Psyllid ID: psy8226

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-----
Protein Sequence
MRTIDPGLLTLYYRPPPKPSTLAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRTD
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccHHHHHHccccccHHHHccccccccEEEEccccccEEEEEEcccccHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccccccccEEEEEccccccccccccEEEccccccccccccccccccccccccEEEEEcHHHHHHcccccHHHHHHccccHHHHHccccccccEEEEEEcccccHEEEEEEccccc
Coil and Loop (DISEMBL)
mrtidpglltlyyrpppkpstlaglkvvgvhnedhrpwtidpipsasaetinprttstfdqfefdgcdncdeflhmknsrdnvynctssnfdgmialmdpkdswVAKWQRIRRTD
Flexible Loop (DISEMBL)
mrtidpglltlyyrpppkpSTLAGLKVVGVHNEDHRpwtidpipsasaetinPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGmialmdpkdswvakwqrirrtd
Low Complexity Region (SEG)
MRTIDPGLLTLYYRPPPKPSTLAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRTD
Disordered region (IsUnstruct)
*******LLTLYYR******TLAGLKVVGVHNEDHRPWTIDPI***********TTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQR*****
Disordered Region (DISOPRED)
*****PG***************************************SAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI****
Disordered Region (DISEMBL)
MRTIDPGLLTLYYRPPPKPSTLAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRTD
Disordered Region (DISPRO)
*RTIDPGLLTLYYRPPPKPSTLAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIR***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MRTIDPGLLTLYYRPPPKPSTLAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRTD
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	115	2.2.26 [Sep-21-2011]
Q6DGQ0	117	Transcription elongation	yes	N/A	0.486	0.478	0.678	1e-19
Q4R941	117	Transcription elongation	N/A	N/A	0.486	0.478	0.660	1e-19
P63272	117	Transcription elongation	yes	N/A	0.486	0.478	0.660	1e-19
Q3SYX6	117	Transcription elongation	yes	N/A	0.486	0.478	0.660	1e-19
P63271	117	Transcription elongation	yes	N/A	0.486	0.478	0.660	1e-19
Q5RFH5	117	Transcription elongation	yes	N/A	0.486	0.478	0.660	2e-19
Q5HZ97	117	Transcription elongation	N/A	N/A	0.486	0.478	0.660	3e-19
Q9TVQ5	116	Transcription elongation	yes	N/A	0.486	0.482	0.714	4e-19
Q9Z199	117	Transcription elongation	yes	N/A	0.469	0.461	0.666	2e-18
Q628A6	120	Transcription elongation	N/A	N/A	0.486	0.466	0.571	6e-16

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

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 38/56 (67%), Positives = 47/56 (83%)

Query: 56  TSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNC+ +L MK +R+ VY CTSS+FDG+IA+M P+DSWVAKWQRI
Sbjct: 22  VKTIDQFEYDGCDNCESYLQMKGNREMVYECTSSSFDGVIAMMSPEDSWVAKWQRI 77

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

 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 37/56 (66%), Positives = 48/56 (85%)

Query: 56  TSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct: 22  VKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 77

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 = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 37/56 (66%), Positives = 48/56 (85%)

Query: 56  TSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct: 22  VKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 77

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 = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 37/56 (66%), Positives = 48/56 (85%)

Query: 56  TSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct: 22  VKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 77

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 = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 37/56 (66%), Positives = 48/56 (85%)

Query: 56  TSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct: 22  VKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 77

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

 Score = 94.0 bits (232), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 37/56 (66%), Positives = 47/56 (83%)

Query: 56  TSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P DSWV+KWQR+
Sbjct: 22  VKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPGDSWVSKWQRV 77

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 = 93.6 bits (231), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 37/56 (66%), Positives = 47/56 (83%)

Query: 56  TSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG++A+M P DSWV+KWQRI
Sbjct: 22  VKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIVAMMSPDDSWVSKWQRI 77

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

 Score = 93.2 bits (230), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 40/56 (71%), Positives = 49/56 (87%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
           +FDQFE DGC+NC+EFL MKN++DNVY+ TS+NFDG+IAL  P DSWVAKWQR+ R
Sbjct: 24  SFDQFETDGCENCEEFLRMKNNKDNVYDHTSNNFDGIIALTTPTDSWVAKWQRLSR 79

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

 Score = 91.3 bits (225), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 36/54 (66%), Positives = 47/54 (87%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
           T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+ A+M P+DSWV+KWQR+
Sbjct: 24  TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGINAMMSPEDSWVSKWQRV 77

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

 Score = 82.8 bits (203), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 32/56 (57%), Positives = 43/56 (76%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
           + D F+ DGC+NCDE LH+K   + VY+CTS+N+DGMIA M   DSWV KWQ+++R
Sbjct: 23  SVDAFQTDGCENCDEVLHLKGDEEKVYDCTSANYDGMIAAMSNDDSWVCKWQKMQR 78

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	115
427786237	118	Putative transcription elongation factor	0.486	0.474	0.857	1e-23
241680460	118	transcription elongation factor SPT4, pu	0.486	0.474	0.857	2e-23
442747457	118	Putative transcription elongation factor	0.486	0.474	0.857	2e-23
321460428	117	hypothetical protein DAPPUDRAFT_308814 [	0.504	0.495	0.775	3e-22
242003564	116	transcription elongation factor SPT4, pu	0.486	0.482	0.821	6e-22
307211608	116	Transcription elongation factor SPT4 [Ha	0.486	0.482	0.821	6e-22
66513379	116	PREDICTED: transcription elongation fact	0.504	0.5	0.793	1e-21
350402496	114	PREDICTED: transcription elongation fact	0.486	0.491	0.821	1e-21
340711990	114	PREDICTED: transcription elongation fact	0.486	0.491	0.821	1e-21
383861308	114	PREDICTED: transcription elongation fact	0.504	0.508	0.793	1e-21

