Psyllid ID: psy1423

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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
MAEPMSLRDSALWSKTRRPKRNLIGSAMLTKKKRTSGDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPYVWRMNLPQDVVKRRELGMS
Secondary Structure (PSIPRED)
cccccccHHHHHHHcccccccccccHHHHHHHHHHccccHHcccccHHHHHHHHHHHHcccccHHHHHHcccHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccHcHHHHHHHHcccHHcccccccccccccccccccccccccHHHHHHHHHHHHcccccHHHHHHccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHccHHHcccc
Coil and Loop (DISEMBL)
maepmslrdsalwsktrrpkrnligsamltkkkrtsgdnkltgLVRQEQALDLLKALQTLNIDLNILTKTHIgmtvnnlrksskddEVINLAKTLIKNWKKFIRPYvwrmnlpqDVVKRRELGMS
Flexible Loop (DISEMBL)
maepmslrdsalwsktrrpkrnligsamltkkkrtsgdnkltgLVRQEQALDLLKALQTLNIDLNiltkthigmtvnnlrksskddevINLAKTLIKNWKkfirpyvwrmnlpqdvvkrrelgms
Low Complexity Region (SEG)
MAEPMSLRDSALWSKTRRPKRNLIGSAMLTKKKRTSGDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPYVWRMNLPQDVVKRRELGMS
Disordered region (IsUnstruct)
*****************************************TGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPYVWRMNLPQDV*********
Disordered Region (DISOPRED)
**************************************************LDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWK*************************
Disordered Region (DISEMBL)
*********SALWSKTRRPKRNLIGSAMLTKKKRTSGDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPYVWRMNLPQDVVKRRELGMS
Disordered Region (DISPRO)
*********************************************RQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPYVWRMNL*************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAEPMSLRDSALWSKTRRPKRNLIGSAMLTKKKRTSGDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPYVWRMNLPQDVVKRRELGMS
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]
P20232	313	Transcription elongation	yes	N/A	0.456	0.182	0.859	3e-21
Q15560	299	Transcription elongation	yes	N/A	0.448	0.187	0.553	3e-11
Q148K0	300	Transcription elongation	yes	N/A	0.448	0.186	0.517	4e-11
Q9QVN7	299	Transcription elongation	no	N/A	0.448	0.187	0.535	2e-10
Q63799	299	Transcription elongation	yes	N/A	0.448	0.187	0.535	2e-10
P10711	301	Transcription elongation	no	N/A	0.432	0.179	0.574	5e-10
P23193	301	Transcription elongation	no	N/A	0.432	0.179	0.555	1e-09
Q4KLL0	301	Transcription elongation	no	N/A	0.432	0.179	0.555	1e-09
Q29RL9	301	Transcription elongation	no	N/A	0.432	0.179	0.555	1e-09
O75764	348	Transcription elongation	no	N/A	0.448	0.160	0.5	1e-09

>sp|P20232|TFS2_DROME Transcription elongation factor S-II OS=Drosophila melanogaster GN=TfIIS PE=2 SV=1

 Score =  100 bits (248), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 49/57 (85%), Positives = 54/57 (94%)

Query: 47  QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           Q+QALDLLKALQTLNI+L+ILTKT IGMTVN LRKSSKDDEVI LAKTLIKNWK+F+
Sbjct: 24  QDQALDLLKALQTLNINLDILTKTRIGMTVNELRKSSKDDEVIALAKTLIKNWKRFL 80

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.
Drosophila melanogaster (taxid: 7227)

>sp|Q15560|TCEA2_HUMAN Transcription elongation factor A protein 2 OS=Homo sapiens GN=TCEA2 PE=1 SV=1

 Score = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 31/56 (55%), Positives = 43/56 (76%)

Query: 48  EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           E A+DLL+ L+ + I L++L  T +GM+VN LRK S D+EVI LAK+LIK+WKK +
Sbjct: 25  EGAMDLLRELKAMPITLHLLQSTRVGMSVNALRKQSSDEEVIALAKSLIKSWKKLL 80

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Homo sapiens (taxid: 9606)

>sp|Q148K0|TCEA2_BOVIN Transcription elongation factor A protein 2 OS=Bos taurus GN=TCEA2 PE=2 SV=1

 Score = 66.6 bits (161), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 43/56 (76%)

Query: 48  EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           E A+DLL+ L+ + + L++L  T +GM+VN LRK S D+EV+ LAK+LIK+WKK +
Sbjct: 25  EGAMDLLRELKAMPVTLHLLQSTRVGMSVNALRKQSSDEEVVTLAKSLIKSWKKLL 80

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Bos taurus (taxid: 9913)

>sp|Q9QVN7|TCEA2_MOUSE Transcription elongation factor A protein 2 OS=Mus musculus GN=Tcea2 PE=2 SV=2

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/56 (53%), Positives = 43/56 (76%)

Query: 48  EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           E A+DLL+ L+ + I L++L  T +GM+VN LRK S D+E+I LAK+LIK+WKK +
Sbjct: 24  EGAMDLLRELKNMPITLHLLQSTRVGMSVNALRKQSSDEELIALAKSLIKSWKKLL 79

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Mus musculus (taxid: 10090)

>sp|Q63799|TCEA2_RAT Transcription elongation factor A protein 2 OS=Rattus norvegicus GN=Tcea2 PE=2 SV=1

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/56 (53%), Positives = 43/56 (76%)

Query: 48  EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           E A+DLL+ L+ + I L++L  T +GM+VN LRK S D+E+I LAK+LIK+WKK +
Sbjct: 24  EGAMDLLRELKNMPITLHLLQSTRVGMSVNALRKQSSDEELIALAKSLIKSWKKLL 79

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Rattus norvegicus (taxid: 10116)

>sp|P10711|TCEA1_MOUSE Transcription elongation factor A protein 1 OS=Mus musculus GN=Tcea1 PE=1 SV=2

 Score = 62.8 bits (151), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 31/54 (57%), Positives = 41/54 (75%)

Query: 50  ALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           ALDLLK L+ + + L +L  T IGM+VN LRK S D+EV +LAK+LIK+WKK +
Sbjct: 24  ALDLLKELKNIPMTLELLQSTRIGMSVNALRKQSTDEEVTSLAKSLIKSWKKLL 77

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Mus musculus (taxid: 10090)

>sp|P23193|TCEA1_HUMAN Transcription elongation factor A protein 1 OS=Homo sapiens GN=TCEA1 PE=1 SV=2

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 41/54 (75%)

Query: 50  ALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           ALDLLK L+ + + L +L  T IGM+VN +RK S D+EV +LAK+LIK+WKK +
Sbjct: 24  ALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLIKSWKKLL 77

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Homo sapiens (taxid: 9606)

>sp|Q4KLL0|TCEA1_RAT Transcription elongation factor A protein 1 OS=Rattus norvegicus GN=Tcea1 PE=2 SV=1

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 41/54 (75%)

