Psyllid ID: psy9417

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-
Protein Sequence
ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHccccccccc
Coil and Loop (DISEMBL)
ellsinstkppiskakITGIVKLALKATHYYKYVVQSVEKFIWKCKsqyklpglyvigewnqellsinstkppiskakITGIVKLALKATHYYKYVVQSVEKFIWKCKsqyklpglyVIDAIIHQARLQFKykdvyaprfarnlyrtfgyvfqcpdedrkk
Flexible Loop (DISEMBL)
ellsinstkppiskakITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSinstkppiskAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTfgyvfqcpdedrkk
Low Complexity Region (SEG)
ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK
Disordered region (IsUnstruct)
**************AKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQC*******
Disordered Region (DISOPRED)
***S****KPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSIN*******KAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQ*P******
Disordered Region (DISEMBL)
ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK
Disordered Region (DISPRO)
*LLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPD*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK
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	161	2.2.26 [Sep-21-2011]
Q9UPN6	1271	Protein SCAF8 OS=Homo sap	yes	N/A	0.652	0.082	0.575	5e-31
Q6DID3	1268	Protein SCAF8 OS=Mus musc	yes	N/A	0.652	0.082	0.575	7e-31
Q63623	1268	Protein SCAF8 OS=Rattus n	yes	N/A	0.652	0.082	0.566	1e-29
O95104	1147	Splicing factor, arginine	no	N/A	0.652	0.091	0.556	1e-28

>sp|Q9UPN6|SCAF8_HUMAN Protein SCAF8 OS=Homo sapiens GN=SCAF8 PE=1 SV=1

 Score =  133 bits (334), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 61/106 (57%), Positives = 82/106 (77%), Gaps = 1/106 (0%)

Query: 57  IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGL 116
           +  +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGL
Sbjct: 4   VKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGL 63

Query: 117 YVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           YVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 64  YVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109

May play a role in mRNA processing.
Homo sapiens (taxid: 9606)

>sp|Q6DID3|SCAF8_MOUSE Protein SCAF8 OS=Mus musculus GN=Scaf8 PE=1 SV=1

 Score =  132 bits (333), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 61/106 (57%), Positives = 82/106 (77%), Gaps = 1/106 (0%)

Query: 57  IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGL 116
           +  +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGL
Sbjct: 4   VKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGL 63

Query: 117 YVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           YVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 64  YVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109

May play a role in mRNA processing.

Mus musculus (taxid: 10090)

>sp|Q63623|SCAF8_RAT Protein SCAF8 OS=Rattus norvegicus GN=Scaf8 PE=1 SV=1

 Score =  128 bits (322), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 60/106 (56%), Positives = 80/106 (75%), Gaps = 1/106 (0%)

Query: 57  IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGL 116
           +  +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGL
Sbjct: 4   VKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGL 63

Query: 117 YVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           YVID+I+ Q+R Q  + KDV APRF+ N+  TF  +++CP +D+ K
Sbjct: 64  YVIDSIVRQSRHQVGQEKDVCAPRFSNNIISTFQNLYRCPGDDKSK 109

May play a role in mRNA processing.

Rattus norvegicus (taxid: 10116)

>sp|O95104|SFR15_HUMAN Splicing factor, arginine/serine-rich 15 OS=Homo sapiens GN=SCAF4 PE=1 SV=3

 Score =  125 bits (315), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 59/106 (55%), Positives = 78/106 (73%), Gaps = 1/106 (0%)

Query: 57  IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGL 116
           +  +NQEL S+   KPPIS+AK+  I K A+KA   YK+VVQ VEKFI KCK +YK+PGL
Sbjct: 4   VNAFNQELFSLMDMKPPISRAKMILITKAAIKAIKLYKHVVQIVEKFIKKCKPEYKVPGL 63

Query: 117 YVIDAIIHQARLQFKY-KDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           YVID+I+ Q+R QF   KDV+ PRF++N+  TF Y++ CP ED+ K
Sbjct: 64  YVIDSIVRQSRHQFGTDKDVFGPRFSKNITATFQYLYLCPSEDKSK 109

May act to physically and functionally link transcription and pre-mRNA processing.

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	161
444732459	1022	Protein SCAF8 [Tupaia chinensis]	0.788	0.124	0.475	6e-33
157167923	1337	hypothetical protein AaeL_AAEL002986 [Ae	0.633	0.076	0.611	3e-31
170050233	1014	conserved hypothetical protein [Culex qu	0.633	0.100	0.611	5e-31
347969782	1392	AGAP003369-PA [Anopheles gambiae str. PE	0.633	0.073	0.601	1e-30
312381414	1644	hypothetical protein AND_06286 [Anophele	0.621	0.060	0.613	1e-30
348517487	1364	PREDICTED: protein SCAF8-like [Oreochrom	0.652	0.076	0.566	1e-29
402867872	1316	PREDICTED: protein SCAF8 isoform 3 [Papi	0.652	0.079	0.575	2e-29
402867868	1349	PREDICTED: protein SCAF8 isoform 1 [Papi	0.652	0.077	0.575	2e-29
332825315	1316	PREDICTED: protein SCAF8 isoform 4 [Pan	0.652	0.079	0.575	2e-29
221044370	1316	unnamed protein product [Homo sapiens]	0.652	0.079	0.575	2e-29

>gi|444732459|gb|ELW72751.1| Protein SCAF8 [Tupaia chinensis]

 Score =  145 bits (365), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 77/162 (47%), Positives = 99/162 (61%), Gaps = 35/162 (21%)

Query: 1   ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEW 60
           EL S+N  KPPISKAK+T I K A+KA   Y                             
Sbjct: 10  ELYSLNDYKPPISKAKMTQITKAAIKAIKLY----------------------------- 40

Query: 61  NQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVID 120
                S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGLYVID
Sbjct: 41  -----SLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVID 95

Query: 121 AIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           +I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 96  SIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 137

Source: Tupaia chinensis

Species: Tupaia chinensis

Genus: Tupaia

Family: Tupaiidae

Order: Scandentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|157167923|ref|XP_001662905.1| hypothetical protein AaeL_AAEL002986 [Aedes aegypti] gi|108881522|gb|EAT45747.1| AAEL002986-PA [Aedes aegypti]

 Score =  139 bits (351), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 63/103 (61%), Positives = 82/103 (79%), Gaps = 1/103 (0%)

Query: 60  WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 119
           +NQEL  +   KPPISKAK+  I + A+KA  +YK+VVQSVEKFI KCKS+YK+PGLYVI
Sbjct: 7   FNQELSGLYEAKPPISKAKMASITRSAMKAIKFYKHVVQSVEKFISKCKSEYKIPGLYVI 66

Query: 120 DAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           D+I+ Q+R QF   KDV+APRFARN+ +TF ++F+CP ED+ K
Sbjct: 67  DSIVRQSRHQFGAEKDVFAPRFARNMEQTFAHLFRCPPEDKSK 109

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170050233|ref|XP_001859912.1| conserved hypothetical protein [Culex quinquefasciatus] gi|167871912|gb|EDS35295.1| conserved hypothetical protein [Culex quinquefasciatus]

 Score =  139 bits (349), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 63/103 (61%), Positives = 81/103 (78%), Gaps = 1/103 (0%)

Query: 60  WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 119
           +NQEL  +   KPPISKAK+  I + A+KA  +YK+VVQSVEKFI KCKS+YK+PGLYVI
Sbjct: 7   FNQELSGLYEAKPPISKAKMASITRSAMKAIKFYKHVVQSVEKFISKCKSEYKIPGLYVI 66

Query: 120 DAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           D+I+ Q+R QF   KDV+APRFARN+  TF ++F+CP ED+ K
Sbjct: 67  DSIVRQSRHQFGTEKDVFAPRFARNMEATFAHLFRCPPEDKSK 109

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347969782|ref|XP_314272.5| AGAP003369-PA [Anopheles gambiae str. PEST] gi|333469268|gb|EAA09643.5| AGAP003369-PA [Anopheles gambiae str. PEST]

 Score =  137 bits (346), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 62/103 (60%), Positives = 81/103 (78%), Gaps = 1/103 (0%)

Query: 60  WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 119
           +NQEL  +  +KPPISKAK+  I + A+KA  +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct: 7   FNQELSGLYESKPPISKAKMASITRSAMKAIKFYKHVVQSVEKFIQKCKCEYKIPGLYVI 66

Query: 120 DAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           D+I+ Q+R QF   KDV+APRFARN+  TF ++F+CP ED+ K
Sbjct: 67  DSIVRQSRHQFGPEKDVFAPRFARNMESTFAHLFRCPPEDKSK 109

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312381414|gb|EFR27170.1| hypothetical protein AND_06286 [Anopheles darlingi]

 Score =  137 bits (346), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 62/101 (61%), Positives = 81/101 (80%), Gaps = 1/101 (0%)

Query: 60  WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 119
           +NQEL  +  +KPPISKAK+  I + A+KA  +YK+VVQSVEKFI KCKS+YK+PGLYVI
Sbjct: 119 FNQELSGLYESKPPISKAKMASITRSAMKAIKFYKHVVQSVEKFIQKCKSEYKIPGLYVI 178

Query: 120 DAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDR 159
           D+I+ Q+R QF   KDV+APRFARN+  TF ++F+CP ED+
Sbjct: 179 DSIVRQSRHQFGPEKDVFAPRFARNMEATFAHLFRCPPEDK 219

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|348517487|ref|XP_003446265.1| PREDICTED: protein SCAF8-like [Oreochromis niloticus]

