

 Score = 51.5 bits (123), Expect = 1e-09
 Identities = 23/46 (50%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 80  ARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
           +RACLGC  +KT + F  DGC NC   L+MK    NV  CTS  F+
Sbjct: 9   SRACLGCGIVKTLNGFRKDGCPNC-PMLNMKGGVTNVEECTSPKFE 53

Length = 112

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	125
KOG3490|consensus	111		99.91
cd07973	98	Spt4 Transcription elongation factor Spt4. Spt4 is	99.81
PF06093	77	Spt4: Spt4/RpoE2 zinc finger; InterPro: IPR022800	99.77
COG5204	112	SPT4 Transcription elongation factor SPT4 [Transcr	99.58
PRK06393	64	rpoE DNA-directed RNA polymerase subunit E''; Vali	96.07
PRK08351	61	DNA-directed RNA polymerase subunit E''; Validated	95.78
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	87.05
PF02591	56	DUF164: Putative zinc ribbon domain; InterPro: IPR	85.8

>KOG3490|consensus

Probab=99.91  E-value=9.5e-26  Score=167.19  Aligned_cols=52  Identities=54%  Similarity=1.025  Sum_probs=50.5

Q ss_pred             cccccccccccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227          73 LAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD  125 (125)
Q Consensus        73 VP~~~R~LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd  125 (125)
                      +|+++|+|||||+||||||.+||+++|||||+ +|+|+||.|+|+||||||||
T Consensus         1 ~~~~~~~lRACllCs~Vkt~~~F~~dGC~Nc~-~l~mkgn~e~V~ecTS~nF~   52 (111)
T KOG3490|consen    1 VPKDLRKLRACLLCSIVKTLNGFRKDGCENCP-MLNMKGNVENVYECTSPNFD   52 (111)
T ss_pred             CcchhhhhhhhhhhhhhhhhhhhhhcCCCCch-hhhhccCcceeEEecCCCcc
Confidence            58889999999999999999999999999999 99999999999999999997

>cd07973 Spt4 Transcription elongation factor Spt4

Probab=99.81  E-value=5.6e-21  Score=137.51  Aligned_cols=48  Identities=60%  Similarity=1.097  Sum_probs=46.6

Q ss_pred             ccccccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227          78 RQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD  125 (125)
Q Consensus        78 R~LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd  125 (125)
                      |++|||+.|++|+|.+||..+|||||+.+|+|+||+++|+||||++|+
T Consensus         1 r~lrAC~~C~~I~~~~qf~~~gCpnC~~~l~~~g~~~~v~~~tT~~f~   48 (98)
T cd07973           1 RGLRACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFE   48 (98)
T ss_pred             CCCchhccCCcccccccccCCCCCCCcchhccCCCccccccccCCCcc
Confidence            689999999999999999999999999999999999999999999996

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 []

Probab=99.77  E-value=3.4e-20  Score=128.33  Aligned_cols=45  Identities=58%  Similarity=1.069  Sum_probs=39.6

Q ss_pred             ccccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227          80 ARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD  125 (125)
Q Consensus        80 LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd  125 (125)
                      ||||+.|++|+|.+||+++||||| ++|+|+||+|++.+|||++|+
T Consensus         1 lrAC~~C~~i~t~~qF~~~gCpnC-~~l~~~~~~~~~~~~tT~~f~   45 (77)
T PF06093_consen    1 LRACLRCRLIKTEDQFRDEGCPNC-PFLQMKGDRDRVSDCTTPNFE   45 (77)
T ss_dssp             EEEETTT-BEECCCHHHHH--TTT-HHHH-TCHCHHCHCCEESSEE
T ss_pred             CcccccCCcccCHhHccCCCCCCC-ccccccCCcCcccccCCCCCc
Confidence            799999999999999999999999 699999999999999999995

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.

>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]

Probab=99.58  E-value=2.7e-16  Score=116.82  Aligned_cols=44  Identities=52%  Similarity=1.041  Sum_probs=42.9

Q ss_pred             cccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227          81 RACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD  125 (125)
Q Consensus        81 RACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd  125 (125)
                      ||||.||||||.+.|.++|||||+ .|.|+|+-+.|.+||||.|+
T Consensus        10 RACl~Cgiv~t~n~F~~dGCpNc~-~l~~~~gV~~ve~~TSp~Fe   53 (112)
T COG5204          10 RACLGCGIVKTLNGFRKDGCPNCP-MLNMKGGVTNVEECTSPKFE   53 (112)
T ss_pred             hhhhhcceeeecccccccCCCCCc-ccccccCccceeeecCcchH
Confidence            999999999999999999999998 89999999999999999996

>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated

Probab=96.07  E-value=0.0025  Score=43.76  Aligned_cols=23  Identities=26%  Similarity=0.517  Sum_probs=19.3