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

 Score =  113 bits (282), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 48/56 (85%), Positives = 54/56 (96%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
           TF+QFEFDGCDNCDE+LHMKN+RD VY+CTSSNFDGMIALM+P+DSWVAKWQRI R
Sbjct: 26  TFEQFEFDGCDNCDEYLHMKNNRDMVYDCTSSNFDGMIALMNPEDSWVAKWQRISR 81

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

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 =  112 bits (281), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 48/56 (85%), Positives = 54/56 (96%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
           TF+QFEFDGCDNCDE+LHMKN+RD VY+CTSSNFDGMIALM+P+DSWVAKWQRI R
Sbjct: 26  TFEQFEFDGCDNCDEYLHMKNNRDMVYDCTSSNFDGMIALMNPEDSWVAKWQRINR 81

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  112 bits (281), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 48/56 (85%), Positives = 54/56 (96%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
           TF+QFEFDGCDNCDE+LHMKN+RD VY+CTSSNFDGMIALM+P+DSWVAKWQRI R
Sbjct: 26  TFEQFEFDGCDNCDEYLHMKNNRDMVYDCTSSNFDGMIALMNPEDSWVAKWQRITR 81

Source: Ixodes ricinus

Species: Ixodes ricinus

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321460428|gb|EFX71470.1| hypothetical protein DAPPUDRAFT_308814 [Daphnia pulex]

 Score =  108 bits (271), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 45/58 (77%), Positives = 53/58 (91%)

Query: 56  TSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
             TF+QFEFDGCDNCDEFL MKN++DN+Y+CTS+NFDGM+ALM P+DSWVAKWQRI R
Sbjct: 22  VKTFEQFEFDGCDNCDEFLRMKNNKDNIYDCTSNNFDGMVALMSPEDSWVAKWQRINR 79

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242003564|ref|XP_002422775.1| transcription elongation factor SPT4, putative [Pediculus humanus corporis] gi|212505633|gb|EEB10037.1| transcription elongation factor SPT4, putative [Pediculus humanus corporis]

 Score =  108 bits (269), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 46/56 (82%), Positives = 52/56 (92%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
           T DQFE+DGCDNCDEFL MKN+R+N+Y+CTSSNFDGMIALM P+DSWVAKWQRI R
Sbjct: 24  TMDQFEYDGCDNCDEFLRMKNNRENIYDCTSSNFDGMIALMSPEDSWVAKWQRINR 79

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  108 bits (269), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 46/56 (82%), Positives = 52/56 (92%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
           TFDQFEFDGCDNCDEFL MKN++DNV++CTSSNFDGMIA+M P+DSWV KWQRI R
Sbjct: 24  TFDQFEFDGCDNCDEFLRMKNNKDNVFDCTSSNFDGMIAVMSPEDSWVCKWQRINR 79

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

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 =  107 bits (267), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 46/58 (79%), Positives = 51/58 (87%)

Query: 56  TSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
             TFDQFEFDGCDNCDEFL MKN++DNV++CTSSNFDGMIA M P+DSWV KWQRI R
Sbjct: 22  VKTFDQFEFDGCDNCDEFLRMKNNKDNVFDCTSSNFDGMIAAMSPEDSWVCKWQRINR 79

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

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 =  107 bits (267), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 46/56 (82%), Positives = 51/56 (91%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
           TFDQFEFDGCDNCDEFL MKN++DNV++CTSSNFDGMIA M P+DSWV KWQRI R
Sbjct: 22  TFDQFEFDGCDNCDEFLRMKNNKDNVFDCTSSNFDGMIAAMSPEDSWVCKWQRINR 77

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

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 =  107 bits (266), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 46/56 (82%), Positives = 51/56 (91%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
           TFDQFEFDGCDNCDEFL MKN++DNV++CTSSNFDGMIA M P+DSWV KWQRI R
Sbjct: 22  TFDQFEFDGCDNCDEFLRMKNNKDNVFDCTSSNFDGMIAAMSPEDSWVCKWQRINR 77

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  107 bits (266), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 46/58 (79%), Positives = 51/58 (87%)

Query: 56  TSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
             TFDQFEFDGCDNCDEFL MKN++DNV++CTSSNFDGMIA M P+DSWV KWQRI R
Sbjct: 20  VKTFDQFEFDGCDNCDEFLRMKNNKDNVFDCTSSNFDGMIAAMSPEDSWVCKWQRINR 77

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	115
UNIPROTKB|F2Z535	96	LOC100515097 "Uncharacterized	0.478	0.572	0.690	5.7e-20
FB|FBgn0028683	116	spt4 "spt4" [Drosophila melano	0.486	0.482	0.714	1.2e-19
UNIPROTKB|J3QSB9	108	SUPT4H1 "Transcription elongat	0.486	0.518	0.660	1.5e-19
UNIPROTKB|Q3SYX6	117	SUPT4H1 "Transcription elongat	0.469	0.461	0.685	1.9e-19
UNIPROTKB|E2RAN9	117	SUPT4H1 "Uncharacterized prote	0.469	0.461	0.685	1.9e-19
UNIPROTKB|P63272	117	SUPT4H1 "Transcription elongat	0.469	0.461	0.685	1.9e-19
UNIPROTKB|K7GKT6	117	LOC100515097 "Uncharacterized	0.469	0.461	0.685	1.9e-19
UNIPROTKB|Q4R941	117	SUPT4H1 "Transcription elongat	0.469	0.461	0.685	1.9e-19
MGI|MGI:107416	117	Supt4a "suppressor of Ty 4A" [	0.469	0.461	0.685	1.9e-19
RGD|1306372	117	Supt4h1 "suppressor of Ty 4 ho	0.469	0.461	0.685	1.9e-19