 Score =  134 bits (336), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 60/106 (56%), Positives = 82/106 (77%), Gaps = 1/106 (0%)

Query: 57  IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGL 116
           +  +N EL S+N  KPPISKAK+T I K  +KA  +YK+VVQSVEKFI KCK +YK+PGL
Sbjct: 4   VKAFNNELYSLNEYKPPISKAKMTQITKSGIKAIKFYKHVVQSVEKFIQKCKPEYKVPGL 63

Query: 117 YVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           YVID+I+ Q+R QF   KDV+APRF++N+  TF ++++CP +D+ K
Sbjct: 64  YVIDSIVRQSRHQFGTEKDVFAPRFSKNIISTFQHLYRCPSDDKSK 109

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|402867872|ref|XP_003898053.1| PREDICTED: protein SCAF8 isoform 3 [Papio anubis]

 Score =  134 bits (336), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/106 (57%), Positives = 82/106 (77%), Gaps = 1/106 (0%)

Query: 57  IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGL 116
           +  +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGL
Sbjct: 49  VKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGL 108

Query: 117 YVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           YVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 109 YVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 154

Source: Papio anubis

Species: Papio anubis

Genus: Papio

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|402867868|ref|XP_003898051.1| PREDICTED: protein SCAF8 isoform 1 [Papio anubis]

 Score =  133 bits (335), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/106 (57%), Positives = 82/106 (77%), Gaps = 1/106 (0%)

Query: 57  IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGL 116
           +  +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGL
Sbjct: 82  VKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGL 141

Query: 117 YVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           YVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 142 YVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 187

Source: Papio anubis

Species: Papio anubis

Genus: Papio

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|332825315|ref|XP_003311605.1| PREDICTED: protein SCAF8 isoform 4 [Pan troglodytes]

 Score =  133 bits (335), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/106 (57%), Positives = 82/106 (77%), Gaps = 1/106 (0%)

Query: 57  IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGL 116
           +  +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGL
Sbjct: 49  VKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGL 108

Query: 117 YVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           YVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 109 YVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 154

Source: Pan troglodytes

Species: Pan troglodytes

Genus: Pan

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|221044370|dbj|BAH13862.1| unnamed protein product [Homo sapiens]

 Score =  133 bits (335), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/106 (57%), Positives = 82/106 (77%), Gaps = 1/106 (0%)

Query: 57  IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGL 116
           +  +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGL
Sbjct: 49  VKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGL 108

Query: 117 YVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           YVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 109 YVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 154

Source: Homo sapiens

Species: Homo sapiens

Genus: Homo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

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	161
UNIPROTKB|F1SB23	1347	SCAF8 "Uncharacterized protein	0.714	0.085	0.537	7.3e-28
UNIPROTKB|F1LPT8	1267	Rbm16 "Protein Rbm16" [Rattus	0.633	0.080	0.592	8.5e-28
MGI|MGI:1925212	1268	Scaf8 "SR-related CTD-associat	0.633	0.080	0.592	8.5e-28
UNIPROTKB|Q9UPN6	1271	SCAF8 "Protein SCAF8" [Homo sa	0.633	0.080	0.592	8.5e-28
ZFIN|ZDB-GENE-030131-4817	1286	wu:fd99c08 "wu:fd99c08" [Danio	0.633	0.079	0.592	1.4e-27
UNIPROTKB|F1NW30	1288	Gga.54017 "Uncharacterized pro	0.670	0.083	0.568	1.8e-27
UNIPROTKB|F1MYK6	1268	LOC540182 "Uncharacterized pro	0.633	0.080	0.572	4.7e-27
UNIPROTKB|F1PC86	1267	SCAF8 "Uncharacterized protein	0.608	0.077	0.595	1.6e-26
RGD|708362	1268	Scaf8 "SR-related CTD-associat	0.633	0.080	0.582	1.6e-26
UNIPROTKB|B7Z888	1337	SCAF8 "Protein SCAF8" [Homo sa	0.608	0.073	0.595	1.8e-26

UNIPROTKB|F1SB23 SCAF8 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 325 (119.5 bits), Expect = 7.3e-28, P = 7.3e-28
 Identities = 65/121 (53%), Positives = 88/121 (72%)

Query:    47 SQYKLPGLYV-----IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVE 101
             S++  PGL       +  +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVE
Sbjct:    67 SRFPGPGLCTDNMEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVE 126

Query:   102 KFIWKCKSQYKLPGLYVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRK 160
             KFI KCK +YK+PGLYVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ 
Sbjct:   127 KFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKS 186

Query:   161 K 161
             K
Sbjct:   187 K 187

GO:0043175 "RNA polymerase core enzyme binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1LPT8 Rbm16 "Protein Rbm16" [Rattus norvegicus (taxid:10116)]

 Score = 324 (119.1 bits), Expect = 8.5e-28, P = 8.5e-28
 Identities = 61/103 (59%), Positives = 81/103 (78%)

Query:    60 WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 119
             +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct:     7 FNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVI 66

Query:   120 DAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
             D+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct:    67 DSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1925212 Scaf8 "SR-related CTD-associated factor 8" [Mus musculus (taxid:10090)]

 Score = 324 (119.1 bits), Expect = 8.5e-28, P = 8.5e-28
 Identities = 61/103 (59%), Positives = 81/103 (78%)

Query:    60 WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 119
             +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct:     7 FNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVI 66

Query:   120 DAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
             D+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct:    67 DSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

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

GO:0006397 "mRNA processing" evidence=ISO

GO:0008380 "RNA splicing" evidence=IEA

GO:0016363 "nuclear matrix" evidence=ISO

GO:0019904 "protein domain specific binding" evidence=ISO

GO:0043175 "RNA polymerase core enzyme binding" evidence=ISO

GO:0070063 "RNA polymerase binding" evidence=ISO

UNIPROTKB|Q9UPN6 SCAF8 "Protein SCAF8" [Homo sapiens (taxid:9606)]

 Score = 324 (119.1 bits), Expect = 8.5e-28, P = 8.5e-28
 Identities = 61/103 (59%), Positives = 81/103 (78%)

Query:    60 WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 119
             +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct:     7 FNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVI 66

Query:   120 DAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
             D+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct:    67 DSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0043175 "RNA polymerase core enzyme binding" evidence=IPI

GO:0016363 "nuclear matrix" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

ZFIN|ZDB-GENE-030131-4817 wu:fd99c08 "wu:fd99c08" [Danio rerio (taxid:7955)]

 Score = 322 (118.4 bits), Expect = 1.4e-27, P = 1.4e-27
 Identities = 61/103 (59%), Positives = 82/103 (79%)

Query:    60 WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 119
             +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct:     7 FNGELYSLNEYKPPISKAKMTQITKSAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVI 66

Query:   120 DAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
             D+I+ Q+R QF + KDV+APRF++N+  TF  +++CP +D+ K
Sbjct:    67 DSIVRQSRHQFGQEKDVFAPRFSKNIIGTFQNLYRCPTDDKSK 109

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0046660 "female sex differentiation" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|F1NW30 Gga.54017 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 321 (118.1 bits), Expect = 1.8e-27, P = 1.8e-27
 Identities = 62/109 (56%), Positives = 82/109 (75%)

Query:    54 LYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKL 113
             L  I  +  EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+
Sbjct:     1 LLPITTYQSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60

Query:   114 PGLYVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
             PGLYVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct:    61 PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0043175 "RNA polymerase core enzyme binding" evidence=IEA

UNIPROTKB|F1MYK6 LOC540182 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 317 (116.6 bits), Expect = 4.7e-27, P = 4.7e-27
 Identities = 59/103 (57%), Positives = 81/103 (78%)

Query:    60 WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 119
             + ++L S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct:     7 FTEDLYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVI 66

Query:   120 DAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
             D+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct:    67 DSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109

GO:0043175 "RNA polymerase core enzyme binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1PC86 SCAF8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 312 (114.9 bits), Expect = 1.6e-26, P = 1.6e-26
 Identities = 59/99 (59%), Positives = 78/99 (78%)

Query:    64 LLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAII 123
             L S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGLYVID+I+
Sbjct:     7 LYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIV 66

Query:   124 HQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
              Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct:    67 RQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 105

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

RGD|708362 Scaf8 "SR-related CTD-associated factor 8" [Rattus norvegicus (taxid:10116)]

 Score = 312 (114.9 bits), Expect = 1.6e-26, P = 1.6e-26
 Identities = 60/103 (58%), Positives = 79/103 (76%)

Query:    60 WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 119
             +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct:     7 FNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVI 66

Query:   120 DAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
             D+I+ Q+R Q  + KDV APRF+ N+  TF  +++CP +D+ K
Sbjct:    67 DSIVRQSRHQVGQEKDVCAPRFSNNIISTFQNLYRCPGDDKSK 109

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=IEA

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

GO:0006397 "mRNA processing" evidence=IMP

GO:0008380 "RNA splicing" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IDA

GO:0019904 "protein domain specific binding" evidence=IMP

GO:0043175 "RNA polymerase core enzyme binding" evidence=ISO

GO:0070063 "RNA polymerase binding" evidence=IPI

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|B7Z888 SCAF8 "Protein SCAF8" [Homo sapiens (taxid:9606)]

 Score = 312 (114.9 bits), Expect = 1.8e-26, P = 1.8e-26
 Identities = 59/99 (59%), Positives = 78/99 (78%)

Query:    64 LLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAII 123
             L S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGLYVID+I+
Sbjct:    77 LYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIV 136

Query:   124 HQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
              Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct:   137 RQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 175