Q ss_pred             ccccccccCCcccchhhhhhcCCCChhh
Q psy8227          78 RQARACLGCSQIKTFDQFEFDGCDNCDE  105 (125)
Q Consensus        78 R~LRACLlCsLVKT~dQF~~dGCpNCe~  105 (125)
                      +.++||..|..|.+     .+.||||.+
T Consensus         3 ~~~~AC~~C~~i~~-----~~~Cp~Cgs   25 (64)
T PRK06393          3 VQYRACKKCKRLTP-----EKTCPVHGD   25 (64)
T ss_pred             chhhhHhhCCcccC-----CCcCCCCCC
Confidence            46899999999995     448999984

>PRK08351 DNA-directed RNA polymerase subunit E''; Validated

Probab=95.78  E-value=0.0039  Score=42.32  Aligned_cols=21  Identities=38%  Similarity=0.784  Sum_probs=17.6

Q ss_pred             ccccccCCcccchhhhhhcCCCChhh
Q psy8227          80 ARACLGCSQIKTFDQFEFDGCDNCDE  105 (125)
Q Consensus        80 LRACLlCsLVKT~dQF~~dGCpNCe~  105 (125)
                      ++||..|+.|.+.+     .||||.+
T Consensus         3 ~kAC~~C~~i~~~~-----~CP~Cgs   23 (61)
T PRK08351          3 EKACRHCHYITTED-----RCPVCGS   23 (61)
T ss_pred             hhhhhhCCcccCCC-----cCCCCcC
Confidence            46999999999655     5999985

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=87.05  E-value=1.6  Score=31.60  Aligned_cols=71  Identities=20%  Similarity=0.427  Sum_probs=44.7

Q ss_pred             heeeecCc----chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCccccccccccccccccccccccCCcccchh
Q psy8227          18 VHVQVGRM----PESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTFD   93 (125)
Q Consensus        18 ~~~~~~~~----~~~~~~~~~~~~~~~c~~~~flw~~v~~~~m~h~~s~~~~~~~s~~~VP~~~R~LRACLlCsLVKT~d   93 (125)
                      |+++||.+    ||+|..-|.                    +..-||--+.++..-- .+|...    -|..|+-.-..+
T Consensus        29 V~l~iG~ls~v~pe~L~f~f~--------------------~~~~~T~~egA~L~I~-~vp~~~----~C~~Cg~~~~~~   83 (113)
T PRK12380         29 VWLEIGALSCVEESAVRFSFE--------------------IVCHGTVAQGCDLHIV-YKPAQA----WCWDCSQVVEIH   83 (113)
T ss_pred             EEEEEcCccccCHHHHHHHHH--------------------HHhCCCccCCCEEEEE-eeCcEE----EcccCCCEEecC
Confidence            78999987    666654332                    1345777777766543 666654    499999555555


Q ss_pred             hhhhcCCCChhhh-hhccCCcc
Q psy8227          94 QFEFDGCDNCDEF-LHMKNSRD  114 (125)
Q Consensus        94 QF~~dGCpNCe~~-L~Mkgn~d  114 (125)
                      ++... ||+|.+. +++.+.++
T Consensus        84 ~~~~~-CP~Cgs~~~~i~~G~E  104 (113)
T PRK12380         84 QHDAQ-CPHCHGERLRVDTGDS  104 (113)
T ss_pred             CcCcc-CcCCCCCCcEEccCCe
Confidence            44443 9999864 35554444

>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function

Probab=85.80  E-value=0.43  Score=30.21  Aligned_cols=27  Identities=30%  Similarity=0.712  Sum_probs=22.1

Q ss_pred             cccccCCcccchhhhhh--cC-----CCChhhhh
Q psy8227          81 RACLGCSQIKTFDQFEF--DG-----CDNCDEFL  107 (125)
Q Consensus        81 RACLlCsLVKT~dQF~~--dG-----CpNCe~~L  107 (125)
                      .+|..|.+..+.+.+.+  .+     ||||..+|
T Consensus        23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRiL   56 (56)
T PF02591_consen   23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCGRIL   56 (56)
T ss_pred             CccCCCCEEcCHHHHHHHHcCCCeEECcCCCccC
Confidence            59999999999988865  23     99998765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	125
3h7h_A	120	Crystal Structure Of The Human Transcription Elonga		7e-16

>pdb|3H7H|A Chain A, Crystal Structure Of The Human Transcription Elongation Factor Dsif, Hspt4HSPT5 (176-273) Length = 120

Iteration: 1
 Score = 79.0 bits (193), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 41/56 (73%)
Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              + K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct: 6   LETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 61

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	125
3h7h_A	120	Transcription elongation factor SPT4; helices surr	3e-21
2exu_A	200	Transcription initiation protein SPT4/SPT5; helixs	2e-16