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

 Score = 237 (88.5 bits), Expect = 5.7e-20, P = 5.7e-20
 Identities = 38/55 (69%), Positives = 49/55 (89%)

Query:    58 TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIR 112
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+R
Sbjct:    21 TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVR 75

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

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

 Score = 234 (87.4 bits), Expect = 1.2e-19, P = 1.2e-19
 Identities = 40/56 (71%), Positives = 49/56 (87%)

Query:    58 TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
             +FDQFE DGC+NC+EFL MKN++DNVY+ TS+NFDG+IAL  P DSWVAKWQR+ R
Sbjct:    24 SFDQFETDGCENCEEFLRMKNNKDNVYDHTSNNFDGIIALTTPTDSWVAKWQRLSR 79

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|J3QSB9 SUPT4H1 "Transcription elongation factor SPT4" [Homo sapiens (taxid:9606)]

 Score = 233 (87.1 bits), Expect = 1.5e-19, P = 1.5e-19
 Identities = 37/56 (66%), Positives = 49/56 (87%)

Query:    56 TSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             + T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct:    13 SQTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 68

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

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

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 37/54 (68%), Positives = 48/54 (88%)

Query:    58 TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct:    24 TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 77

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 = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 37/54 (68%), Positives = 48/54 (88%)

Query:    58 TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct:    24 TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 77

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

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 37/54 (68%), Positives = 48/54 (88%)

Query:    58 TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct:    24 TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 77

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

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 37/54 (68%), Positives = 48/54 (88%)

Query:    58 TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct:    24 TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 77

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 = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 37/54 (68%), Positives = 48/54 (88%)

Query:    58 TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct:    24 TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 77

GO:0032044 "DSIF complex" evidence=ISS

MGI|MGI:107416 Supt4a "suppressor of Ty 4A" [Mus musculus (taxid:10090)]

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 37/54 (68%), Positives = 48/54 (88%)

Query:    58 TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct:    24 TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 77

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

GO:0005634 "nucleus" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032044 "DSIF complex" evidence=ISO

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

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

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

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=ISO

RGD|1306372 Supt4h1 "suppressor of Ty 4 homolog 1 (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 37/54 (68%), Positives = 48/54 (88%)

Query:    58 TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct:    24 TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 77

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

GO:0005634 "nucleus" evidence=ISO

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032044 "DSIF complex" evidence=IEA;ISO

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

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

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

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

GO:0046982 "protein heterodimerization activity" evidence=IEA;ISO

---

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)
P0CR68	SPT4_CRYNJ	No assigned EC number	0.52	0.4347	0.4424	yes	N/A
Q9Z199	SPT42_MOUSE	No assigned EC number	0.6666	0.4695	0.4615	yes	N/A
Q6DGQ0	SPT4H_DANRE	No assigned EC number	0.6785	0.4869	0.4786	yes	N/A
Q9TVQ5	SPT4H_DROME	No assigned EC number	0.7142	0.4869	0.4827	yes	N/A
P63272	SPT4H_HUMAN	No assigned EC number	0.6607	0.4869	0.4786	yes	N/A
P63271	SPT41_MOUSE	No assigned EC number	0.6607	0.4869	0.4786	yes	N/A
Q5RFH5	SPT4H_PONAB	No assigned EC number	0.6607	0.4869	0.4786	yes	N/A
Q3SYX6	SPT4H_BOVIN	No assigned EC number	0.6607	0.4869	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	115
cd07973	98	cd07973, Spt4, Transcription elongation factor Spt	6e-33
pfam06093	77	pfam06093, Spt4, Spt4/RpoE2 zinc finger	4e-28
COG5204	112	COG5204, SPT4, Transcription elongation factor SPT	1e-14

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

 Score =  110 bits (277), Expect = 6e-33
 Identities = 35/54 (64%), Positives = 44/54 (81%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
           T DQFE DGC NC+ +L MK + + VY+CTS NF+G+IALMDP+ SWVA+WQRI
Sbjct: 14  TEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFEGIIALMDPEKSWVARWQRI 67

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 = 97.4 bits (243), Expect = 4e-28
 Identities = 35/54 (64%), Positives = 43/54 (79%), Gaps = 1/54 (1%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
           T DQFE DGC NC EFLHMK  R+ V  CTS NF+G++A++DP+ SWVAKWQR+
Sbjct: 12  TEDQFEDDGCPNC-EFLHMKGDRERVSECTSENFEGLVAILDPEKSWVAKWQRL 64

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 = 64.2 bits (156), Expect = 1e-14
 Identities = 28/54 (51%), Positives = 36/54 (66%), Gaps = 1/54 (1%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
           T + F  DGC NC   L+MK    NV  CTS  F+G++A++ P +SWVAKWQRI
Sbjct: 20  TLNGFRKDGCPNC-PMLNMKGGVTNVEECTSPKFEGVVAMLQPTNSWVAKWQRI 72