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

---

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)
Q6DID3	SCAF8_MOUSE	No assigned EC number	0.5754	0.6521	0.0828	yes	N/A
Q63623	SCAF8_RAT	No assigned EC number	0.5660	0.6521	0.0828	yes	N/A
Q9UPN6	SCAF8_HUMAN	No assigned EC number	0.5754	0.6521	0.0826	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	161
cd03562	114	cd03562, CID, CID (CTD-Interacting Domain) domain	8e-15
smart00582	124	smart00582, RPR, domain present in proteins, which	4e-14
cd03562	114	cd03562, CID, CID (CTD-Interacting Domain) domain	3e-10
smart00582	124	smart00582, RPR, domain present in proteins, which	4e-07
pfam04818	64	pfam04818, CTD_bind, RNA polymerase II-binding dom	9e-05

>gnl|CDD|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1

 Score = 66.1 bits (162), Expect = 8e-15
 Identities = 26/89 (29%), Positives = 46/89 (51%), Gaps = 7/89 (7%)

Query: 74  ISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYK 133
            S+  I  + KLA++   + K +V+ +EK I KC  + KLP LY++D+I+     ++K  
Sbjct: 16  NSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKEF 75

Query: 134 DVYAPRFARNLYRTFGYVFQ-CPDEDRKK 161
                 F+  L   F   ++   ++ RKK
Sbjct: 76  ------FSEFLVPLFLDAYEKVDEKTRKK 98

Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. Length = 114

>gnl|CDD|214731 smart00582, RPR, domain present in proteins, which are involved in regulation of nuclear pre-mRNA

 Score = 64.6 bits (158), Expect = 4e-14
 Identities = 27/90 (30%), Positives = 46/90 (51%), Gaps = 5/90 (5%)

Query: 74  ISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFK-- 131
            S+  I  + K A++   + K +V+  EK+I K     KLP LY++D+I+  ++ ++   
Sbjct: 11  NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSE 70

Query: 132 YKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           + D   P F   L R  G     P+E +KK
Sbjct: 71  FGDELGPVFQDALRRVLGA---APEELKKK 97

Length = 124

>gnl|CDD|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1

 Score = 54.5 bits (132), Expect = 3e-10
 Identities = 17/46 (36%), Positives = 28/46 (60%)

Query: 12 ISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 57
           S+  I  + KLA++   + K +V+ +EK I KC  + KLP LY++
Sbjct: 16 NSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLL 61

Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. Length = 114

>gnl|CDD|214731 smart00582, RPR, domain present in proteins, which are involved in regulation of nuclear pre-mRNA

 Score = 46.1 bits (110), Expect = 4e-07
 Identities = 15/46 (32%), Positives = 25/46 (54%)

Query: 12 ISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 57
           S+  I  + K A++   + K +V+  EK+I K     KLP LY++
Sbjct: 11 NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLL 56

Length = 124

>gnl|CDD|218279 pfam04818, CTD_bind, RNA polymerase II-binding domain

 Score = 38.3 bits (90), Expect = 9e-05
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 112 KLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           KLP LY+ + ++  ++   K KD +   F+  L   F +V++  DE+ KK
Sbjct: 1   KLPLLYLANDVVQNSKH--KNKDEFVKAFSPVLPDAFAHVYKEGDEEVKK 48

This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. Length = 64

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	161
KOG0132|consensus	894		100.0
KOG0132|consensus	894		99.93
cd03562	114	CID CID (CTD-Interacting Domain) domain family; CI	99.86
KOG2071|consensus	579		99.73
smart00582	121	RPR domain present in proteins, which are involved	99.7
cd03562	114	CID CID (CTD-Interacting Domain) domain family; CI	98.97
smart00582	121	RPR domain present in proteins, which are involved	98.72
PF04818	64	CTD_bind: RNA polymerase II-binding domain.; Inter	98.6
cd00197	115	VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamil	97.97
KOG2669|consensus	325		97.5
PF12243	139	CTK3: CTD kinase subunit gamma CTK3	97.09
KOG2071|consensus	579		96.31
PF00790	140	VHS: VHS domain; InterPro: IPR002014 The VHS domai	95.46
cd03561	133	VHS VHS domain family; The VHS domain is present i	94.73
KOG0151|consensus	877		94.49
cd03572	122	ENTH_epsin_related ENTH domain, Epsin Related fami	88.16
smart00288	133	VHS Domain present in VPS-27, Hrs and STAM. Unpubl	86.8
PF01417	125	ENTH: ENTH domain; InterPro: IPR001026 The ENTH (E	86.24

>KOG0132|consensus

Probab=100.00  E-value=9.9e-35  Score=273.74  Aligned_cols=107  Identities=54%  Similarity=0.874  Sum_probs=104.6

Q ss_pred             HHHHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhc-cc
Q psy9417          55 YVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFK-YK  133 (161)
Q Consensus        55 yvIDef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~-~k  133 (161)
                      .+|.+|+.||+||.++|+||||+||..||++|++|++.|+|||+.||+||+||+|+||||+|||||||||+++||++ +|
T Consensus         2 e~v~~Fn~eL~SL~DsK~~IS~sKi~~ITkaAikaIk~ykhVVqsVeKfi~kCkpe~Kl~gLYVIDSIVRqsrhq~~~~k   81 (894)
T KOG0132|consen    2 DAVKEFNGELDSLEDSKPGISGSKILKITKAAIKAIKLYKHVVQSVEKFIKKCKPEYKLPGLYVIDSIVRQSRHQFGKEK   81 (894)
T ss_pred             hHHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccCeeEEehHHHHHHHHhhcccc
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999 99


Q ss_pred             CccHHhhHHHHHHHHhhhhcCCCcccCC
Q psy9417         134 DVYAPRFARNLYRTFGYVFQCPDEDRKK  161 (161)
Q Consensus       134 d~Y~~rF~~nl~~tf~~~~~c~~~dk~k  161 (161)
                      |+|++||.+|+..||+++|+|+.+||++
T Consensus        82 d~F~prf~~n~~~tf~~L~~c~~edks~  109 (894)
T KOG0132|consen   82 DVFGPRFSKNFTGTFQNLYECPQEDKSD  109 (894)
T ss_pred             cccCCccchhHHHHHHHHHhcCHHHHHH
Confidence            9999999999999999999999999864

>KOG0132|consensus

Probab=99.93  E-value=7.9e-27  Score=220.54  Aligned_cols=86  Identities=48%  Similarity=0.594  Sum_probs=73.7

Q ss_pred             CcccccCCCCCchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHhhhhhc-C----CCCCc
Q psy9417           1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINS-T----KPPIS   75 (161)
Q Consensus         1 ~l~~~~~~~~~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL~sL~~-~----k~~iS   75 (161)
                      ||.||+|+||+||++||..|||+||||||+||||||+|||||+||||+||||||||||++++...+-+. .    .+..|
T Consensus        10 eL~SL~DsK~~IS~sKi~~ITkaAikaIk~ykhVVqsVeKfi~kCkpe~Kl~gLYVIDSIVRqsrhq~~~~kd~F~prf~   89 (894)
T KOG0132|consen   10 ELDSLEDSKPGISGSKILKITKAAIKAIKLYKHVVQSVEKFIKKCKPEYKLPGLYVIDSIVRQSRHQFGKEKDVFGPRFS   89 (894)
T ss_pred             HHHHhhccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccCeeEEehHHHHHHHHhhcccccccCCccc
Confidence            799999999999999999999999999999999999999999999999999999999999998866554 1    23455


Q ss_pred             HHHHHHHHHHH
Q psy9417          76 KAKITGIVKLA   86 (161)
Q Consensus        76 rskI~~LT~lA   86 (161)
                      +..+..+..++
T Consensus        90 ~n~~~tf~~L~  100 (894)
T KOG0132|consen   90 KNFTGTFQNLY  100 (894)
T ss_pred             hhHHHHHHHHH
Confidence            55555444443

>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1

Probab=99.86  E-value=9.4e-22  Score=145.20  Aligned_cols=94  Identities=29%  Similarity=0.425  Sum_probs=85.2

Q ss_pred             HhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccH
Q psy9417          58 GEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYA  137 (161)
Q Consensus        58 Def~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~  137 (161)
                      .+|...|++|..++  +|++.|++||.+|++|.++++.||+.++++|++|+|++||++|||+|||+||++++      |.
T Consensus         2 ~~~~~~l~~L~~~~--~S~~~I~~lt~~a~~~~~~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~~~~------~~   73 (114)
T cd03562           2 FDYNALLEKLTFNK--NSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRK------YK   73 (114)
T ss_pred             ccHHHHHHHHHcCc--ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHcccc------hH
Confidence            57888899998865  89999999999999999999999999999999999999999999999999999987      55


Q ss_pred             HhhHHHHHHHHhhhh-cCCCccc
Q psy9417         138 PRFARNLYRTFGYVF-QCPDEDR  159 (161)
Q Consensus       138 ~rF~~nl~~tf~~~~-~c~~~dk  159 (161)
                      ..|+..+.++|.+++ +|+++.|
T Consensus        74 ~~~~~~~~~~f~~~~~~~~~~~r   96 (114)
T cd03562          74 EFFSEFLVPLFLDAYEKVDEKTR   96 (114)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHH
Confidence            888888899999888 5666554

Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.