>3h7h_A Transcription elongation factor SPT4; helices surrounding beta sheet, activator, ME binding, nucleus, repressor, transcription regulation; 1.55A {Homo sapiens} Length = 120

 Score = 81.2 bits (200), Expect = 3e-21
 Identities = 33/56 (58%), Positives = 41/56 (73%)

Query: 70  FNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              + K  R  RACL CS +KT DQFE+DGCDNCD +L MK +R+ VY+CTSS+FD
Sbjct: 6   LETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 61

>2exu_A Transcription initiation protein SPT4/SPT5; helixs surrounding beta sheet; 2.23A {Saccharomyces cerevisiae} Length = 200

 Score = 70.5 bits (172), Expect = 2e-16
 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 2/48 (4%)

Query: 78  RQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
              RAC+ C  ++T ++F  DGC NC           +   CTS +F+
Sbjct: 2   SSERACMLCGIVQTTNEFNRDGCPNCQGIFEEA--GVSTMECTSPSFE 47

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	125
3h7h_A	120	Transcription elongation factor SPT4; helices surr	99.88
2exu_A	200	Transcription initiation protein SPT4/SPT5; helixs	99.75
3lpe_B	59	DNA-directed RNA polymerase subunit E''; transcrip	98.77
3p8b_A	81	DNA-directed RNA polymerase, subunit E''; transcri	98.17
1ryq_A	69	DNA-directed RNA polymerase, subunit E''; structur	97.77
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	84.05

>3h7h_A Transcription elongation factor SPT4; helices surrounding beta sheet, activator, ME binding, nucleus, repressor, transcription regulation; 1.55A {Homo sapiens}

Probab=99.88  E-value=1.8e-24  Score=159.75  Aligned_cols=58  Identities=57%  Similarity=1.101  Sum_probs=55.5

Q ss_pred             ccccccccccccccccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227          68 DDFNNLAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD  125 (125)
Q Consensus        68 ~s~~~VP~~~R~LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd  125 (125)
                      +++.+||+++|+||||+.|++|+|.+||+++|||||++||+|+||+|+|++|||++|+
T Consensus         4 m~~~~iP~~~r~lrAC~~C~~V~t~~qF~~~gCpnC~~~l~m~~~~d~v~~ctT~~f~   61 (120)
T 3h7h_A            4 GALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD   61 (120)
T ss_dssp             CCGGGSCSSSTTEEEETTTCBEEEHHHHHHHCCTTTHHHHCCTTCHHHHHHHEESCEE
T ss_pred             cccccCCCccccCeeeccCCceechhhccCCCCCCCcchhhccCCcccccccccCCcc
Confidence            4567999999999999999999999999999999999999999999999999999995

>2exu_A Transcription initiation protein SPT4/SPT5; helixs surrounding beta sheet; 2.23A {Saccharomyces cerevisiae}

Probab=99.75  E-value=1.1e-19  Score=142.14  Aligned_cols=47  Identities=32%  Similarity=0.785  Sum_probs=44.0

Q ss_pred             cccccccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227          77 FRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD  125 (125)
Q Consensus        77 ~R~LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd  125 (125)
                      .|+||||+.|++|||.+||+.+|||||++||  +||+++|+||||++|+
T Consensus         1 ~~~lrAC~~C~~i~t~~qf~~~gCpnC~~~l--~g~~~~v~~cts~~f~   47 (200)
T 2exu_A            1 MSSERACMLCGIVQTTNEFNRDGCPNCQGIF--EEAGVSTMECTSPSFE   47 (200)
T ss_dssp             --CEEEETTTCBEEEHHHHHHHCCTTTHHHH--HHHTCCSGGGEESCEE
T ss_pred             CCcceecccCCceechhHhccCCCCCCcccc--CCCcceeeecccCCee
Confidence            3789999999999999999999999999999  9999999999999995

>3lpe_B DNA-directed RNA polymerase subunit E''; transcription regulation, SPT4, SPT5, NUSG, archaea, evoluti directed RNA polymerase; 1.90A {Methanocaldococcus jannaschii} SCOP: g.41.9.0

Probab=98.77  E-value=7.9e-10  Score=72.94  Aligned_cols=28  Identities=36%  Similarity=0.635  Sum_probs=24.4

Q ss_pred             ccccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227          80 ARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD  125 (125)
Q Consensus        80 LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd  125 (125)
                      ||||+.|++|+|.+     |||||++             |||++|+
T Consensus         1 lrAC~~C~~v~~~~-----~CpnC~~-------------~tt~~~~   28 (59)
T 3lpe_B            1 MRACLKCKYLTNDE-----ICPICHS-------------PTSENWI   28 (59)
T ss_dssp             CEEETTTCBEESSS-----BCTTTCC-------------BEESCEE
T ss_pred             CcccccCCcccCCC-----CCCCCCC-------------CccCCEe
Confidence            79999999999887     8999983             6888874