Length = 112

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	115
KOG3490|consensus	111		100.0
cd07973	98	Spt4 Transcription elongation factor Spt4. Spt4 is	100.0
PF06093	77	Spt4: Spt4/RpoE2 zinc finger; InterPro: IPR022800	99.98
COG5204	112	SPT4 Transcription elongation factor SPT4 [Transcr	99.94
PRK06393	64	rpoE DNA-directed RNA polymerase subunit E''; Vali	99.84
PRK08351	61	DNA-directed RNA polymerase subunit E''; Validated	99.73
COG2093	64	DNA-directed RNA polymerase, subunit E'' [Transcri	99.47
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	90.63
PF09845	131	DUF2072: Zn-ribbon containing protein (DUF2072); I	88.21
PRK11788	389	tetratricopeptide repeat protein; Provisional	88.01
PF02591	56	DUF164: Putative zinc ribbon domain; InterPro: IPR	87.21
COG3364	112	Zn-ribbon containing protein [General function pre	87.09
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	85.83
COG0675	364	Transposase and inactivated derivatives [DNA repli	85.3
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	82.87
PF13248	26	zf-ribbon_3: zinc-ribbon domain	81.02

>KOG3490|consensus

Probab=100.00  E-value=8.5e-35  Score=211.35  Aligned_cols=68  Identities=50%  Similarity=0.943  Sum_probs=66.1

Q ss_pred             ccccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhccccC
Q psy8226          46 ASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRT  114 (115)
Q Consensus        46 ~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k~  114 (115)
                      +..||+-|++|||.++|.++|||||+ +|+|+||.++|+||||+||+|+||+|+|.+|||||||||++|
T Consensus         7 ~lRACllCs~Vkt~~~F~~dGC~Nc~-~l~mkgn~e~V~ecTS~nF~GiIa~m~Pt~SWVakWqri~~f   74 (111)
T KOG3490|consen    7 KLRACLLCSIVKTLNGFRKDGCENCP-MLNMKGNVENVYECTSPNFDGIIAMMSPTESWVAKWQRIGRF   74 (111)
T ss_pred             hhhhhhhhhhhhhhhhhhhcCCCCch-hhhhccCcceeEEecCCCccceeeeeCccHHHHHHHHhhccc
Confidence            45689999999999999999999999 999999999999999999999999999999999999999998

>cd07973 Spt4 Transcription elongation factor Spt4

Probab=100.00  E-value=3.5e-34  Score=203.69  Aligned_cols=68  Identities=51%  Similarity=0.970  Sum_probs=65.9

Q ss_pred             cccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhccccC
Q psy8226          47 SAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRT  114 (115)
Q Consensus        47 ~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k~  114 (115)
                      .+||++|++|+|.+||..+|||||+.+|+|+|++++|+||||++|+|+|+||||++|||||||||++|
T Consensus         3 lrAC~~C~~I~~~~qf~~~gCpnC~~~l~~~g~~~~v~~~tT~~f~G~i~i~dP~~SwVAk~l~i~~~   70 (98)
T cd07973           3 LRACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFEGIIALMDPEKSWVARWQRIDKF   70 (98)
T ss_pred             CchhccCCcccccccccCCCCCCCcchhccCCCccccccccCCCcceEEEEECCchhHHHHHhCCCCC
Confidence            46899999999999999999999998999999999999999999999999999999999999999976

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=99.98  E-value=4.1e-34  Score=195.65  Aligned_cols=66  Identities=53%  Similarity=0.993  Sum_probs=58.2

Q ss_pred             ccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhccccC
Q psy8226          48 AETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRT  114 (115)
Q Consensus        48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k~  114 (115)
                      +||++|++|+|.+||+++||||| .||+|+||++++.+|||++|+|+|+||||++||||||||+++|
T Consensus         2 rAC~~C~~i~t~~qF~~~gCpnC-~~l~~~~~~~~~~~~tT~~f~G~i~i~~P~~SwvAk~~rl~~~   67 (77)
T PF06093_consen    2 RACLRCRLIKTEDQFRDEGCPNC-PFLQMKGDRDRVSDCTTPNFEGMIAIMDPEKSWVAKWQRLGKF   67 (77)
T ss_dssp             EEETTT-BEECCCHHHHH--TTT-HHHH-TCHCHHCHCCEESSEEEEEEES-TTT-HHHHHTTCTTS
T ss_pred             cccccCCcccCHhHccCCCCCCC-ccccccCCcCcccccCCCCCcCEEEECCCchhHHHHhhccCCC
Confidence            68999999999999999999999 5999999999999999999999999999999999999999986

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=99.94  E-value=4.5e-28  Score=175.54  Aligned_cols=69  Identities=42%  Similarity=0.826  Sum_probs=66.4

Q ss_pred             CccccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhccccC
Q psy8226          45 SASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRT  114 (115)
Q Consensus        45 ~~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k~  114 (115)
                      +.+.||+-|++|+|.+.|.++|||||+ .|.|+|+-+.+.+|||+.|+|+|||+.|.+|||||||||+.|
T Consensus         7 t~sRACl~Cgiv~t~n~F~~dGCpNc~-~l~~~~gV~~ve~~TSp~FeGvvam~~Pt~SWVakWqrid~f   75 (112)
T COG5204           7 TLSRACLGCGIVKTLNGFRKDGCPNCP-MLNMKGGVTNVEECTSPKFEGVVAMLQPTNSWVAKWQRIDEF   75 (112)
T ss_pred             hhhhhhhhcceeeecccccccCCCCCc-ccccccCccceeeecCcchHHHHHHhcccHHHHHHHhhhccc
Confidence            567899999999999999999999999 799999999999999999999999999999999999999987