>KOG2071|consensus

Probab=99.73  E-value=3.5e-18  Score=158.42  Aligned_cols=92  Identities=29%  Similarity=0.436  Sum_probs=85.3

Q ss_pred             HHHHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccC
Q psy9417          55 YVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKD  134 (161)
Q Consensus        55 yvIDef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd  134 (161)
                      -+..+|...|++|+.    ||++.|++||.+|.||..+++.||..||+||.||+|..||+++|++|||++|+|.+     
T Consensus         4 ~~~~dy~s~ledltf----nskp~i~~lt~la~En~~~a~~iv~~iE~hi~kcpp~~kL~~~y~~dsi~knvg~p-----   74 (579)
T KOG2071|consen    4 DACRDYQSSLEDLTF----NSKPIINTLTILAEENLPFAKSIVSAIEAHIAKCPPSQKLPVMYLLDSIVKNVGSP-----   74 (579)
T ss_pred             HhHHHHHHHHHHHhc----CCcchhHHhhHhhhhcccccHHHHHHHHHHHhhCCcccccchhhhhHHHHhhcCCc-----
Confidence            456789999999984    88999999999999999999999999999999999999999999999999999998     


Q ss_pred             ccHHhhHHHHHHHHhhhhcCCC
Q psy9417         135 VYAPRFARNLYRTFGYVFQCPD  156 (161)
Q Consensus       135 ~Y~~rF~~nl~~tf~~~~~c~~  156 (161)
                       |+-.|++||+.||+++|.--+
T Consensus        75 -y~~~fs~~l~a~f~~~~~~vd   95 (579)
T KOG2071|consen   75 -YTTAFSRNLVATFICAFTKVD   95 (579)
T ss_pred             -chhhhhhhHHHHHHHHHhhcc
Confidence             779999999999999996543

>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA

Probab=99.70  E-value=1e-16  Score=118.69  Aligned_cols=87  Identities=25%  Similarity=0.397  Sum_probs=74.6

Q ss_pred             hhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHH
Q psy9417          59 EWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAP  138 (161)
Q Consensus        59 ef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~  138 (161)
                      +|++.|++|.     +|++.|+++|..|++|.+++++||+.+++++++++|++||+.|||+|+|++|++.+++  ..|..
T Consensus         1 ~f~~~L~~L~-----~s~~~I~~lt~~~~~~~~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~~~~~~--~~f~~   73 (121)
T smart00582        1 AFEQKLESLN-----NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNSKRKYG--SEFGD   73 (121)
T ss_pred             ChHHHHHhcc-----ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHHhhccH--HHHHH
Confidence            4788899986     7999999999999999999999999999999999999999999999999999998854  23445


Q ss_pred             hhHHHHHHHHhhhh
Q psy9417         139 RFARNLYRTFGYVF  152 (161)
Q Consensus       139 rF~~nl~~tf~~~~  152 (161)
                      -|.+.+..+|.+++
T Consensus        74 ~~~~~~~~~~~~~~   87 (121)
T smart00582       74 ELGPVFQDALRDVL   87 (121)
T ss_pred             HHHHHHHHHHHHHH
Confidence            55555555666665

>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1

Probab=98.97  E-value=2.6e-09  Score=78.76  Aligned_cols=53  Identities=32%  Similarity=0.474  Sum_probs=50.8

Q ss_pred             chHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHh
Q psy9417          12 ISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQEL   64 (161)
Q Consensus        12 ~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL   64 (161)
                      .|+..|+.+|.-|+.+.++++++|+.++++|.+|.|+.|+|+|||+|+.....
T Consensus        16 ~S~~~I~~lt~~a~~~~~~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~   68 (114)
T cd03562          16 NSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNV   68 (114)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHc
Confidence            59999999999999999999999999999999999999999999999988764

Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.

>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA

Probab=98.72  E-value=5.2e-08  Score=72.07  Aligned_cols=54  Identities=30%  Similarity=0.325  Sum_probs=51.3

Q ss_pred             CchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHh
Q psy9417          11 PISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQEL   64 (161)
Q Consensus        11 ~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL   64 (161)
                      ..||..|+++|.-|+.+.++++++|+.+++.+.+|.|+.|++.|||+|+....-
T Consensus        10 ~~s~~~I~~lt~~~~~~~~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~   63 (121)
T smart00582       10 NNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNS   63 (121)
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHH
Confidence            389999999999999999999999999999999999999999999999987755

>PF04818 CTD_bind: RNA polymerase II-binding domain

Probab=98.60  E-value=1.3e-08  Score=68.78  Aligned_cols=46  Identities=28%  Similarity=0.474  Sum_probs=40.0

Q ss_pred             cchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHHHhhhhcC-CCccc
Q psy9417         112 KLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQC-PDEDR  159 (161)
Q Consensus       112 KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~tf~~~~~c-~~~dk  159 (161)
                      ||+.|||+|+|++|++.+  ..|.|++.|++.|..+|.+++++ +++++
T Consensus         1 KL~~lYl~ndI~q~sk~k--~~~~f~~~F~~~l~~~~~~~~~~~~~~~~   47 (64)
T PF04818_consen    1 KLALLYLANDILQNSKRK--NPDEFAPAFSPVLPDAFAHAYKNVDPEVR   47 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHH--TTHCHHHHHHCCHHHHHHHHCCCS-HHHH
T ss_pred             CcceeehHHHHHHHhhhc--ChHHHHHHHHHHHHHHHHHHHhcCCHHHH
Confidence            799999999999999876  45789999999999999999988 55544

; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....

>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain

Probab=97.97  E-value=2.5e-05  Score=57.65  Aligned_cols=69  Identities=17%  Similarity=0.125  Sum_probs=59.9

Q ss_pred             CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHH
Q psy9417          73 PISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRT  147 (161)
Q Consensus        73 ~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~t  147 (161)
                      +-+.+.|..|+.+.-++...++.++..|.++|....|...+.+|+++|++++|.+.+|      ...|+.+.+-.
T Consensus        15 ~p~~~~i~~i~d~~~~~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g~~f------~~~i~~~~~~~   83 (115)
T cd00197          15 GPDWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERF------HQEVASNDFAV   83 (115)
T ss_pred             CCCHHHHHHHHHHHHCCCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHccHHH------HHHHHHhHHHH
Confidence            6788999999999988878899999999999999999999999999999999999874      45666654433

The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra

>KOG2669|consensus

Probab=97.50  E-value=0.00054  Score=60.94  Aligned_cols=90  Identities=12%  Similarity=0.207  Sum_probs=77.7

Q ss_pred             hHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHHh
Q psy9417          60 WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPR  139 (161)
Q Consensus        60 f~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~r  139 (161)
                      |...|..|.     +|...|+++..-.+.|-+++..||+.=.+.+++....+||..||++.-++-|++.+   .+.|.+-
T Consensus         9 l~~kL~~L~-----~TQeSIqtlS~Wli~hkk~a~~IV~~Wl~~~~~~~~~~Kl~llYLaNDVvQnskrk---~~ef~~e   80 (325)
T KOG2669|consen    9 LEKKLAELS-----NTQESIQTLSLWLIHHKKHARLIVDVWLKELKKSSVNHKLTLLYLANDVVQNSKRK---GPEFVDE   80 (325)
T ss_pred             HHHHHHhcc-----chHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCCCceeeehhhhHHHHHHhhhc---CchhHHH
Confidence            444455553     68899999999999999999999999999999999999999999999999999433   4679999


Q ss_pred             hHHHHHHHHhhhh-cCCCc
Q psy9417         140 FARNLYRTFGYVF-QCPDE  157 (161)
Q Consensus       140 F~~nl~~tf~~~~-~c~~~  157 (161)
                      |.+-+.+-|.+++ +|+.+
T Consensus        81 f~~v~~~a~~~i~~~~~~~   99 (325)
T KOG2669|consen   81 FWPVVLKAFAHIVEETDVK   99 (325)
T ss_pred             HHHHHHHHHHHHHHhcchh
Confidence            9999999999998 55554

>PF12243 CTK3: CTD kinase subunit gamma CTK3

Probab=97.09  E-value=0.005  Score=48.73  Aligned_cols=91  Identities=21%  Similarity=0.230  Sum_probs=77.1

Q ss_pred             HHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCcc
Q psy9417          57 IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVY  136 (161)
Q Consensus        57 IDef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y  136 (161)
                      =-.|.+-|+.|.     .|...|+..|..|++|......+..+|-..+.+..=.-|...+|.||++|-.+...-+....|
T Consensus         7 r~~F~~~L~~L~-----aS~qSi~kaa~fAlk~~~~~edL~~cIle~le~~~lN~R~nI~~fID~l~e~~~~~~~~~~~Y   81 (139)
T PF12243_consen    7 RMQFTQLLRRLN-----ASQQSIQKAAQFALKNRDMEEDLWSCILEQLEKENLNTRINIFYFIDSLCESSQKSKKYNYPY   81 (139)
T ss_pred             HHHHHHHHHHcc-----hhHHHHHHHHHHHHHccccHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHhcccccchh
Confidence            334555566654     477889999999999999999999999999999988889999999999999988776567899


Q ss_pred             HHhhHHHHHHHHhhhh
Q psy9417         137 APRFARNLYRTFGYVF  152 (161)
Q Consensus       137 ~~rF~~nl~~tf~~~~  152 (161)
                      ...-.++|..+...+.
T Consensus        82 v~~l~~dL~~Iv~~V~   97 (139)
T PF12243_consen   82 VSMLQRDLPRIVDAVA   97 (139)
T ss_pred             HHHHHHHHHHHHHHhC
Confidence            9999999999887764

>KOG2071|consensus

Probab=96.31  E-value=0.004  Score=59.14  Aligned_cols=58  Identities=28%  Similarity=0.322  Sum_probs=53.2