Query: 50  ALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           ALDLLK L+ + + L +L  T IGM+VN +RK S D+EV +LAK+LIK+WKK +
Sbjct: 24  ALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLIKSWKKLL 77

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Rattus norvegicus (taxid: 10116)

>sp|Q29RL9|TCEA1_BOVIN Transcription elongation factor A protein 1 OS=Bos taurus GN=TCEA1 PE=2 SV=1

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 41/54 (75%)

Query: 50  ALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           ALDLLK L+ + + L +L  T IGM+VN +RK S D+EV +LAK+LIK+WKK +
Sbjct: 24  ALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLIKSWKKLL 77

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Bos taurus (taxid: 9913)

>sp|O75764|TCEA3_HUMAN Transcription elongation factor A protein 3 OS=Homo sapiens GN=TCEA3 PE=2 SV=2

 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/56 (50%), Positives = 38/56 (67%)

Query: 48  EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           E ALDLLK L +  + + +L  T IG+ VN +RK   D EV++LAK LIKNWK+ +
Sbjct: 24  EGALDLLKKLHSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLL 79

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Homo sapiens (taxid: 9606)

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
195030242	350	GH10818 [Drosophila grimshawi] gi|193903	0.456	0.162	0.877	5e-20
125987179	313	GA17632 [Drosophila pseudoobscura pseudo	0.456	0.182	0.877	6e-20
17136888	313	RNA polymerase II elongation factor, iso	0.456	0.182	0.859	1e-19
194857365	313	GG24225 [Drosophila erecta] gi|190660804	0.456	0.182	0.859	1e-19
195475592	313	GE19417 [Drosophila yakuba] gi|194176169	0.456	0.182	0.859	2e-19
195115581	323	GI17330 [Drosophila mojavensis] gi|19391	0.456	0.176	0.859	2e-19
8050580	324	transcription elongation factor TFIIS [D	0.456	0.175	0.859	2e-19
195385615	324	TfIIS [Drosophila virilis] gi|194147957|	0.456	0.175	0.859	2e-19
91084035	294	PREDICTED: similar to transcription elon	0.456	0.193	0.842	5e-19
195338531	311	GM14545 [Drosophila sechellia] gi|194129	0.456	0.183	0.842	6e-19

>gi|195030242|ref|XP_001987977.1| GH10818 [Drosophila grimshawi] gi|193903977|gb|EDW02844.1| GH10818 [Drosophila grimshawi]

 Score =  101 bits (252), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 50/57 (87%), Positives = 53/57 (92%)

Query: 47  QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           QEQALDLLKALQTLNI+L ILTKT IGMTVN LRKSSKDDEVI LAKTLIKNWK+F+
Sbjct: 26  QEQALDLLKALQTLNINLEILTKTRIGMTVNELRKSSKDDEVIALAKTLIKNWKRFL 82

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125987179|ref|XP_001357352.1| GA17632 [Drosophila pseudoobscura pseudoobscura] gi|195155927|ref|XP_002018852.1| GL25727 [Drosophila persimilis] gi|54645683|gb|EAL34421.1| GA17632 [Drosophila pseudoobscura pseudoobscura] gi|194115005|gb|EDW37048.1| GL25727 [Drosophila persimilis]

 Score =  101 bits (251), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 50/57 (87%), Positives = 53/57 (92%)

Query: 47  QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           QEQALDLLKALQTLNI+L ILTKT IGMTVN LRKSSKDDEVI LAKTLIKNWK+F+
Sbjct: 26  QEQALDLLKALQTLNINLEILTKTRIGMTVNELRKSSKDDEVIALAKTLIKNWKRFL 82

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17136888|ref|NP_476967.1| RNA polymerase II elongation factor, isoform A [Drosophila melanogaster] gi|442627872|ref|NP_001260457.1| RNA polymerase II elongation factor, isoform B [Drosophila melanogaster] gi|135660|sp|P20232.1|TFS2_DROME RecName: Full=Transcription elongation factor S-II; AltName: Full=RNA polymerase II elongation factor DMS-II; AltName: Full=TFIIS gi|7921|emb|CAA37710.1| unnamed protein product [Drosophila melanogaster] gi|6713129|gb|AAA92864.2| transcription elongation factor [Drosophila melanogaster] gi|7298202|gb|AAF53436.1| RNA polymerase II elongation factor, isoform A [Drosophila melanogaster] gi|15291997|gb|AAK93267.1| LD34766p [Drosophila melanogaster] gi|220942248|gb|ACL83667.1| TfIIS-PA [synthetic construct] gi|440213800|gb|AGB92992.1| RNA polymerase II elongation factor, isoform B [Drosophila melanogaster]

 Score =  100 bits (248), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 49/57 (85%), Positives = 54/57 (94%)

Query: 47  QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           Q+QALDLLKALQTLNI+L+ILTKT IGMTVN LRKSSKDDEVI LAKTLIKNWK+F+
Sbjct: 24  QDQALDLLKALQTLNINLDILTKTRIGMTVNELRKSSKDDEVIALAKTLIKNWKRFL 80

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194857365|ref|XP_001968937.1| GG24225 [Drosophila erecta] gi|190660804|gb|EDV57996.1| GG24225 [Drosophila erecta]

 Score =  100 bits (248), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 49/57 (85%), Positives = 54/57 (94%)

Query: 47  QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           Q+QALDLLKALQTLNI+L+ILTKT IGMTVN LRKSSKDDEVI LAKTLIKNWK+F+
Sbjct: 24  QDQALDLLKALQTLNINLDILTKTRIGMTVNELRKSSKDDEVIALAKTLIKNWKRFL 80

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195475592|ref|XP_002090068.1| GE19417 [Drosophila yakuba] gi|194176169|gb|EDW89780.1| GE19417 [Drosophila yakuba]

 Score =  100 bits (248), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 49/57 (85%), Positives = 54/57 (94%)

Query: 47  QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           Q+QALDLLKALQTLNI+L+ILTKT IGMTVN LRKSSKDDEVI LAKTLIKNWK+F+
Sbjct: 24  QDQALDLLKALQTLNINLDILTKTRIGMTVNELRKSSKDDEVIALAKTLIKNWKRFL 80

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195115581|ref|XP_002002335.1| GI17330 [Drosophila mojavensis] gi|193912910|gb|EDW11777.1| GI17330 [Drosophila mojavensis]

 Score = 99.8 bits (247), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 49/57 (85%), Positives = 53/57 (92%)

Query: 47  QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           Q+QALDLLKALQTLNI+L ILTKT IGMTVN LRKSSKDDEVI LAKTLIKNWK+F+
Sbjct: 26  QDQALDLLKALQTLNINLEILTKTRIGMTVNELRKSSKDDEVIALAKTLIKNWKRFL 82

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|8050580|gb|AAF71710.1|AF220261_1 transcription elongation factor TFIIS [Drosophila virilis]