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

Probab=99.84  E-value=1.4e-21  Score=130.88  Aligned_cols=51  Identities=16%  Similarity=0.270  Sum_probs=45.0

Q ss_pred             ccccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhcccc
Q psy8226          46 ASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR  113 (115)
Q Consensus        46 ~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k  113 (115)
                      ..+||++||+|.+.++     ||+|++       ++     ||++|+|+|+|+||++|||||||||+.
T Consensus         4 ~~~AC~~C~~i~~~~~-----Cp~Cgs-------~~-----~S~~w~G~v~i~dPe~S~vAk~~~i~~   54 (64)
T PRK06393          4 QYRACKKCKRLTPEKT-----CPVHGD-------EK-----TTTEWFGFLIITEPEGSAIAKRAGITE   54 (64)
T ss_pred             hhhhHhhCCcccCCCc-----CCCCCC-------Cc-----CCcCcceEEEEECCchhHHHHHhCCCC
Confidence            4579999999996554     999985       44     899999999999999999999999983

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

Probab=99.73  E-value=2.3e-18  Score=114.27  Aligned_cols=49  Identities=22%  Similarity=0.344  Sum_probs=43.8

Q ss_pred             ccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhcccc
Q psy8226          48 AETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR  113 (115)
Q Consensus        48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k  113 (115)
                      +||++|++|++.++     ||||++       ++     +|++|.|+|+|+||++|||||+++|++
T Consensus         4 kAC~~C~~i~~~~~-----CP~Cgs-------~~-----~T~~W~G~viI~dPe~S~IAk~l~i~~   52 (61)
T PRK08351          4 KACRHCHYITTEDR-----CPVCGS-------RD-----LSDEWFDLVIIIDVENSRIAKKLGAKV   52 (61)
T ss_pred             hhhhhCCcccCCCc-----CCCCcC-------Cc-----cccccccEEEEeCCcHhHHHHHhCCCC
Confidence            59999999997765     999986       33     788999999999999999999999974

>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]

Probab=99.47  E-value=2.2e-14  Score=96.34  Aligned_cols=53  Identities=23%  Similarity=0.397  Sum_probs=47.0

Q ss_pred             ccccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhcccc
Q psy8226          46 ASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR  113 (115)
Q Consensus        46 ~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k  113 (115)
                      ..+||.+|+.|.+.|+   +-||+|++       ++     +|++|.|+|.|+||++|.+||.+++++
T Consensus         3 ~~kAC~~Ck~l~~~d~---e~CP~Cgs-------~~-----~te~W~G~~iIidpe~SeIAkrlgi~~   55 (64)
T COG2093           3 TEKACKNCKRLTPEDT---EICPVCGS-------TD-----LTEEWFGLLIIIDPEKSEIAKRLGIKI   55 (64)
T ss_pred             hhHHHhhccccCCCCC---ccCCCCCC-------cc-----cchhhccEEEEEcCcHHHHHHHhCCCC
Confidence            4579999999999887   46999985       44     899999999999999999999999874

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=90.63  E-value=0.11  Score=31.55  Aligned_cols=34  Identities=12%  Similarity=0.159  Sum_probs=26.1

Q ss_pred             ccccCCcccccccccc-cCCCCCchhhhcccCCCC
Q psy8226          48 AETINPRTTSTFDQFE-FDGCDNCDEFLHMKNSRD   81 (115)
Q Consensus        48 ~ACl~C~lVkT~dQF~-~~GCPNC~~~L~m~gd~d   81 (115)
                      ..|.+|+...+.++.. .--||+|++-+.++..+.
T Consensus         4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~~   38 (46)
T PRK00398          4 YKCARCGREVELDEYGTGVRCPYCGYRILFKERPP   38 (46)
T ss_pred             EECCCCCCEEEECCCCCceECCCCCCeEEEccCCC
Confidence            4699999998888765 357999998666666554

>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function

Probab=88.21  E-value=0.2  Score=37.89  Aligned_cols=24  Identities=13%  Similarity=0.210  Sum_probs=18.5

Q ss_pred             cccCCcccccccc-cccCCCCCchh
Q psy8226          49 ETINPRTTSTFDQ-FEFDGCDNCDE   72 (115)
Q Consensus        49 ACl~C~lVkT~dQ-F~~~GCPNC~~   72 (115)
                      .|.+|+-+-.... -..+|||+|+.
T Consensus         3 ~Ct~Cg~~f~dgs~eil~GCP~CGg   27 (131)
T PF09845_consen    3 QCTKCGRVFEDGSKEILSGCPECGG   27 (131)
T ss_pred             ccCcCCCCcCCCcHHHHccCcccCC
Confidence            5999998865443 45689999986

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=88.01  E-value=0.26  Score=38.66  Aligned_cols=28  Identities=14%  Similarity=0.202  Sum_probs=22.5

Q ss_pred             CCCccccccCCcccccccccccCCCCCchhh
Q psy8226          43 IPSASAETINPRTTSTFDQFEFDGCDNCDEF   73 (115)
Q Consensus        43 ~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~   73 (115)
                      .++...+|.+|+++.+.=+|.   ||||+++
T Consensus       350 ~~~p~~~c~~cg~~~~~~~~~---c~~c~~~  377 (389)
T PRK11788        350 KRKPRYRCRNCGFTARTLYWH---CPSCKAW  377 (389)
T ss_pred             hCCCCEECCCCCCCCccceeE---CcCCCCc
Confidence            444457899999998887774   9999975

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

Probab=87.21  E-value=0.23  Score=31.21  Aligned_cols=27  Identities=15%  Similarity=0.224  Sum_probs=20.6