Q ss_pred             CchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHhhhhh
Q psy9417          11 PISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSIN   68 (161)
Q Consensus        11 ~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL~sL~   68 (161)
                      .=||-.|+-.|..|..-+.+=+-+|..+|.-|+||.|-.|||++|++|++..-+.+=+
T Consensus        18 fnskp~i~~lt~la~En~~~a~~iv~~iE~hi~kcpp~~kL~~~y~~dsi~knvg~py   75 (579)
T KOG2071|consen   18 FNSKPIINTLTILAEENLPFAKSIVSAIEAHIAKCPPSQKLPVMYLLDSIVKNVGSPY   75 (579)
T ss_pred             cCCcchhHHhhHhhhhcccccHHHHHHHHHHHhhCCcccccchhhhhHHHHhhcCCcc
Confidence            5688899999999999999999999999999999999999999999999988775533

>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM

Probab=95.46  E-value=0.027  Score=43.27  Aligned_cols=75  Identities=17%  Similarity=0.222  Sum_probs=57.4

Q ss_pred             cHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHHHhh
Q psy9417          75 SKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGY  150 (161)
Q Consensus        75 SrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~tf~~  150 (161)
                      .=+.|-.|.+..-.+....+.++..|.++++...|..-+.+|.|+|++++|.|.++. .-+=..+|...|.+++..
T Consensus        22 Dw~~~l~icD~i~~~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~-~ev~~~~fl~~l~~l~~~   96 (140)
T PF00790_consen   22 DWSLILEICDLINSSPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFH-REVASKEFLDELVKLIKS   96 (140)
T ss_dssp             -HHHHHHHHHHHHTSTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHH-HHHTSHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHH-HHHhHHHHHHHHHHHHcc
Confidence            345667777777777778999999999999999999999999999999999998865 011123466666665543

Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....

>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule)

Probab=94.73  E-value=0.041  Score=42.00  Aligned_cols=57  Identities=14%  Similarity=0.095  Sum_probs=47.8

Q ss_pred             cHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhc
Q psy9417          75 SKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFK  131 (161)
Q Consensus        75 SrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~  131 (161)
                      .-+-|-.|.++.-..-...+..++.|.++|+...|.--+.+|.++|++++|.|+++.
T Consensus        17 D~~~il~icd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~   73 (133)
T cd03561          17 DWALNLELCDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFH   73 (133)
T ss_pred             cHHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHH
Confidence            345566666666656667899999999999999999999999999999999998754

It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me

>KOG0151|consensus

Probab=94.49  E-value=0.12  Score=50.81  Aligned_cols=88  Identities=16%  Similarity=0.229  Sum_probs=69.5

Q ss_pred             hHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHH--HhhcCCCCcchhHHHHHHHHHHHhhhhcccCccH
Q psy9417          60 WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKF--IWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYA  137 (161)
Q Consensus        60 f~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~--I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~  137 (161)
                      |..-|++|+     --|+.|..+.--|++|.+.+-.||.+|..-  +...+-.-|+.-||+|.-|.-|.-..-..--.|.
T Consensus       436 lE~liR~LT-----pEk~sIg~aM~FalenA~aa~EI~eci~eSlt~~~t~~~kKiarLyLvsDIL~N~sarv~nas~YR  510 (877)
T KOG0151|consen  436 LEDLIRGLT-----PEKSSIGDAMVFALENADAAGEIVECITESLTNKETPLPKKIARLYLVSDILHNSSARVANASAYR  510 (877)
T ss_pred             HHHHHHhcC-----cccchHHHHHHHHHhhhhhHHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHhhhhhhhhHHHHHH
Confidence            444445554     357789999999999999999999999864  4778888999999999999988865533334577


Q ss_pred             HhhHHHHHHHHhhhh
Q psy9417         138 PRFARNLYRTFGYVF  152 (161)
Q Consensus       138 ~rF~~nl~~tf~~~~  152 (161)
                      .-|-..|..+|.+++
T Consensus       511 ~~FEa~L~~Ifd~l~  525 (877)
T KOG0151|consen  511 KSFEATLEDIFDDLN  525 (877)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            888888888887765

>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain

Probab=88.16  E-value=2.9  Score=32.47  Aligned_cols=58  Identities=17%  Similarity=0.170  Sum_probs=53.7

Q ss_pred             CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhh
Q psy9417          72 PPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQ  129 (161)
Q Consensus        72 ~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~  129 (161)
                      .|-++....+|+.+..++......|++.|-+.+++..|.-|+-+|=|||-+|++....
T Consensus        15 ~p~pgy~~~Eia~~t~~s~~~~~ei~d~L~kRL~~~~~hVK~K~Lrilk~l~~~G~~~   72 (122)
T cd03572          15 EPTPGYLYEEIAKLTRKSVGSCQELLEYLLKRLKRSSPHVKLKVLKIIKHLCEKGNSD   72 (122)
T ss_pred             CCCchHHHHHHHHHHHcCHHHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHhhCCHH
Confidence            3889999999999999998889999999999999999999999999999999998654

The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t

>smart00288 VHS Domain present in VPS-27, Hrs and STAM

Probab=86.80  E-value=0.72  Score=35.35  Aligned_cols=57  Identities=19%  Similarity=0.153  Sum_probs=45.6

Q ss_pred             cHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhc
Q psy9417          75 SKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFK  131 (161)
Q Consensus        75 SrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~  131 (161)
                      .-+.|-.+.++.-......+..+..|-+.++.-.|.--+-+|-++|++++|.|.++.
T Consensus        17 dw~~~l~icD~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~   73 (133)
T smart00288       17 DWELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFH   73 (133)
T ss_pred             CHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHH
Confidence            334455555555555556788899999999999999999999999999999998754

Unpublished observations. Domain of unknown function.

>PF01417 ENTH: ENTH domain; InterPro: IPR001026 The ENTH (Epsin N-terminal homology) domain is approximately 150 amino acids in length and is always found located at the N-termini of proteins

Probab=86.24  E-value=2.4  Score=31.68  Aligned_cols=56  Identities=7%  Similarity=0.046  Sum_probs=45.1

Q ss_pred             CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHH---hhcCCCCcchhHHHHHHHHHHHhhh
Q psy9417          73 PISKAKITGIVKLALKATHYYKYVVQSVEKFI---WKCKSQYKLPGLYVIDAIIHQARLQ  129 (161)
Q Consensus        73 ~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I---~k~~p~~KL~~LYVIDSIvRn~~~~  129 (161)
                      |.++..+..|+...-+. ..+..|+..|-+.+   ....+.+++-+|.+|+-+++|....
T Consensus        18 gp~~~~l~eIa~~t~~~-~~~~~I~~~l~kRL~~~~~k~wr~~~KaL~ll~yLl~nG~~~   76 (125)
T PF01417_consen   18 GPPGKLLAEIAQLTYNS-KDCQEIMDVLWKRLSKSDGKNWRHVYKALTLLEYLLKNGSER   76 (125)
T ss_dssp             S--HHHHHHHHHHTTSC-HHHHHHHHHHHHHHHSSTSSGHHHHHHHHHHHHHHHHHS-HH
T ss_pred             CcCHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHHHHCCHH
Confidence            67777777777776555 89999999999999   7777788999999999999998654

The domain forms a compact globular structure, composed of 9 alpha-helices connected by loops of varying length. The general topology is determined by three helical hairpins that are stacked consecutively with a right hand twist []. An N-terminal helix folds back, forming a deep basic groove that forms the binding pocket for the Ins(1,4,5)P3 ligand []. The ligand is coordinated by residues from surrounding alpha-helices and all three phosphates are multiply coordinated. The coordination of Ins(1,4,5)P3 suggests that ENTH is specific for particular head groups. Proteins containing this domain have been found to bind PtdIns(4,5)P2 and PtdIns(1,4,5)P3 suggesting that the domain may be a membrane interacting module. The main function of proteins containing this domain appears to be to act as accessory clathrin adaptors in endocytosis, Epsin is able to recruit and promote clathrin polymerisation on a lipid monolayer, but may have additional roles in signalling and actin regulation []. Epsin causes a strong degree of membrane curvature and tubulation, even fragmentation of membranes with a high PtdIns(4,5)P2 content. Epsin binding to membranes facilitates their deformation by insertion of the N-terminal helix into the outer leaflet of the bilayer, pushing the head groups apart. This would reduce the energy needed to curve the membrane into a vesicle, making it easier for the clathrin cage to fix and stabilise the curved membrane. This points to a pioneering role for epsin in vesicle budding as it provides both a driving force and a link between membrane invagination and clathrin polymerisation. ; PDB: 1H0A_A 1EYH_A 1EDU_A 2QY7_B 1XGW_A 2V8S_E 1VDY_A 2DCP_A 1INZ_A 3ONL_B ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	161
2diw_A	152	Solution Structure Of The Rpr Domain Of Putative Rn		5e-31
3d9p_A	145	Snapshots Of The Rna Processing Factor Scaf8 Bound		5e-31
3d9j_A	145	Snapshots Of The Rna Processing Factor Scaf8 Bound		6e-31
3d9i_A	145	Snapshots Of The Rna Processing Factor Scaf8 Bound		2e-30
3d9o_A	145	Snapshots Of The Rna Processing Factor Scaf8 Bound		7e-30

>pdb|2DIW|A Chain A, Solution Structure Of The Rpr Domain Of Putative Rna- Binding Protein 16 Length = 152

Iteration: 1
 Score =  130 bits (326), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 61/109 (55%), Positives = 83/109 (76%), Gaps = 1/109 (0%)
Query: 54  LYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKL 113
           +  +  +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+
Sbjct: 10  MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 69
Query: 114 PGLYVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           PGLYVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 70  PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 118