 Score = 99.4 bits (246), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 49/57 (85%), Positives = 53/57 (92%)

Query: 47  QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           Q+QALDLLKALQTLNI+L ILTKT IGMTVN LRKSSKDDEVI LAKTLIKNWK+F+
Sbjct: 26  QDQALDLLKALQTLNINLEILTKTRIGMTVNELRKSSKDDEVIALAKTLIKNWKRFL 82

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195385615|ref|XP_002051500.1| TfIIS [Drosophila virilis] gi|194147957|gb|EDW63655.1| TfIIS [Drosophila virilis]

 Score = 99.4 bits (246), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 49/57 (85%), Positives = 53/57 (92%)

Query: 47  QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           Q+QALDLLKALQTLNI+L ILTKT IGMTVN LRKSSKDDEVI LAKTLIKNWK+F+
Sbjct: 26  QDQALDLLKALQTLNINLEILTKTRIGMTVNELRKSSKDDEVIALAKTLIKNWKRFL 82

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91084035|ref|XP_966732.1| PREDICTED: similar to transcription elongation factor S-II [Tribolium castaneum] gi|270008004|gb|EFA04452.1| hypothetical protein TcasGA2_TC014756 [Tribolium castaneum]

 Score = 98.2 bits (243), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 48/57 (84%), Positives = 53/57 (92%)

Query: 47  QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           QEQALDLLK LQTLNI+L +LTKT IGMTVN LRKSSKDDEVI+L+KTLIKNWKKF+
Sbjct: 25  QEQALDLLKQLQTLNINLEVLTKTRIGMTVNALRKSSKDDEVISLSKTLIKNWKKFL 81

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195338531|ref|XP_002035878.1| GM14545 [Drosophila sechellia] gi|194129758|gb|EDW51801.1| GM14545 [Drosophila sechellia]

 Score = 98.2 bits (243), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 48/57 (84%), Positives = 53/57 (92%)

Query: 47  QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           Q+QALDLLK LQTLNI+L+ILTKT IGMTVN LRKSSKDDEVI LAKTLIKNWK+F+
Sbjct: 24  QDQALDLLKTLQTLNINLDILTKTRIGMTVNELRKSSKDDEVIALAKTLIKNWKRFL 80

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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|FBgn0010422	313	TfIIS "RNA polymerase II elong	0.456	0.182	0.859	1.3e-20
UNIPROTKB|Q86VL0	242	TCEA2 "TCEA2 protein" [Homo sa	0.448	0.231	0.553	1.3e-11
UNIPROTKB|F1NBF9	312	TCEA2 "Uncharacterized protein	0.52	0.208	0.492	3e-11
UNIPROTKB|F1PPX8	274	TCEA2 "Uncharacterized protein	0.448	0.204	0.535	3.1e-11
UNIPROTKB|Q15560	299	TCEA2 "Transcription elongatio	0.448	0.187	0.553	3.4e-11
UNIPROTKB|Q148K0	300	TCEA2 "Transcription elongatio	0.448	0.186	0.517	3.4e-11
UNIPROTKB|G1K224	303	TCEA2 "Transcription elongatio	0.448	0.184	0.517	3.5e-11
MGI|MGI:107368	299	Tcea2 "transcription elongatio	0.52	0.217	0.476	5.7e-11
RGD|61825	299	Tcea2 "transcription elongatio	0.52	0.217	0.476	5.7e-11
UNIPROTKB|Q63799	299	Tcea2 "Transcription elongatio	0.52	0.217	0.476	5.7e-11

FB|FBgn0010422 TfIIS "RNA polymerase II elongation factor" [Drosophila melanogaster (taxid:7227)]

 Score = 243 (90.6 bits), Expect = 1.3e-20, P = 1.3e-20
 Identities = 49/57 (85%), Positives = 54/57 (94%)

Query:    47 QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
             Q+QALDLLKALQTLNI+L+ILTKT IGMTVN LRKSSKDDEVI LAKTLIKNWK+F+
Sbjct:    24 QDQALDLLKALQTLNINLDILTKTRIGMTVNELRKSSKDDEVIALAKTLIKNWKRFL 80

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

GO:0005634 "nucleus" evidence=ISS;NAS

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

UNIPROTKB|Q86VL0 TCEA2 "TCEA2 protein" [Homo sapiens (taxid:9606)]

 Score = 158 (60.7 bits), Expect = 1.3e-11, P = 1.3e-11
 Identities = 31/56 (55%), Positives = 43/56 (76%)

Query:    48 EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
             E A+DLL+ L+ + I L++L  T +GM+VN LRK S D+EVI LAK+LIK+WKK +
Sbjct:    25 EGAMDLLRELKAMPITLHLLQSTRVGMSVNALRKQSSDEEVIALAKSLIKSWKKLL 80

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0003746 "translation elongation factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005813 "centrosome" evidence=IDA

UNIPROTKB|F1NBF9 TCEA2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 159 (61.0 bits), Expect = 3.0e-11, P = 3.0e-11
 Identities = 32/65 (49%), Positives = 47/65 (72%)

Query:    39 NKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKN 98
             +K+      + A+DLLK L+++ + L++L  T IGM+VN LRK S D+EVI LAK+LIK+
Sbjct:    41 DKMVAKKSADGAMDLLKELKSMPMTLDLLQSTRIGMSVNALRKQSSDEEVIALAKSLIKS 100

Query:    99 WKKFI 103
             WKK +
Sbjct:   101 WKKLL 105

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0005813 "centrosome" evidence=IEA

UNIPROTKB|F1PPX8 TCEA2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 157 (60.3 bits), Expect = 3.1e-11, P = 3.1e-11
 Identities = 30/56 (53%), Positives = 43/56 (76%)

Query:    48 EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
             E A+DLL+ L+ + + L++L  T +GM+VN LRK S D+EVI LAK+LIK+WKK +
Sbjct:     1 EGAMDLLRELKAMPVTLHLLQSTRVGMSVNALRKQSSDEEVIALAKSLIKSWKKLL 56

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q15560 TCEA2 "Transcription elongation factor A protein 2" [Homo sapiens (taxid:9606)]

 Score = 158 (60.7 bits), Expect = 3.4e-11, P = 3.4e-11
 Identities = 31/56 (55%), Positives = 43/56 (76%)

Query:    48 EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
             E A+DLL+ L+ + I L++L  T +GM+VN LRK S D+EVI LAK+LIK+WKK +
Sbjct:    25 EGAMDLLRELKAMPITLHLLQSTRVGMSVNALRKQSSDEEVIALAKSLIKSWKKLL 80

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=NAS

GO:0006354 "DNA-dependent transcription, elongation" evidence=NAS

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005813 "centrosome" evidence=IDA

UNIPROTKB|Q148K0 TCEA2 "Transcription elongation factor A protein 2" [Bos taurus (taxid:9913)]

 Score = 158 (60.7 bits), Expect = 3.4e-11, P = 3.4e-11
 Identities = 29/56 (51%), Positives = 43/56 (76%)