Q ss_pred             ccccCCccccccccccc--C-----CCCCchhhh
Q psy8226          48 AETINPRTTSTFDQFEF--D-----GCDNCDEFL   74 (115)
Q Consensus        48 ~ACl~C~lVkT~dQF~~--~-----GCPNC~~~L   74 (115)
                      .+|..|++..+.+.+.+  .     -||||+.+|
T Consensus        23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRiL   56 (56)
T PF02591_consen   23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCGRIL   56 (56)
T ss_pred             CccCCCCEEcCHHHHHHHHcCCCeEECcCCCccC
Confidence            37999999998886643  2     499998654

>COG3364 Zn-ribbon containing protein [General function prediction only]

Probab=87.09  E-value=0.22  Score=36.91  Aligned_cols=25  Identities=12%  Similarity=0.151  Sum_probs=20.1

Q ss_pred             cccCCcccccc-cccccCCCCCchhh
Q psy8226          49 ETINPRTTSTF-DQFEFDGCDNCDEF   73 (115)
Q Consensus        49 ACl~C~lVkT~-dQF~~~GCPNC~~~   73 (115)
                      .|.+|+-|-.. +.-...|||+|+.-
T Consensus         4 ~CtrCG~vf~~g~~~il~GCp~CG~n   29 (112)
T COG3364           4 QCTRCGEVFDDGSEEILSGCPKCGCN   29 (112)
T ss_pred             eecccccccccccHHHHccCccccch
Confidence            59999988766 66666899999863

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=85.83  E-value=0.4  Score=26.78  Aligned_cols=22  Identities=14%  Similarity=0.064  Sum_probs=15.2

Q ss_pred             ccCCcccccccc-cccCCCCCch
Q psy8226          50 TINPRTTSTFDQ-FEFDGCDNCD   71 (115)
Q Consensus        50 Cl~C~lVkT~dQ-F~~~GCPNC~   71 (115)
                      |.+|+....... ...--||||+
T Consensus         1 C~sC~~~i~~r~~~v~f~CPnCG   23 (24)
T PF07754_consen    1 CTSCGRPIAPREQAVPFPCPNCG   23 (24)
T ss_pred             CccCCCcccCcccCceEeCCCCC
Confidence            678877665544 4445799997

It is likely to bind zinc via its four well-conserved cysteine residues.

>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=85.30  E-value=0.58  Score=35.69  Aligned_cols=35  Identities=14%  Similarity=0.023  Sum_probs=25.9

Q ss_pred             CCceeEcCCCCccccccCCcccccccccccCCCCCchhh
Q psy8226          35 HRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEF   73 (115)
Q Consensus        35 ~~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~   73 (115)
                      |-+..+.+...+|.-|-.|+. .....|   -||+|+..
T Consensus       297 ~~~v~~~~~~~tS~~C~~cg~-~~~r~~---~C~~cg~~  331 (364)
T COG0675         297 GIVVKVVPPYYTSKTCPCCGH-LSGRLF---KCPRCGFV  331 (364)
T ss_pred             CeEEEECCCCCCcccccccCC-ccceeE---ECCCCCCe
Confidence            345566777788899999999 444445   39999964

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=82.87  E-value=0.89  Score=27.64  Aligned_cols=29  Identities=14%  Similarity=0.059  Sum_probs=18.6

Q ss_pred             CCccccccCCccccccccccc----CCCCCchh
Q psy8226          44 PSASAETINPRTTSTFDQFEF----DGCDNCDE   72 (115)
Q Consensus        44 ~~~~~ACl~C~lVkT~dQF~~----~GCPNC~~   72 (115)
                      |.-...|..|+..-+..+-..    .-||+|++
T Consensus         2 P~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~   34 (52)
T TIGR02605         2 PIYEYRCTACGHRFEVLQKMSDDPLATCPECGG   34 (52)
T ss_pred             CCEEEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence            445678999997544433211    26999995

This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=81.02  E-value=0.59  Score=25.61  Aligned_cols=20  Identities=25%  Similarity=0.356  Sum_probs=13.6

Q ss_pred             cccCCccccc-ccccccCCCCCchh
Q psy8226          49 ETINPRTTST-FDQFEFDGCDNCDE   72 (115)
Q Consensus        49 ACl~C~lVkT-~dQF~~~GCPNC~~   72 (115)
                      .|.+|+.... .+.|    ||+|+.
T Consensus         4 ~Cp~Cg~~~~~~~~f----C~~CG~   24 (26)
T PF13248_consen    4 FCPNCGAEIDPDAKF----CPNCGA   24 (26)
T ss_pred             CCcccCCcCCccccc----ChhhCC
Confidence            5888888533 3345    999984

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	115
3h7h_A	120	Crystal Structure Of The Human Transcription Elonga		1e-20
2exu_A	200	Crystal Structure Of Saccharomyces Cerevisiae Trans		5e-06

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

Iteration: 1
 Score = 94.7 bits (234), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 37/54 (68%), Positives = 48/54 (88%)
Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
           T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+
Sbjct: 27  TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRV 80

>pdb|2EXU|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae Transcription Elongation Factors Spt4-Spt5ngn Domain Length = 200

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 56  TSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
             T ++F  DGC NC        +  +   CTS +F+G++ +  P  SWVAKW  +
Sbjct: 13  VQTTNEFNRDGCPNCQGIFE--EAGVSTMECTSPSFEGLVGMCKPTKSWVAKWLSV 66