>pdb|3D9P|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To Different Phosphorylated Forms Of The Carboxy-Terminal Domain Of Rna-Polymerase Ii Length = 145

Iteration: 1
 Score =  129 bits (325), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 61/109 (55%), Positives = 83/109 (76%), Gaps = 1/109 (0%)
Query: 54  LYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKL 113
           +  +  +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+
Sbjct: 1   MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60
Query: 114 PGLYVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           PGLYVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 61  PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109

>pdb|3D9J|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To Different Phosphorylated Forms Of The Carboxy-Terminal Domain Of Rna-Polymerase Ii Length = 145

Iteration: 1
 Score =  129 bits (325), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 61/109 (55%), Positives = 83/109 (76%), Gaps = 1/109 (0%)
Query: 54  LYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKL 113
           +  +  +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+
Sbjct: 1   MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60
Query: 114 PGLYVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           PGLYVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 61  PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109

>pdb|3D9I|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To Different Phosphorylated Forms Of The Carboxy-Terminal Domain Of Rna-Polymerase Ii Length = 145

Iteration: 1
 Score =  127 bits (320), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 60/109 (55%), Positives = 82/109 (75%), Gaps = 1/109 (0%)
Query: 54  LYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKL 113
           +  +  +N EL S+   KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+
Sbjct: 1   MEAVKTFNSELYSLMDMKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60
Query: 114 PGLYVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           PGLYVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 61  PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109

>pdb|3D9O|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To Different Phosphorylated Forms Of The Carboxy-Terminal Domain Of Rna-Polymerase Ii Length = 145

Iteration: 1
 Score =  126 bits (316), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 60/106 (56%), Positives = 80/106 (75%), Gaps = 1/106 (0%)
Query: 57  IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGL 116
           +  +N EL S+   KPPISKAK T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGL
Sbjct: 4   VKTFNSELYSLXDXKPPISKAKXTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGL 63
Query: 117 YVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           YVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 64  YVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	161
3d9j_A	145	RNA-binding protein 16; SCAF8, RNA polymerase II C	9e-27
3d9j_A	145	RNA-binding protein 16; SCAF8, RNA polymerase II C	4e-13
3clj_A	157	Protein NRD1; CTD-interacting domain, nucleus, pho	7e-21
3clj_A	157	Protein NRD1; CTD-interacting domain, nucleus, pho	6e-13
1sz9_A	144	PCF11 protein; RNA polymerase II CTD interacting d	2e-16
1sz9_A	144	PCF11 protein; RNA polymerase II CTD interacting d	1e-05
4fld_A	135	Regulation of nuclear PRE-mRNA domain-containing 1	1e-12
4fld_A	135	Regulation of nuclear PRE-mRNA domain-containing 1	2e-04
4flb_A	132	Regulation of nuclear PRE-mRNA domain-containing;	4e-11
4flb_A	132	Regulation of nuclear PRE-mRNA domain-containing;	2e-04
2km4_A	142	Regulator of TY1 transposition protein 103; CTD-in	2e-08

>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A Length = 145

 Score = 97.5 bits (242), Expect = 9e-27
 Identities = 61/107 (57%), Positives = 82/107 (76%), Gaps = 1/107 (0%)

Query: 56  VIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPG 115
            +  +N EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PG
Sbjct: 3   AVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPG 62

Query: 116 LYVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           LYVID+I+ Q+R QF + KDV+APRF+ N+  TF  +++CP +D+ K
Sbjct: 63  LYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109

>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A Length = 145

 Score = 62.1 bits (150), Expect = 4e-13
 Identities = 44/128 (34%), Positives = 67/128 (52%), Gaps = 7/128 (5%)

Query: 1   ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEW 60
           EL S+N  KPPISKAK+T I K A+KA  +YK+VVQSVEKFI KCK +YK+PGLYVI   
Sbjct: 10  ELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSI 69

Query: 61  NQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKF-----IWKCKSQYKLPG 115
            ++       +  +   + +  +       + Y+       K      +W+  + +K   
Sbjct: 70  VRQSRHQFGQEKDVFAPRFSNNIISTF--QNLYRCPGDDKSKIVRVLNLWQKNNVFKSEI 127

Query: 116 LYVIDAII 123
           +  +  + 
Sbjct: 128 IQPLLDMA 135

>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA polymer binding protein, RNA binding protein; 2.10A {Saccharomyces cerevisiae} Length = 157

 Score = 82.5 bits (203), Expect = 7e-21
 Identities = 17/115 (14%), Positives = 34/115 (29%), Gaps = 12/115 (10%)

Query: 59  EWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYV 118
            +   L S    K  IS ++I  +   AL        ++  +  +   C   +KL  LY+
Sbjct: 5   NFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYI 64

Query: 119 IDAIIHQARLQFKYKDV-----------YAPRFARNLYRTFGYVFQC-PDEDRKK 161
           ID+I      + +                       +             + ++K
Sbjct: 65  IDSIGRAYLDETRSNSNSSSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKEK 119

>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA polymer binding protein, RNA binding protein; 2.10A {Saccharomyces cerevisiae} Length = 157

 Score = 61.7 bits (149), Expect = 6e-13
 Identities = 14/57 (24%), Positives = 23/57 (40%)

Query: 1  ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 57
           L S    K  IS ++I  +   AL        ++  +  +   C   +KL  LY+I
Sbjct: 9  TLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYII 65

>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm repeats, transcription; 2.10A {Saccharomyces cerevisiae} SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X Length = 144

 Score = 70.5 bits (172), Expect = 2e-16
 Identities = 26/106 (24%), Positives = 44/106 (41%), Gaps = 10/106 (9%)

Query: 56  VIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPG 115
           ++ ++N  L  +     PI    IT + KLA +     +Y V ++E  I KC  + KL  
Sbjct: 8   IVKDFNSILEELTFNSRPI----ITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYA 63

Query: 116 LYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
            Y +D+I             Y   F+RNL+  +   +   D   + 
Sbjct: 64  FYALDSICKNV------GSPYTIYFSRNLFNLYKRTYLLVDNTTRT 103

>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm repeats, transcription; 2.10A {Saccharomyces cerevisiae} SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X Length = 144

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 4/57 (7%)

Query: 1  ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 57
           L  +     PI    IT + KLA +     +Y V ++E  I KC  + KL   Y +
Sbjct: 15 ILEELTFNSRPI----ITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYAL 67

>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural genomics consortium, SGC, protein binding; 1.80A {Homo sapiens} Length = 132

 Score = 56.5 bits (136), Expect = 4e-11
 Identities = 14/101 (13%), Positives = 35/101 (34%), Gaps = 9/101 (8%)

Query: 61  NQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVID 120
           +++  S+ +T   I            ++   ++  +V    K++ +    ++L   Y+ +
Sbjct: 11  DRKFQSVTNTMESIQGLS-----SWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLAN 65

Query: 121 AIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
            +I   +   K   ++   FA  L      V        K 
Sbjct: 66  DVIQNCK--RKNAIIFRESFADVLPEAAALV--KDPSVSKS 102

>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural genomics consortium, SGC, protein binding; 1.80A {Homo sapiens} Length = 132

 Score = 38.4 bits (89), Expect = 2e-04
 Identities = 8/62 (12%), Positives = 23/62 (37%), Gaps = 5/62 (8%)

Query: 1  ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEW 60
          +  S+ +T   I            ++   ++  +V    K++ +    ++L   Y+  + 
Sbjct: 13 KFQSVTNTMESIQGLS-----SWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDV 67

Query: 61 NQ 62
           Q
Sbjct: 68 IQ 69

>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain, RNA polymerase II binding protein, phosphoprotein; NMR {Saccharomyces cerevisiae} PDB: 2l0i_A* Length = 142

 Score = 49.6 bits (118), Expect = 2e-08
 Identities = 20/103 (19%), Positives = 42/103 (40%), Gaps = 9/103 (8%)

Query: 61  NQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIW--KCKSQYKLPGLYV 118
             +L ++  ++  IS A      K  L        V +  ++++      ++ KL GLY+
Sbjct: 9   TTKLNTLEDSQESISSAS-----KWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYL 63

Query: 119 IDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           ++ ++ QA+   +    +   F +      G + Q    D KK
Sbjct: 64  MNHVVQQAK--GQKIIQFQDSFGKVAAEVLGRINQEFPRDLKK 104

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	161
3d9j_A	145	RNA-binding protein 16; SCAF8, RNA polymerase II C	99.97
3clj_A	157	Protein NRD1; CTD-interacting domain, nucleus, pho	99.97
1sz9_A	144	PCF11 protein; RNA polymerase II CTD interacting d	99.93
3clj_A	157	Protein NRD1; CTD-interacting domain, nucleus, pho	99.79
4fu3_A	135	Regulation of nuclear PRE-mRNA domain-containing 1	99.7
4flb_A	132	Regulation of nuclear PRE-mRNA domain-containing;	99.69
3d9j_A	145	RNA-binding protein 16; SCAF8, RNA polymerase II C	99.67
1sz9_A	144	PCF11 protein; RNA polymerase II CTD interacting d	99.37
2km4_A	142	Regulator of TY1 transposition protein 103; CTD-in	99.22
4fu3_A	135	Regulation of nuclear PRE-mRNA domain-containing 1	98.66
4flb_A	132	Regulation of nuclear PRE-mRNA domain-containing;	98.62
2km4_A	142	Regulator of TY1 transposition protein 103; CTD-in	96.9
1vdy_A	140	Hypothetical protein (RAFL09-17-B18); structural g	90.16
1x5b_A	163	Signal transducing adaptor molecule 2; VHS domain,	86.02
1mhq_A	148	ADP-ribosylation factor binding protein GGA2; supe	81.51
3ldz_A	140	STAM-1, signal transducing adapter molecule 1; ubi	80.92