Query:    48 EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
             E A+DLL+ L+ + + L++L  T +GM+VN LRK S D+EV+ LAK+LIK+WKK +
Sbjct:    25 EGAMDLLRELKAMPVTLHLLQSTRVGMSVNALRKQSSDEEVVTLAKSLIKSWKKLL 80

GO:0005634 "nucleus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|G1K224 TCEA2 "Transcription elongation factor A protein 2" [Bos taurus (taxid:9913)]

 Score = 158 (60.7 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 29/56 (51%), Positives = 43/56 (76%)

Query:    48 EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
             E A+DLL+ L+ + + L++L  T +GM+VN LRK S D+EV+ LAK+LIK+WKK +
Sbjct:    25 EGAMDLLRELKAMPVTLHLLQSTRVGMSVNALRKQSSDEEVVTLAKSLIKSWKKLL 80

GO:0005813 "centrosome" evidence=IEA

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

MGI|MGI:107368 Tcea2 "transcription elongation factor A (SII), 2" [Mus musculus (taxid:10090)]

 Score = 156 (60.0 bits), Expect = 5.7e-11, P = 5.7e-11
 Identities = 31/65 (47%), Positives = 46/65 (70%)

Query:    39 NKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKN 98
             +K+      E A+DLL+ L+ + I L++L  T +GM+VN LRK S D+E+I LAK+LIK+
Sbjct:    15 DKMVTRKNAEGAMDLLRELKNMPITLHLLQSTRVGMSVNALRKQSSDEELIALAKSLIKS 74

Query:    99 WKKFI 103
             WKK +
Sbjct:    75 WKKLL 79

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003746 "translation elongation factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0006414 "translational elongation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

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

GO:0046872 "metal ion binding" evidence=IEA

RGD|61825 Tcea2 "transcription elongation factor A (SII), 2" [Rattus norvegicus (taxid:10116)]

 Score = 156 (60.0 bits), Expect = 5.7e-11, P = 5.7e-11
 Identities = 31/65 (47%), Positives = 46/65 (70%)

Query:    39 NKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKN 98
             +K+      E A+DLL+ L+ + I L++L  T +GM+VN LRK S D+E+I LAK+LIK+
Sbjct:    15 DKMVTRKNAEGAMDLLRELKNMPITLHLLQSTRVGMSVNALRKQSSDEELIALAKSLIKS 74

Query:    99 WKKFI 103
             WKK +
Sbjct:    75 WKKLL 79

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO;TAS

GO:0005813 "centrosome" evidence=IEA;ISO

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

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

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q63799 Tcea2 "Transcription elongation factor A protein 2" [Rattus norvegicus (taxid:10116)]

 Score = 156 (60.0 bits), Expect = 5.7e-11, P = 5.7e-11
 Identities = 31/65 (47%), Positives = 46/65 (70%)

Query:    39 NKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKN 98
             +K+      E A+DLL+ L+ + I L++L  T +GM+VN LRK S D+E+I LAK+LIK+
Sbjct:    15 DKMVTRKNAEGAMDLLRELKNMPITLHLLQSTRVGMSVNALRKQSSDEELIALAKSLIKS 74

Query:    99 WKKFI 103
             WKK +
Sbjct:    75 WKKLL 79

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA

---

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)
Q15560	TCEA2_HUMAN	No assigned EC number	0.5535	0.448	0.1872	yes	N/A
Q63799	TCEA2_RAT	No assigned EC number	0.5357	0.448	0.1872	yes	N/A
Q148K0	TCEA2_BOVIN	No assigned EC number	0.5178	0.448	0.1866	yes	N/A
P20232	TFS2_DROME	No assigned EC number	0.8596	0.456	0.1821	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
cd00183	76	cd00183, TFIIS_I, N-terminal domain (domain I) of	6e-14
smart00509	75	smart00509, TFS2N, Domain in the N-terminus of tra	3e-13
pfam08711	51	pfam08711, Med26, TFIIS helical bundle-like domain	3e-12
TIGR01385	299	TIGR01385, TFSII, transcription elongation factor	6e-09

>gnl|CDD|238107 cd00183, TFIIS_I, N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme

 Score = 61.6 bits (150), Expect = 6e-14
 Identities = 26/57 (45%), Positives = 39/57 (68%), Gaps = 1/57 (1%)

Query: 48  EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR 104
            + LDLL+ L+ L + + IL +T IG  VN+LRK S ++++  LAK LIK+WKK + 
Sbjct: 21  SRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHS-NEKIRKLAKALIKSWKKLVD 76

Length = 76

>gnl|CDD|197766 smart00509, TFS2N, Domain in the N-terminus of transcription elongation factor S-II (and elsewhere)

 Score = 60.0 bits (146), Expect = 3e-13
 Identities = 27/58 (46%), Positives = 39/58 (67%), Gaps = 1/58 (1%)

Query: 48  EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRP 105
            + LD+LK L+ L I +++L +T IG  VN LRK  K++E+  LAK LIK+WKK +  
Sbjct: 19  SRCLDILKKLKKLPITVDLLEETRIGKKVNGLRK-HKNEEIRKLAKKLIKSWKKLVYS 75

Length = 75

>gnl|CDD|204037 pfam08711, Med26, TFIIS helical bundle-like domain

 Score = 56.8 bits (138), Expect = 3e-12
 Identities = 25/52 (48%), Positives = 34/52 (65%), Gaps = 1/52 (1%)

Query: 52  DLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           +LLK L+ L I   +L +T IG  VN LRK  +++EV  LAK LIK WK+ +
Sbjct: 1   ELLKELKKLPITEELLRETGIGKAVNKLRK-HENEEVKKLAKKLIKKWKRLV 51

Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5. Length = 51

>gnl|CDD|233390 TIGR01385, TFSII, transcription elongation factor S-II

 Score = 52.1 bits (125), Expect = 6e-09
 Identities = 23/56 (41%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 48  EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           EQ LD+L  L+       +L +T +G+ VN LRK   +D +  LAK +IK+WKK +
Sbjct: 21  EQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNED-ISKLAKKIIKSWKKVV 75

This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end. Length = 299

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	125
smart00509	75	TFS2N Domain in the N-terminus of transcription el	99.78
cd00183	76	TFIIS_I N-terminal domain (domain I) of transcript	99.78
TIGR01385	299	TFSII transcription elongation factor S-II. This m	99.71
PF08711	53	Med26: TFIIS helical bundle-like domain; InterPro:	99.66
KOG1105|consensus	296		99.54
KOG2821|consensus	433		97.92
PF11467	106	LEDGF: Lens epithelium-derived growth factor (LEDG	97.02
KOG1793|consensus	417		95.77
COG5139	397	Uncharacterized conserved protein [Function unknow	95.31
PLN02976	1713	amine oxidase	89.47

>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere)