>3p8b_A DNA-directed RNA polymerase, subunit E''; transcription elongation factor, RNA polymerase, transferase transcription complex; 1.80A {Pyrococcus furiosus}

Probab=98.17  E-value=2.7e-07  Score=64.67  Aligned_cols=38  Identities=21%  Similarity=0.365  Sum_probs=24.5

Q ss_pred             cccc-cccccccccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227          71 NNLA-KYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD  125 (125)
Q Consensus        71 ~~VP-~~~R~LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd  125 (125)
                      --|| .+...+|||+.|++|++.+     |||||..            ++||++|+
T Consensus        13 ~~~~~~~~m~~rAC~~C~~v~~~d-----~CPnCgs------------~~~T~~w~   51 (81)
T 3p8b_A           13 GLVPRGSHMSEKACRHCHYITSED-----RCPVCGS------------RDLSEEWF   51 (81)
T ss_dssp             ---------CCEEETTTCBEESSS-----SCTTTCC------------CCEESCEE
T ss_pred             ccccCCcchhHHHHhhCCCccCCC-----CCCCCCC------------CccCCccc
Confidence            3466 3456799999999999764     7999974            45777764

>1ryq_A DNA-directed RNA polymerase, subunit E''; structural genomics, zinc, PSI, protein structure initiative; 1.38A {Pyrococcus furiosus} SCOP: g.41.9.3 PDB: 3qqc_E

Probab=97.77  E-value=3.8e-06  Score=57.14  Aligned_cols=30  Identities=27%  Similarity=0.506  Sum_probs=24.4

Q ss_pred             cccccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227          79 QARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD  125 (125)
Q Consensus        79 ~LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd  125 (125)
                      ..+||..|..|.     ..+|||||+.            +|||++|+
T Consensus        10 ~~~AC~~C~~~~-----~~~~CPnC~s------------~~tS~~w~   39 (69)
T 1ryq_A           10 SEKACRHCHYIT-----SEDRCPVCGS------------RDLSEEWF   39 (69)
T ss_dssp             -CEEETTTCBEE-----SSSSCTTTCC------------CCEESCEE
T ss_pred             hhhhHHhCCccc-----cCCcCCCccC------------CccCCccc
Confidence            468999999987     7889999983            47888874

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=84.05  E-value=0.32  Score=37.37  Aligned_cols=30  Identities=23%  Similarity=0.438  Sum_probs=24.2

Q ss_pred             cccccCCcccchhhhhh----c---CCCChhhhhhcc
Q psy8227          81 RACLGCSQIKTFDQFEF----D---GCDNCDEFLHMK  110 (125)
Q Consensus        81 RACLlCsLVKT~dQF~~----d---GCpNCe~~L~Mk  110 (125)
                      ++|.+|.+..++..+..    +   -||||..+|=..
T Consensus       199 ~~C~GC~~~lppq~~~~i~~~~~Iv~Cp~CgRIL~~~  235 (256)
T 3na7_A          199 QACGGCFIRLNDKIYTEVLTSGDMITCPYCGRILYAE  235 (256)
T ss_dssp             TBCTTTCCBCCHHHHHHHHHSSSCEECTTTCCEEECS
T ss_pred             CccCCCCeeeCHHHHHHHHCCCCEEECCCCCeeEEeC
Confidence            69999999999988854    2   399999988443

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	125
d1ryqa_	67	putative DNA-directed RNA polymerase subunit E'' (	98.27

>d1ryqa_ g.41.9.3 (A:) putative DNA-directed RNA polymerase subunit E'' (RpoE2) {Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: RNA polymerase subunits
family: RpoE2-like
domain: putative DNA-directed RNA polymerase subunit E'' (RpoE2)
species: Pyrococcus furiosus [TaxId: 2261]

Probab=98.27  E-value=4.7e-08  Score=64.44  Aligned_cols=32  Identities=25%  Similarity=0.432  Sum_probs=25.0

Q ss_pred             cccccccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227          77 FRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD  125 (125)
Q Consensus        77 ~R~LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd  125 (125)
                      -.+.|||+.|++|++.+     +||||++            +|||++|+
T Consensus         6 g~~~rAC~~C~~i~~~~-----~CpnC~s------------~~~S~~~~   37 (67)
T d1ryqa_           6 GSSEKACRHCHYITSED-----RCPVCGS------------RDLSEEWF   37 (67)
T ss_dssp             ---CEEETTTCBEESSS-----SCTTTCC------------CCEESCEE
T ss_pred             CccChhHhhCCCccCCC-----CCCCCcC------------CcCCCCcc
Confidence            35789999999999865     5999973            78998884