>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A

Probab=99.97  E-value=1.1e-31  Score=208.00  Aligned_cols=105  Identities=57%  Similarity=0.968  Sum_probs=100.9

Q ss_pred             HHHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhc-ccC
Q psy9417          56 VIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFK-YKD  134 (161)
Q Consensus        56 vIDef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~-~kd  134 (161)
                      ++++|++.|++|.+++|+|||++|++||.+|++|+++|++||+.++++|++|+|++|||+|||+||||||++++.+ ++|
T Consensus         3 ~v~~f~~~L~~L~~~k~~~S~~~I~~LT~~a~~~~~~~~~IV~~~~~~i~k~~~~~KL~~LYL~DsIvrn~~~k~~~~~~   82 (145)
T 3d9j_A            3 AVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKD   82 (145)
T ss_dssp             HHHHHHHHHHGGGGSCSSCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHCTTTC
T ss_pred             HHHHHHHHHHHHHhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceeehhhhhHHHHHHhhhhcCCccc
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999999987 578


Q ss_pred             ccHHhhHHHHHHHHhhhhcCCCcccC
Q psy9417         135 VYAPRFARNLYRTFGYVFQCPDEDRK  160 (161)
Q Consensus       135 ~Y~~rF~~nl~~tf~~~~~c~~~dk~  160 (161)
                      .|+++|+++|.++|.++|+|++++|.
T Consensus        83 ~f~~~F~~~L~~~f~~~~~~~~~~r~  108 (145)
T 3d9j_A           83 VFAPRFSNNIISTFQNLYRCPGDDKS  108 (145)
T ss_dssp             SHHHHHHHHHHHHHHHHTSSCGGGHH
T ss_pred             cHHHHHHHHHHHHHHHHHhCCHHHHH
Confidence            99999999999999999999987764

>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA polymer binding protein, RNA binding protein; 2.10A {Saccharomyces cerevisiae}

Probab=99.97  E-value=2e-31  Score=211.60  Aligned_cols=104  Identities=16%  Similarity=0.224  Sum_probs=95.0

Q ss_pred             HHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcc----
Q psy9417          57 IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKY----  132 (161)
Q Consensus        57 IDef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~----  132 (161)
                      +++|+++|++|.+++|||||++|++||++|++|+++|++||+.||+||++|||+||||+|||||||+||++++++.    
T Consensus         3 v~ef~~~L~sL~~lkp~iS~skI~~LT~~A~~nv~~~~~iv~~l~~~ikk~p~~hKL~~LYVvDSIvR~~~~~~~k~g~~   82 (157)
T 3clj_A            3 FQNFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYIIDSIGRAYLDETRSNSNS   82 (157)
T ss_dssp             HHHHHHHHHGGGGCSSSCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHTCCC-
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhCCCcceeeeeeehHHHHHHHHHHHHhcCCc
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999999853    


Q ss_pred             ----cCccH---HhhHHHHHHHHhhhhc-CCCcccC
Q psy9417         133 ----KDVYA---PRFARNLYRTFGYVFQ-CPDEDRK  160 (161)
Q Consensus       133 ----kd~Y~---~rF~~nl~~tf~~~~~-c~~~dk~  160 (161)
                          ++.|+   .||+.++..+|.++++ ||+++|.
T Consensus        83 ~~a~~gt~a~~v~~~~e~i~~l~~~~~~~~~~~~k~  118 (157)
T 3clj_A           83 SSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKE  118 (157)
T ss_dssp             ---STTSHHHHHHHHHHHHHHHHHHHHHHSCHHHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence                25685   6889999999999996 5666664

>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm repeats, transcription; 2.10A {Saccharomyces cerevisiae} SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X

Probab=99.93  E-value=2e-26  Score=178.68  Aligned_cols=97  Identities=26%  Similarity=0.400  Sum_probs=88.4

Q ss_pred             hHHHHHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcc
Q psy9417          53 GLYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKY  132 (161)
Q Consensus        53 ~lyvIDef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~  132 (161)
                      +--++++|...|++|.    .+||++|++||.+|++|++++++||+.|+++|++|+|+||||+|||+||||||+|++   
T Consensus         5 ~~~~~~~f~~~L~~L~----~nSk~~I~~LT~~a~~~~~~a~~Iv~~i~~~i~k~~p~~KL~~LYL~DsIvkN~g~~---   77 (144)
T 1sz9_A            5 TEVIVKDFNSILEELT----FNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNVGSP---   77 (144)
T ss_dssp             HHHHHHHHHHHHTTCS----SCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTCTT---
T ss_pred             HHHHHHHHHHHHHHhc----cccHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHhhHHHHHHHHHHHHHhccch---
Confidence            3457899999999885    489999999999999999999999999999999999999999999999999999876   


Q ss_pred             cCccHHhhHHHHHHHHhhhhcC-CCccc
Q psy9417         133 KDVYAPRFARNLYRTFGYVFQC-PDEDR  159 (161)
Q Consensus       133 kd~Y~~rF~~nl~~tf~~~~~c-~~~dk  159 (161)
                         |...|+++|.++|+++|.+ +++.|
T Consensus        78 ---y~~~F~~~l~~~f~~~~~~~d~~~r  102 (144)
T 1sz9_A           78 ---YTIYFSRNLFNLYKRTYLLVDNTTR  102 (144)
T ss_dssp             ---HHHHHHTTHHHHHHHHHHTSCHHHH
T ss_pred             ---HHHHHHHHHHHHHHHHHHhCCHHHH
Confidence               7799999999999999964 55554

>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA polymer binding protein, RNA binding protein; 2.10A {Saccharomyces cerevisiae}

Probab=99.79  E-value=1.1e-20  Score=149.87  Aligned_cols=68  Identities=22%  Similarity=0.312  Sum_probs=64.6

Q ss_pred             CcccccCCCCCchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHhhhhh
Q psy9417           1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSIN   68 (161)
Q Consensus         1 ~l~~~~~~~~~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL~sL~   68 (161)
                      +|++|.+++|++|+.||..||+.|++++++|+||||.||+||++|.|++|||||||||+..+.+.+-.
T Consensus         9 ~L~sL~~lkp~iS~skI~~LT~~A~~nv~~~~~iv~~l~~~ikk~p~~hKL~~LYVvDSIvR~~~~~~   76 (157)
T 3clj_A            9 TLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYIIDSIGRAYLDET   76 (157)
T ss_dssp             HHHGGGGCSSSCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhCCCcceeeeeeehHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999999999999999999986544

>4fu3_A Regulation of nuclear PRE-mRNA domain-containing 1B; structural genomics consortium, SGC, domain swapping, transc; HET: MSE; 1.90A {Homo sapiens} PDB: 4fld_A*

Probab=99.70  E-value=2e-17  Score=123.97  Aligned_cols=94  Identities=16%  Similarity=0.224  Sum_probs=83.9

Q ss_pred             HhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccH
Q psy9417          58 GEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYA  137 (161)
Q Consensus        58 Def~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~  137 (161)
                      |.|.+.|++|.     .|+..|++++..|++|.++++.||+++++++++++|++||+.|||+|+|++|++.+   .+.|+
T Consensus         7 ~~l~~~L~~L~-----~s~~sI~~~s~w~l~~~~~a~~iv~~i~~~l~~~~~~~KL~~LYLindIl~ns~~~---~~~y~   78 (135)
T 4fu3_A            7 SALEKKLSELS-----NSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRK---GPEFT   78 (135)
T ss_dssp             HHHHHHHHHCC-----SSTTHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCTTTHHHHHHHHHHHHHHHTTT---CSHHH
T ss_pred             HHHHHHHHHcc-----ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHhc---CHHHH
Confidence            67888888885     58899999999999999999999999999999999999999999999999999754   36799


Q ss_pred             HhhHHHHHHHHhhhhc-CCCccc
Q psy9417         138 PRFARNLYRTFGYVFQ-CPDEDR  159 (161)
Q Consensus       138 ~rF~~nl~~tf~~~~~-c~~~dk  159 (161)
                      ..|++.|..+|.+++. ++++.|
T Consensus        79 ~~f~~~l~~~~~~~~~~~~~~~k  101 (135)
T 4fu3_A           79 REFESVLVDAFSHVAREADEGCK  101 (135)
T ss_dssp             HHHHTTHHHHHHHHHHHHHTTSS
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHH
Confidence            9999999999999984 555444

>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural genomics consortium, SGC, protein binding; 1.80A {Homo sapiens}

Probab=99.69  E-value=2.6e-17  Score=123.43  Aligned_cols=93  Identities=13%  Similarity=0.194  Sum_probs=81.6

Q ss_pred             HhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccH
Q psy9417          58 GEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYA  137 (161)
Q Consensus        58 Def~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~  137 (161)
                      ++|.+.|++|.     .|+..|++++..|++|.++++.||+++++++++++|++||+.|||+|+|++|++.+++  +.|.
T Consensus         8 ~~l~~~L~~L~-----~s~~sI~~~s~w~l~h~~~a~~Iv~~i~~~l~~~~~~~KL~~LYL~ndIl~ns~~~~~--~~f~   80 (132)
T 4flb_A            8 SSLDRKFQSVT-----NTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNA--IIFR   80 (132)
T ss_dssp             HHHHHHHHHCC-----SSHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTTTTC--THHH
T ss_pred             HHHHHHHHHCc-----ccHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHhcccCh--HHHH
Confidence            56777777774     6999999999999999999999999999999999999999999999999999988754  6788