Probab=99.78  E-value=5.7e-19  Score=119.57  Aligned_cols=71  Identities=39%  Similarity=0.638  Sum_probs=64.0

Q ss_pred             HHHhhhHhhcCC-CCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423          33 KRTSGDNKLTGL-VRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR  104 (125)
Q Consensus        33 El~~~lek~~~~-~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~  104 (125)
                      ++.+.++++.++ .+.+.|+++|+.|+.++||.++|++|+||++||+|||| +|++|+.+|+.||++||++|+
T Consensus         3 ~~~k~~~k~~~~~~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh-~~~~I~~~A~~Li~~WK~~v~   74 (75)
T smart00509        3 RAAKKLDKVANNGKEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKH-KNEEIRKLAKKLIKSWKKLVY   74 (75)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcC-CcHHHHHHHHHHHHHHHHHhc
Confidence            344577777664 56789999999999999999999999999999999999 899999999999999999985

>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme

Probab=99.78  E-value=6e-19  Score=119.23  Aligned_cols=67  Identities=39%  Similarity=0.603  Sum_probs=62.0

Q ss_pred             hhHhhcCCCCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423          37 GDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR  104 (125)
Q Consensus        37 ~lek~~~~~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~  104 (125)
                      .|++..++.+.+.++++|+.|+.+|||.++|++|+||+.||+|||| ++++|+.+|+.||++||++|+
T Consensus        10 ~l~~~~~~~~~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh-~~~~i~~~A~~Lv~~Wk~~v~   76 (76)
T cd00183          10 KLEKKDSNEEVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKH-SNEKIRKLAKALIKSWKKLVD   76 (76)
T ss_pred             HhhccccCCCHHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcC-CcHHHHHHHHHHHHHHHHhcC
Confidence            6666666678999999999999999999999999999999999999 789999999999999999874

>TIGR01385 TFSII transcription elongation factor S-II

Probab=99.71  E-value=2.6e-17  Score=136.24  Aligned_cols=71  Identities=32%  Similarity=0.532  Sum_probs=66.7

Q ss_pred             HhhhHhhcCCCCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhhhh
Q psy1423          35 TSGDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPY  106 (125)
Q Consensus        35 ~~~lek~~~~~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~~~  106 (125)
                      .+.|+++.++.+.+.++++|++|+.++||.|+|++|+||++||+|||| ++++|+.+|+.||++||++|..+
T Consensus         8 ~k~L~k~~~~~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh-~~~~I~~lAk~li~~WK~~v~~~   78 (299)
T TIGR01385         8 AKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKH-PNEDISKLAKKIIKSWKKVVDKN   78 (299)
T ss_pred             HHHhhhhccCCCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcC-CcHHHHHHHHHHHHHHHHHHhhh
Confidence            338888888888899999999999999999999999999999999999 89999999999999999999775

This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.

>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription

Probab=99.66  E-value=1.8e-16  Score=99.94  Aligned_cols=53  Identities=45%  Similarity=0.763  Sum_probs=48.3

Q ss_pred             HHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423          52 DLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR  104 (125)
Q Consensus        52 ~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~  104 (125)
                      ++|+.|+.+|||.++|++|+||++||.|+||+++++|+++|+.||++||++|+
T Consensus         1 ~iL~~L~~l~it~~~L~~T~IGk~V~~l~k~~~~~~i~~~A~~Li~~Wk~~v~   53 (53)
T PF08711_consen    1 EILKVLEKLPITVELLKSTGIGKAVNKLRKHSENPEIRKLAKELIKKWKRIVD   53 (53)
T ss_dssp             HHHHHHHCSS-SHHHHHHHSHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHH-
T ss_pred             CHHHHhhcCCCCHHHHHhCChhHHHHHHHcCCCCHHHHHHHHHHHHHHhHhcC
Confidence            58999999999999999999999999999998899999999999999999874

The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.

>KOG1105|consensus

Probab=99.54  E-value=1.8e-14  Score=119.53  Aligned_cols=76  Identities=38%  Similarity=0.537  Sum_probs=69.0

Q ss_pred             hHHHHh---hhHhhcCCCCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhhhh
Q psy1423          31 KKKRTS---GDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPY  106 (125)
Q Consensus        31 ~~El~~---~lek~~~~~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~~~  106 (125)
                      .+|+++   .++++.++.+.+.++++|.+|+++|||.++|++|+||+.||.+||+++|++|+++|+.||+.||++|...
T Consensus         3 ~e~~~r~ak~l~~~~~~~n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~~   81 (296)
T KOG1105|consen    3 EEEALRAAKALEKDKQSKNVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDKS   81 (296)
T ss_pred             cHHHHHHHHHHHhhcccccHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhcc
Confidence            345555   8899999899999999999999999999999999999999977777799999999999999999999863

>KOG2821|consensus

Probab=97.92  E-value=7.8e-06  Score=71.28  Aligned_cols=73  Identities=23%  Similarity=0.216  Sum_probs=61.6

Q ss_pred             HHHHhhhHhhcCC-CCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhhhhh
Q psy1423          32 KKRTSGDNKLTGL-VRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPYV  107 (125)
Q Consensus        32 ~El~~~lek~~~~-~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~~~~  107 (125)
                      .+.++.++..+++ .++..++..|..|.++|++++.|.+|++|+.|+.||++ .  .+..+|.+++..||++|-...
T Consensus         8 l~~Vr~lQ~~l~~~~dpkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~-~--~~g~~~~Dl~~~WK~~v~~d~   81 (433)
T KOG2821|consen    8 LGAVRKLQARLENRIDPKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKI-S--HVGKLAFDLVALWKDLVLVDF   81 (433)
T ss_pred             HHHHHHHHHHHHhCccHHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHh-h--cccccccchHHHHHHhccccc
Confidence            4455544444443 48899999999999999999999999999999999999 2  799999999999999995444

>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis

Probab=97.02  E-value=0.0019  Score=46.77  Aligned_cols=62  Identities=18%  Similarity=0.266  Sum_probs=51.1

Q ss_pred             CCCCHHHHHHHHHHHhcCcCCHHHhh-cccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423          43 GLVRQEQALDLLKALQTLNIDLNILT-KTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR  104 (125)
Q Consensus        43 ~~~~~~~il~~L~~L~~~~iT~elL~-~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~  104 (125)
                      ...+.+.|+++|..|..+++|.-+|+ -+.+--++.++|+.-.|..|.+.|..|..+-|.++-
T Consensus        18 ~~~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnkfK~~f~   80 (106)
T PF11467_consen   18 DNPDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNKFKSLFL   80 (106)
T ss_dssp             TEE-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHhC
Confidence            67889999999999999999998876 567888999999988889999999999999999994

It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.