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	115
3h7h_A	120	Transcription elongation factor SPT4; helices surr	2e-28
2exu_A	200	Transcription initiation protein SPT4/SPT5; helixs	5e-23
1ryq_A	69	DNA-directed RNA polymerase, subunit E''; structur	6e-05
3p8b_A	81	DNA-directed RNA polymerase, subunit E''; transcri	9e-05

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

 Score = 99.3 bits (247), Expect = 2e-28
 Identities = 37/56 (66%), Positives = 48/56 (85%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
           T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+  
Sbjct: 27  TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSN 82

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

 Score = 87.4 bits (216), Expect = 5e-23
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
           T ++F  DGC NC           +   CTS +F+G++ +  P  SWVAKW  +
Sbjct: 15  TTNEFNRDGCPNCQGIFEEA--GVSTMECTSPSFEGLVGMCKPTKSWVAKWLSV 66

>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 Length = 69

 Score = 37.4 bits (87), Expect = 6e-05
 Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 8/51 (15%)

Query: 67  CDNCDEFLHMKNSRDNVYNC----TSSNFDGMIALMDPKDSWVAKWQRIRR 113
           C +C    H   S D    C     S  +  ++ ++D ++S +AK    + 
Sbjct: 14  CRHC----HYITSEDRCPVCGSRDLSEEWFDLVIIVDVENSEIAKKIGAKV 60

>3p8b_A DNA-directed RNA polymerase, subunit E''; transcription elongation factor, RNA polymerase, transferase transcription complex; 1.80A {Pyrococcus furiosus} Length = 81

 Score = 37.1 bits (86), Expect = 9e-05
 Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 12/47 (25%)

Query: 65  DGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
           D C  C                 S  +  ++ ++D ++S +AK    
Sbjct: 36  DRCPVCGS------------RDLSEEWFDLVIIVDVENSEIAKKIGA 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	115
3h7h_A	120	Transcription elongation factor SPT4; helices surr	100.0
2exu_A	200	Transcription initiation protein SPT4/SPT5; helixs	99.96
3lpe_B	59	DNA-directed RNA polymerase subunit E''; transcrip	99.89
1ryq_A	69	DNA-directed RNA polymerase, subunit E''; structur	99.86
3p8b_A	81	DNA-directed RNA polymerase, subunit E''; transcri	99.83
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	82.25

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

Probab=100.00  E-value=8.6e-35  Score=212.46  Aligned_cols=75  Identities=51%  Similarity=0.971  Sum_probs=70.4

Q ss_pred             EcCCCCcc-ccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhccccC
Q psy8226          40 IDPIPSAS-AETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRT  114 (115)
Q Consensus        40 i~p~~~~~-~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k~  114 (115)
                      .+|.+.+. +||++|++|+|.+||+++|||||++||+|+||+|+|++|||++|+|+|+||||++|||||||||++|
T Consensus         8 ~iP~~~r~lrAC~~C~~V~t~~qF~~~gCpnC~~~l~m~~~~d~v~~ctT~~f~G~I~i~dP~~SwVAk~~~i~~~   83 (120)
T 3h7h_A            8 TVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNF   83 (120)
T ss_dssp             GSCSSSTTEEEETTTCBEEEHHHHHHHCCTTTHHHHCCTTCHHHHHHHEESCEEEEEEESCGGGCHHHHHTTCTTS
T ss_pred             cCCCccccCeeeccCCceechhhccCCCCCCCcchhhccCCcccccccccCCcceEEEEeCCcHHHHHHHhccCCC
Confidence            35677766 4799999999999999999999999999999999999999999999999999999999999999986

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

Probab=99.96  E-value=8.6e-31  Score=203.55  Aligned_cols=66  Identities=29%  Similarity=0.697  Sum_probs=63.9

Q ss_pred             cccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhccccC
Q psy8226          47 SAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRT  114 (115)
Q Consensus        47 ~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k~  114 (115)
                      .+||+.|++|+|.+||..+|||||++||  +||+++|+||||++|+|+|+||||++|||||||||++|
T Consensus         4 lrAC~~C~~i~t~~qf~~~gCpnC~~~l--~g~~~~v~~cts~~f~G~i~i~dp~~Swvakw~rl~~y   69 (200)
T 2exu_A            4 ERACMLCGIVQTTNEFNRDGCPNCQGIF--EEAGVSTMECTSPSFEGLVGMCKPTKSWVAKWLSVDHS   69 (200)
T ss_dssp             EEEETTTCBEEEHHHHHHHCCTTTHHHH--HHHTCCSGGGEESCEEEEEEESCTTTCHHHHHTTCTTS
T ss_pred             ceecccCCceechhHhccCCCCCCcccc--CCCcceeeecccCCeeeEEEEeCCcchHHHHHHhcccc
Confidence            4689999999999999999999999999  89999999999999999999999999999999999987

>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=99.89  E-value=2.7e-24  Score=140.46  Aligned_cols=48  Identities=23%  Similarity=0.352  Sum_probs=44.3

Q ss_pred             ccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhcccc
Q psy8226          48 AETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR  113 (115)
Q Consensus        48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k  113 (115)
                      +||++||+|++.+     |||||++             |||++|+|+|+||||++|||||||||+.
T Consensus         2 rAC~~C~~v~~~~-----~CpnC~~-------------~tt~~~~G~v~i~dP~~SwvAk~~~i~~   49 (59)
T 3lpe_B            2 RACLKCKYLTNDE-----ICPICHS-------------PTSENWIGLLIVINPEKSEIAKKAGIDI   49 (59)
T ss_dssp             EEETTTCBEESSS-----BCTTTCC-------------BEESCEECEEEESCTTTCHHHHHTTCCS
T ss_pred             cccccCCcccCCC-----CCCCCCC-------------CccCCEeeEEEEeCCchhHHHHHhCCCC
Confidence            6899999999887     6999984             6899999999999999999999999973