>KOG1793|consensus

Probab=95.77  E-value=0.0092  Score=52.05  Aligned_cols=53  Identities=36%  Similarity=0.478  Sum_probs=46.9

Q ss_pred             HHHHHHHhcCcCCH-HHhhcccchhhhhhhhcCC-CcHHHHHHHHHHHHHHHHhh
Q psy1423          51 LDLLKALQTLNIDL-NILTKTHIGMTVNNLRKSS-KDDEVINLAKTLIKNWKKFI  103 (125)
Q Consensus        51 l~~L~~L~~~~iT~-elL~~T~IGk~VnkLRKhs-~d~~I~~lAk~LV~kWKk~v  103 (125)
                      ..+|.-|..+||-. |.|+..+||++|-=|-||- ...+++.+|..||..|-.-+
T Consensus       236 ~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI  290 (417)
T KOG1793|consen  236 KSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPI  290 (417)
T ss_pred             HHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccc
Confidence            56788888999988 9999999999999999983 44789999999999998776

>COG5139 Uncharacterized conserved protein [Function unknown]

Probab=95.31  E-value=0.019  Score=49.01  Aligned_cols=52  Identities=33%  Similarity=0.521  Sum_probs=44.0

Q ss_pred             HHHHHHHhcCcCCHHHhhcccchhhhh--hhhcCCCcHHHHHHHHHHHHHHHHhh
Q psy1423          51 LDLLKALQTLNIDLNILTKTHIGMTVN--NLRKSSKDDEVINLAKTLIKNWKKFI  103 (125)
Q Consensus        51 l~~L~~L~~~~iT~elL~~T~IGk~Vn--kLRKhs~d~~I~~lAk~LV~kWKk~v  103 (125)
                      -.+|..|..+||-.|.|++.+||+.|.  .+.|. +.++|+.+|+.||..|-.-+
T Consensus       233 ksL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk-~e~~v~r~A~~LV~eWtrpI  286 (397)
T COG5139         233 KSLLDVLKTLPIHTEHLVESGVGRIVYFYTISKK-EEKEVRRSAKALVQEWTRPI  286 (397)
T ss_pred             HHHHHHHhhCCchHHHhhhcCCceEEEEEecCCc-ccHHHHHHHHHHHHHhhccc
Confidence            456777889999999999999998774  44555 77899999999999998765

>PLN02976 amine oxidase

Probab=89.47  E-value=0.9  Score=45.92  Aligned_cols=60  Identities=18%  Similarity=0.272  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHHhcCcCCHHHhhcccchhhhh-hhhcCCCcHHHHHHHHHHHHHHHHhhhhhh
Q psy1423          47 QEQALDLLKALQTLNIDLNILTKTHIGMTVN-NLRKSSKDDEVINLAKTLIKNWKKFIRPYV  107 (125)
Q Consensus        47 ~~~il~~L~~L~~~~iT~elL~~T~IGk~Vn-kLRKhs~d~~I~~lAk~LV~kWKk~v~~~~  107 (125)
                      ++-+..+|+-|=.++..+..++..+||++|. ++.-| .+.+|..+|+.|+..|-+.+..+.
T Consensus      1300 ~~l~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h-~~~~~r~~a~~~~~~w~~~~~~~~ 1360 (1713)
T PLN02976       1300 TQLLRHCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVH-TSRDIRAIASQLVSVWLEVFRREK 1360 (1713)
T ss_pred             HHHHHHHHHHHhhcchhHHHHHhccchHHHHhhhhhc-ccHHHHHHHHHHHHHHHHHHHHhh
Confidence            4445566777777888888999999999985 67888 788999999999999999996554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	125
1wjt_A	103	Solution Structure Of The N-Terminal Domain I Of Mo		2e-10

>pdb|1WJT|A Chain A, Solution Structure Of The N-Terminal Domain I Of Mouse Transcription Elongation Factor S-Ii Protein 3 Length = 103

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/58 (48%), Positives = 39/58 (67%)
Query: 46  RQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           + E ALDLLK L +  + + +L  T IG+ VN +RK   D EV++LAK LIKNWK+ +
Sbjct: 29  KTEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLL 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	125
1wjt_A	103	Transcription elongation factor S-II protein 3; fo	5e-16
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	4e-10

>1wjt_A Transcription elongation factor S-II protein 3; four-helix bundle, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.48.3.1 Length = 103

 Score = 67.4 bits (164), Expect = 5e-16
 Identities = 28/57 (49%), Positives = 38/57 (66%)

Query: 47  QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
            E ALDLLK L +  + + +L  T IG+ VN +RK   D EV++LAK LIKNWK+ +
Sbjct: 30  TEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLL 86

>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A Length = 309

 Score = 54.8 bits (130), Expect = 4e-10
 Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 47  QEQALDLLKALQT-LNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRP 105
               L++L  L         +L +T +G+ VN  +KS+ + E+  L K +I +WK  I  
Sbjct: 20  DAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKST-NVEISKLVKKMISSWKDAINK 78

Query: 106 YVWRMN 111
                 
Sbjct: 79  NKRSRQ 84

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	125
1wjt_A	103	Transcription elongation factor S-II protein 3; fo	99.9
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	99.7
2xpp_A	145	IWS1, ECU08_0440; transcription, elongation, histo	98.12
3nfq_A	170	Transcription factor IWS1; SPN1, RNA polymerase II	97.92
2b4j_C	98	PC4 and SFRS1 interacting protein; HIV, integratio	96.59
1z9e_A	127	PC4 and SFRS1 interacting protein 2; heat repeat-l	95.97

>1wjt_A Transcription elongation factor S-II protein 3; four-helix bundle, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.48.3.1

Probab=99.90  E-value=2.6e-24  Score=152.99  Aligned_cols=86  Identities=36%  Similarity=0.511  Sum_probs=77.7

Q ss_pred             cccccCchHHHHh---hhHhhcCCCCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHH
Q psy1423          24 IGSAMLTKKKRTS---GDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWK  100 (125)
Q Consensus        24 ~g~~m~~~~El~~---~lek~~~~~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWK  100 (125)
                      -||+|+.++||++   .|+++.+..+++.++++|++|+.++||.|+|++|+||++||+||||++|++|+.+|+.||++||
T Consensus         4 ~~~~M~~e~ev~~i~k~L~k~~~~~~~~~~l~~L~~L~~~~iT~e~L~~T~IGk~Vn~LrKh~~~~~V~~lAk~Lv~~WK   83 (103)
T 1wjt_A            4 GSSGMGLEEELLRIAKKLEKMVSRKKTEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWK   83 (103)
T ss_dssp             SCCSSCSHHHHHHHHHHHHHHHHTTCCSSHHHHHHHHHTSCCCHHHHHHTCHHHHHHHHHHHCCCSHHHHHHHHHHHHHH
T ss_pred             cccccchHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhCCCCCHHHHHHcchhHHHHHHHccCCcHHHHHHHHHHHHHHH
Confidence            3678998888877   7888777777889999999999999999999999999999999999899999999999999999


Q ss_pred             HhhhhhhcC
Q psy1423         101 KFIRPYVWR  109 (125)
Q Consensus       101 k~v~~~~~s  109 (125)
                      ++|..+...
T Consensus        84 ~~v~~~~~~   92 (103)
T 1wjt_A           84 RLLDSPRTT   92 (103)
T ss_dssp             HHTCCSCCC
T ss_pred             HHHHHhccc
Confidence            999876543

>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A

Probab=99.70  E-value=3.8e-17  Score=133.69  Aligned_cols=75  Identities=25%  Similarity=0.397  Sum_probs=66.7

Q ss_pred             hHHHHh---hhHhhcCCCCHHHHHHHHHHH-hcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhhhh
Q psy1423          31 KKKRTS---GDNKLTGLVRQEQALDLLKAL-QTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPY  106 (125)
Q Consensus        31 ~~El~~---~lek~~~~~~~~~il~~L~~L-~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~~~  106 (125)
                      ++||.+   .|++  ...+.+.++++|++| +.++||.|+|++|+||++||+|||| ++++|+.+|+.||++||++|..+
T Consensus         3 ~~el~~~~~~L~k--~~~~~~~~l~~L~~L~~~~~it~~~L~~T~IG~~Vn~lrkh-~~~~v~~~Ak~Li~~WK~~v~~~   79 (309)
T 1pqv_S            3 SKEVLVHVKNLEK--NKSNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKS-TNVEISKLVKKMISSWKDAINKN   79 (309)
T ss_pred             HHHHHHHHHHHhc--cCCCHHHHHHHHHHHHhcCCCCHHHHHhCChhHHHHHHHcC-CCHHHHHHHHHHHHHHHHHHHHh
Confidence            566666   6666  456788999999999 9999999999999999999999999 99999999999999999999765


Q ss_pred             hc
Q psy1423         107 VW  108 (125)
Q Consensus       107 ~~  108 (125)
                      ..
T Consensus        80 ~~   81 (309)
T 1pqv_S           80 KR   81 (309)
T ss_pred             cc
Confidence            43

>2xpp_A IWS1, ECU08_0440; transcription, elongation, histone chaperone, RNA polymerase mRNA export; 1.74A {Encephalitozoon cuniculi} PDB: 2xpo_A 2xpn_A 2xpl_A

Probab=98.12  E-value=3.6e-06  Score=62.70  Aligned_cols=59  Identities=24%  Similarity=0.330  Sum_probs=52.4

Q ss_pred             CCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCC-CcHHHHHHHHHHHHHHHHhh
Q psy1423          45 VRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSS-KDDEVINLAKTLIKNWKKFI  103 (125)
Q Consensus        45 ~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs-~d~~I~~lAk~LV~kWKk~v  103 (125)
                      .+..---.+|+-|..+||+.|.|++++||++|.-+.||. ..++++++|+.||.+|..-+
T Consensus        79 P~~~Ir~~lL~~L~~lPI~~e~Lk~SglGkvv~~l~k~~~et~~nk~la~~Li~~WsRpi  138 (145)
T 2xpp_A           79 PNIKIRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEV  138 (145)
T ss_dssp             CCHHHHHHHHHHHHTSCCCHHHHHHHCHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCCCCHHHhhcCCCCcchhhhhcCCccCHHHHHHHHHHHHHHHHHH
Confidence            455566788999999999999999999999999999983 55789999999999998876

>3nfq_A Transcription factor IWS1; SPN1, RNA polymerase II; 1.85A {Saccharomyces cerevisiae} PDB: 3o8z_A 3oak_A

Probab=97.92  E-value=1.1e-05  Score=61.60  Aligned_cols=59  Identities=27%  Similarity=0.369  Sum_probs=50.8

Q ss_pred             CCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCC-CcHHHHHHHHHHHHHHHHhh
Q psy1423          45 VRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSS-KDDEVINLAKTLIKNWKKFI  103 (125)
Q Consensus        45 ~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs-~d~~I~~lAk~LV~kWKk~v  103 (125)
                      .+..---.+|+-|..+||+.+.|++++||++|.-+.||. ..++++++|..||.+|..-+
T Consensus        94 P~~~Ir~~lL~~L~~lPI~~e~Lk~SglGkvV~~l~k~~~et~~nkrla~~Li~~WsRpI  153 (170)
T 3nfq_A           94 PSFEIQKSLFAALNDLPVKTEHLKESGLGRVVIFYTKSKRVEAQLARLAEKLIAEWTRPI  153 (170)
T ss_dssp             CCHHHHHHHHHHHHTSCCCHHHHHHHSHHHHHHHHHHCTTSCHHHHHHHHHHHHHHTCCC
T ss_pred             CcHHHHHHHHHHHHHCCCCHHHHhhCCCCceeeehhcCCcccHHHHHHHHHHHHHHHHHH
Confidence            445555788888999999999999999999999999983 55889999999999996655

>2b4j_C PC4 and SFRS1 interacting protein; HIV, integration, transcription, viral protein, recombinatio; 2.02A {Homo sapiens} SCOP: a.48.4.1 PDB: 3f9k_C 3hpg_G 3u88_C* 3hph_E

Probab=96.59  E-value=0.0068  Score=42.46  Aligned_cols=62  Identities=13%  Similarity=0.283  Sum_probs=54.6

Q ss_pred             CCCCHHHHHHHHHHHhcCcCCHHHh-hcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423          43 GLVRQEQALDLLKALQTLNIDLNIL-TKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR  104 (125)
Q Consensus        43 ~~~~~~~il~~L~~L~~~~iT~elL-~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~  104 (125)
                      ...+...++++|.+|.++++|.-+| +-+.+--++.++|+.-.+..|.+.|..|+.+.|.++.
T Consensus        22 ~~~Dv~kcl~~L~~l~~l~~T~~mL~rnpe~V~t~kklRry~g~q~Ir~kA~~iY~kfK~~f~   84 (98)
T 2b4j_C           22 DNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFL   84 (98)
T ss_dssp             TSCCHHHHHHHHHHHHTCCCCHHHHHTTHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHC--
T ss_pred             CCCCHHHHHHHHHHHhcccccHHHHhhChHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHh
Confidence            4789999999999999999999855 5678888999999987889999999999999999985

>1z9e_A PC4 and SFRS1 interacting protein 2; heat repeat-like, ledgf, protein binding/transcription complex; NMR {Homo sapiens} SCOP: a.48.4.1

Probab=95.97  E-value=0.011  Score=43.24  Aligned_cols=62  Identities=13%  Similarity=0.283  Sum_probs=55.8

Q ss_pred             CCCCHHHHHHHHHHHhcCcCCHHHhh-cccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423          43 GLVRQEQALDLLKALQTLNIDLNILT-KTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR  104 (125)
Q Consensus        43 ~~~~~~~il~~L~~L~~~~iT~elL~-~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~  104 (125)
                      ...+...|+++|..|..+++|.-+|+ -+.+--++.+||+.-.+..|.+.|..|+.+.|.++.
T Consensus        22 ~~~Dv~kCl~~Leel~~l~vT~~mL~Rnpe~V~TlkklRrY~gnq~Ir~kA~~iY~kFK~lf~   84 (127)
T 1z9e_A           22 DNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFL   84 (127)
T ss_dssp             GGCCHHHHHHHHHHHHHSCCCHHHHGGGHHHHHHHHHHTTCTTCSSHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHccccccHHHHhhChHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHh
Confidence            46889999999999999999998554 678888999999987778999999999999999995