>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=99.86  E-value=9.8e-23  Score=137.03  Aligned_cols=52  Identities=17%  Similarity=0.210  Sum_probs=44.3

Q ss_pred             CccccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhcccc
Q psy8226          45 SASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR  113 (115)
Q Consensus        45 ~~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k  113 (115)
                      +..+||++|++|.     ..+|||||++            .|||++|+|+|+||||++|||||||+++.
T Consensus         9 ~~~~AC~~C~~~~-----~~~~CPnC~s------------~~tS~~w~G~ViI~dPe~S~IAK~l~i~~   60 (69)
T 1ryq_A            9 SSEKACRHCHYIT-----SEDRCPVCGS------------RDLSEEWFDLVIIVDVENSEIAKKIGAKV   60 (69)
T ss_dssp             --CEEETTTCBEE-----SSSSCTTTCC------------CCEESCEEEEEEESCGGGCHHHHHHTCCS
T ss_pred             chhhhHHhCCccc-----cCCcCCCccC------------CccCCccceEEEEeCCchhHHHHHhCCCC
Confidence            4558999999988     3458999984            26999999999999999999999999863

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

Probab=99.83  E-value=1e-21  Score=135.57  Aligned_cols=50  Identities=16%  Similarity=0.205  Sum_probs=44.7

Q ss_pred             cccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhcccc
Q psy8226          47 SAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR  113 (115)
Q Consensus        47 ~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k  113 (115)
                      .+||++|++|++.+     +||||++            ++||++|+|+|+|+||++|||||||+|++
T Consensus        23 ~rAC~~C~~v~~~d-----~CPnCgs------------~~~T~~w~G~ViI~dPe~S~IAk~l~i~~   72 (81)
T 3p8b_A           23 EKACRHCHYITSED-----RCPVCGS------------RDLSEEWFDLVIIVDVENSEIAKKIGAKV   72 (81)
T ss_dssp             CEEETTTCBEESSS-----SCTTTCC------------CCEESCEEEEEEESCTTTCHHHHHHTCCS
T ss_pred             HHHHhhCCCccCCC-----CCCCCCC------------CccCCccceEEEEeCChHhHHHHHhCCCC
Confidence            47999999999876     5999984            24899999999999999999999999973

>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii}

Probab=82.25  E-value=0.62  Score=33.18  Aligned_cols=44  Identities=14%  Similarity=0.111  Sum_probs=27.6

Q ss_pred             cccceEEEeecCCCCceeEcCCCCccccccCCcccccccccccCCCCCchh
Q psy8226          22 LAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDE   72 (115)
Q Consensus        22 ~~~~~~~~~~~e~~~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~   72 (115)
                      ..|++|+|+. +-.     .-.-+..+.|..|+-+-+... ...-||.|++
T Consensus       113 ~~Gv~v~~~~-~~i-----~~~~~~~y~C~~Cg~~~~~~~-~~~~Cp~CG~  156 (165)
T 2lcq_A          113 LLGLRFRTLK-RGI-----KKVIKWRYVCIGCGRKFSTLP-PGGVCPDCGS  156 (165)
T ss_dssp             HTTCCEECCS-CCC-----SSCCCCCEEESSSCCEESSCC-GGGBCTTTCC
T ss_pred             HCCCeEEchh-hhc-----cccccEEEECCCCCCcccCCC-CCCcCCCCCC
Confidence            4588888876 322     223344578999998765321 1123999996

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	115
d1ryqa_	67	g.41.9.3 (A:) putative DNA-directed RNA polymerase	4e-13

>d1ryqa_ g.41.9.3 (A:) putative DNA-directed RNA polymerase subunit E'' (RpoE2) {Pyrococcus furiosus [TaxId: 2261]} Length = 67

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]

 Score = 57.4 bits (139), Expect = 4e-13
 Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 12/47 (25%)

Query: 65  DGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
           D C  C                 S  +  ++ ++D ++S +AK    
Sbjct: 22  DRCPVCGS------------RDLSEEWFDLVIIVDVENSEIAKKIGA 56

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	115
d1ryqa_	67	putative DNA-directed RNA polymerase subunit E'' (	99.88

>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=99.88  E-value=4.5e-24  Score=141.04  Aligned_cols=52  Identities=17%  Similarity=0.235  Sum_probs=46.0

Q ss_pred             CccccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhcccc
Q psy8226          45 SASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR  113 (115)
Q Consensus        45 ~~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k  113 (115)
                      ++.+||++|++|++.+|     ||||++            +|||++|+|+|+||||++|||||||+|++
T Consensus         7 ~~~rAC~~C~~i~~~~~-----CpnC~s------------~~~S~~~~G~v~i~dP~~S~iAk~l~i~~   58 (67)
T d1ryqa_           7 SSEKACRHCHYITSEDR-----CPVCGS------------RDLSEEWFDLVIIVDVENSEIAKKIGAKV   58 (67)
T ss_dssp             --CEEETTTCBEESSSS-----CTTTCC------------CCEESCEEEEEEESCGGGCHHHHHHTCCS
T ss_pred             ccChhHhhCCCccCCCC-----CCCCcC------------CcCCCCcccEEEEECchHHHHHHHcCCCC
Confidence            45689999999999876     999984            47999999999999999999999999974