---

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	125
d1wjta_	103	a.48.3.1 (A:) Transcription elongation factor S-II	2e-15
d1eo0a_	77	a.48.3.1 (A:) Transcription elongation factor TFII	4e-11

>d1wjta_ a.48.3.1 (A:) Transcription elongation factor S-II protein 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 103

class: All alpha proteins
fold: N-cbl like
superfamily: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
family: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
domain: Transcription elongation factor S-II protein 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.5 bits (157), Expect = 2e-15
 Identities = 28/57 (49%), Positives = 38/57 (66%)

Query: 48  EQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR 104
           E ALDLLK L +  + + +L  T IG+ VN +RK   D EV++LAK LIKNWK+ + 
Sbjct: 31  EGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLLD 87

>d1eo0a_ a.48.3.1 (A:) Transcription elongation factor TFIIS N-domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 77

class: All alpha proteins
fold: N-cbl like
superfamily: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
family: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
domain: Transcription elongation factor TFIIS N-domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 52.8 bits (127), Expect = 4e-11
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 2/57 (3%)

Query: 48  EQALDLLKALQT-LNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
              L++L  L         +L +T +G+ VN  +K S + E+  L K +I +WK  I
Sbjct: 21  AAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKK-STNVEISKLVKKMISSWKDAI 76

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	125
d1wjta_	103	Transcription elongation factor S-II protein 3 {Mo	99.88
d1eo0a_	77	Transcription elongation factor TFIIS N-domain {Ba	99.8
d2b4jc1	81	PC4 and SFRS1-interacting protein, PSIP1 {Human (H	97.7

>d1wjta_ a.48.3.1 (A:) Transcription elongation factor S-II protein 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: N-cbl like
superfamily: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
family: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
domain: Transcription elongation factor S-II protein 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.88  E-value=8.6e-24  Score=148.45  Aligned_cols=84  Identities=36%  Similarity=0.525  Sum_probs=76.9

Q ss_pred             ccCchHHHHh---hhHhhcCCCCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhh
Q psy1423          27 AMLTKKKRTS---GDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI  103 (125)
Q Consensus        27 ~m~~~~El~~---~lek~~~~~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v  103 (125)
                      +|+.++|+++   .|+++.+..+.+.++++|+.|+.++||.++|++|+||++||+||||+++++|+.+|+.||++||++|
T Consensus         7 ~m~~eeei~~i~k~L~~~~~~~~~~~vl~~L~~L~~~~it~e~L~~T~IGk~Vn~LrK~~~~~~v~~lAk~Lv~~WK~~v   86 (103)
T d1wjta_           7 GMGLEEELLRIAKKLEKMVSRKKTEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLL   86 (103)
T ss_dssp             SSCSHHHHHHHHHHHHHHHHTTCCSSHHHHHHHHHTSCCCHHHHHHTCHHHHHHHHHHHCCCSHHHHHHHHHHHHHHHHT
T ss_pred             CCcHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHcCCCCHHHHHhCCccHhHHHHHccCCCHHHHHHHHHHHHHHHHHH
Confidence            4999999988   7888888888899999999999999999999999999999999999888999999999999999999


Q ss_pred             hhhhcCC
Q psy1423         104 RPYVWRM  110 (125)
Q Consensus       104 ~~~~~s~  110 (125)
                      ..+....
T Consensus        87 ~~~~~~~   93 (103)
T d1wjta_          87 DSPRTTK   93 (103)
T ss_dssp             CCSCCCC
T ss_pred             HhhccCC
Confidence            7766443

>d1eo0a_ a.48.3.1 (A:) Transcription elongation factor TFIIS N-domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: N-cbl like
superfamily: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
family: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
domain: Transcription elongation factor TFIIS N-domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.80  E-value=8.3e-21  Score=127.54  Aligned_cols=71  Identities=27%  Similarity=0.436  Sum_probs=62.6

Q ss_pred             hHHHHh---hhHhhcCCCCHHHHHHHHHHHhc-CcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423          31 KKKRTS---GDNKLTGLVRQEQALDLLKALQT-LNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR  104 (125)
Q Consensus        31 ~~El~~---~lek~~~~~~~~~il~~L~~L~~-~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~  104 (125)
                      .+|+++   .|++..  .+.+.++++|+.|++ ++||.|+|++|+||++||+|||| ++++|+++|+.||++||++|+
T Consensus         3 ~~ev~~~~k~Lek~~--~~~~~~l~~L~~L~~~~~it~d~L~~T~iG~~Vn~LRkh-~~~~v~~lAk~Lv~~WK~~Vd   77 (77)
T d1eo0a_           3 SKEVLVHVKNLEKNK--SNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKS-TNVEISKLVKKMISSWKDAIN   77 (77)
T ss_dssp             HHHHHHHHHHHHHHC--SSSHHHHHHHHHHTTTCSCSTTHHHHHHHHHHHHHCCSS-SCTTHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhccc--CCHHHHHHHHHHHHhcCCCcHHHHHHCCccHHHHHHhcC-CcHHHHHHHHHHHHHHHHhcC
Confidence            455655   666653  466899999999997 99999999999999999999999 899999999999999999884

>d2b4jc1 a.48.4.1 (C:346-426) PC4 and SFRS1-interacting protein, PSIP1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: N-cbl like
superfamily: HIV integrase-binding domain
family: HIV integrase-binding domain
domain: PC4 and SFRS1-interacting protein, PSIP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.70  E-value=5.1e-05  Score=50.08  Aligned_cols=60  Identities=13%  Similarity=0.299  Sum_probs=54.8

Q ss_pred             CCCCHHHHHHHHHHHhcCcCCHHHhh-cccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHh
Q psy1423          43 GLVRQEQALDLLKALQTLNIDLNILT-KTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKF  102 (125)
Q Consensus        43 ~~~~~~~il~~L~~L~~~~iT~elL~-~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~  102 (125)
                      ...+...++++|.+|.++++|.-+|. .+.+--++.++|++-.|.+|.+.|..|..+||++
T Consensus        21 ~~~dv~kcL~~L~~l~~l~vt~~mL~kn~e~V~tikklRry~gn~~Ir~kA~~ly~kfKsl   81 (81)
T d2b4jc1          21 DNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNM   81 (81)
T ss_dssp             TSCCHHHHHHHHHHHHTCCCCHHHHHTTHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHChHHHHHHHHHHHHhccHHHHHHHHHHHHHhccC
Confidence            57899999999999999999998776 5678899999999988899999999999999974