Q ss_pred             HhhHHHHHHHHhhhhcCCCccc
Q psy9417         138 PRFARNLYRTFGYVFQCPDEDR  159 (161)
Q Consensus       138 ~rF~~nl~~tf~~~~~c~~~dk  159 (161)
                      +.|.+.|..+|.++  |+++.|
T Consensus        81 ~~f~~~l~~~~~~~--~~~~~~  100 (132)
T 4flb_A           81 ESFADVLPEAAALV--KDPSVS  100 (132)
T ss_dssp             HHHHTTHHHHHHTT--CSTTTH
T ss_pred             HHHHHHHHHHHHHh--CCHHHH
Confidence            88999998888876  455544

>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A

Probab=99.67  E-value=1.4e-16  Score=123.08  Aligned_cols=104  Identities=45%  Similarity=0.611  Sum_probs=84.1

Q ss_pred             cccccCCCCCchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHhhhhh-------------
Q psy9417           2 LLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSIN-------------   68 (161)
Q Consensus         2 l~~~~~~~~~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL~sL~-------------   68 (161)
                      |++|.+++||+|+.+|+.+|..|+.++++++|||+.+|++|.||.|++|||+|||+|+..+...+-.             
T Consensus        11 L~~L~~~k~~~S~~~I~~LT~~a~~~~~~~~~IV~~~~~~i~k~~~~~KL~~LYL~DsIvrn~~~k~~~~~~~f~~~F~~   90 (145)
T 3d9j_A           11 LYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSN   90 (145)
T ss_dssp             HHGGGGSCSSCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHCTTTCSHHHHHHH
T ss_pred             HHHHHhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceeehhhhhHHHHHHhhhhcCCccccHHHHHHH
Confidence            7899999999999999999999999999999999999999999999999999999998776554311             


Q ss_pred             ---c------CCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHh
Q psy9417          69 ---S------TKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIW  105 (161)
Q Consensus        69 ---~------~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~  105 (161)
                         .      ..++-.|.+|..|..++.++-=+-..+++.|+..+.
T Consensus        91 ~L~~~f~~~~~~~~~~r~kl~rLl~iW~~r~vF~~~~l~~l~~~l~  136 (145)
T 3d9j_A           91 NIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAA  136 (145)
T ss_dssp             HHHHHHHHHTSSCGGGHHHHHHHHHHHHHTTSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhc
Confidence               0      234566777777777777666565666666666654

>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm repeats, transcription; 2.10A {Saccharomyces cerevisiae} SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X

Probab=99.37  E-value=5.9e-13  Score=102.92  Aligned_cols=99  Identities=22%  Similarity=0.309  Sum_probs=81.0

Q ss_pred             CchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHh----------------hhhhcCCCCC
Q psy9417          11 PISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQEL----------------LSINSTKPPI   74 (161)
Q Consensus        11 ~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL----------------~sL~~~k~~i   74 (161)
                      +.||..|+++|..|+.++++++|||+.+|++|.+|.|++|+|+|||+|++++-.                .+.....+..
T Consensus        21 ~nSk~~I~~LT~~a~~~~~~a~~Iv~~i~~~i~k~~p~~KL~~LYL~DsIvkN~g~~y~~~F~~~l~~~f~~~~~~~d~~  100 (144)
T 1sz9_A           21 FNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNT  100 (144)
T ss_dssp             SCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTCTTHHHHHHTTHHHHHHHHHHTSCHH
T ss_pred             cccHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHhhHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhCCHH
Confidence            479999999999999999999999999999999999999999999999976632                1222223456


Q ss_pred             cHHHHHHHHHHHHHh-----hHHHHHHHHHHHHHHhhcCC
Q psy9417          75 SKAKITGIVKLALKA-----THYYKYVVQSVEKFIWKCKS  109 (161)
Q Consensus        75 SrskI~~LT~lA~en-----ik~~k~IV~~Ie~~I~k~~p  109 (161)
                      .|.+|..|..++.++     -=+-+.+++.|+.++.+.++
T Consensus       101 ~r~k~~rL~~~W~~~~~~~~~vF~~~~l~~i~~~l~~a~~  140 (144)
T 1sz9_A          101 TRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLIKASA  140 (144)
T ss_dssp             HHHHHHHHHHHHTSGGGCSSCSSCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhCcccCCCCCCCHHHHHHHHHHHHhhhh
Confidence            788888888888877     55667777888888877665

>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain, RNA polymerase II binding protein, phosphoprotein; NMR {Saccharomyces cerevisiae} PDB: 2l0i_A*

Probab=99.22  E-value=9.7e-12  Score=95.23  Aligned_cols=95  Identities=19%  Similarity=0.285  Sum_probs=84.1

Q ss_pred             HhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhc--CCCCcchhHHHHHHHHHHHhhhhcccCc
Q psy9417          58 GEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKC--KSQYKLPGLYVIDAIIHQARLQFKYKDV  135 (161)
Q Consensus        58 Def~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~--~p~~KL~~LYVIDSIvRn~~~~~~~kd~  135 (161)
                      |.|.+.|++|.     .|+..|++++.-++.|.++++.||+++.+++.+.  +|++||+.||+++.|+.|+..+.+  +.
T Consensus         6 ~~l~~kL~~L~-----~sq~sIq~~s~W~l~h~~~a~~iv~~~~~~l~~~~~~~~kKL~~lYL~NDVlqnsk~k~~--~~   78 (142)
T 2km4_A            6 EQFTTKLNTLE-----DSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYLMNHVVQQAKGQKI--IQ   78 (142)
T ss_dssp             HHHHHHHHTCC-----SCHHHHHHHHHHHHTCGGGHHHHHHHHHHHHTSSSSCHHHHHHHHHHHHHHHHHHGGGTC--CH
T ss_pred             HHHHHHHHhcc-----ccHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcCCCccceehhhhhHHHHHHHHhhcCc--hH
Confidence            66777888875     4899999999999999999999999999999997  889999999999999999986543  67


Q ss_pred             cHHhhHHHHHHHHhhhhc-CCCccc
Q psy9417         136 YAPRFARNLYRTFGYVFQ-CPDEDR  159 (161)
Q Consensus       136 Y~~rF~~nl~~tf~~~~~-c~~~dk  159 (161)
                      |...|++.|.+.|.+++. ++++.+
T Consensus        79 f~~~F~~~L~~~~~~~~~~~~~~~~  103 (142)
T 2km4_A           79 FQDSFGKVAAEVLGRINQEFPRDLK  103 (142)
T ss_dssp             HHHHHHHTHHHHHHHHHHHSCHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHH
Confidence            999999999999999996 555544

>4fu3_A Regulation of nuclear PRE-mRNA domain-containing 1B; structural genomics consortium, SGC, domain swapping, transc; HET: MSE; 1.90A {Homo sapiens} PDB: 4fld_A*

Probab=98.66  E-value=3.3e-08  Score=73.60  Aligned_cols=53  Identities=19%  Similarity=0.147  Sum_probs=49.4

Q ss_pred             CchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHH
Q psy9417          11 PISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQE   63 (161)
Q Consensus        11 ~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~e   63 (161)
                      +-|+..|+..|.-++.+.+++++||+.+++.+.+|.|+.|++.||++|++...
T Consensus        17 ~~s~~sI~~~s~w~l~~~~~a~~iv~~i~~~l~~~~~~~KL~~LYLindIl~n   69 (135)
T 4fu3_A           17 SNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQN   69 (135)
T ss_dssp             CSSTTHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCTTTHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHH
Confidence            34788999999999999999999999999999999999999999999998653

>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural genomics consortium, SGC, protein binding; 1.80A {Homo sapiens}

Probab=98.62  E-value=8.8e-08  Score=71.34  Aligned_cols=53  Identities=13%  Similarity=0.176  Sum_probs=49.7

Q ss_pred             CchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHH
Q psy9417          11 PISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQE   63 (161)
Q Consensus        11 ~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~e   63 (161)
                      +-|+..|+.+|.-+|.+.+++++||+.+++.|.+|.|+.|++.||++|++...
T Consensus        18 ~~s~~sI~~~s~w~l~h~~~a~~Iv~~i~~~l~~~~~~~KL~~LYL~ndIl~n   70 (132)
T 4flb_A           18 TNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQN   70 (132)
T ss_dssp             CSSHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCChhhHHHHHHHHHHHHHH
Confidence            45899999999999999999999999999999999999999999999997653

>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain, RNA polymerase II binding protein, phosphoprotein; NMR {Saccharomyces cerevisiae} PDB: 2l0i_A*

Probab=96.90  E-value=0.001  Score=50.46  Aligned_cols=54  Identities=20%  Similarity=0.227  Sum_probs=48.7

Q ss_pred             CchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhc--cCCCCCchHHHHHhhHHHh
Q psy9417          11 PISKAKITGIVKLALKATHYYKYVVQSVEKFIWKC--KSQYKLPGLYVIGEWNQEL   64 (161)
Q Consensus        11 ~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~--~~~~~~~~lyvIDef~~eL   64 (161)
                      +-|+.-|+..+.-.|.+.++++.+|+..++.+.+.  .|+.|++.||++++...-.
T Consensus        16 ~~sq~sIq~~s~W~l~h~~~a~~iv~~~~~~l~~~~~~~~kKL~~lYL~NDVlqns   71 (142)
T 2km4_A           16 EDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYLMNHVVQQA   71 (142)
T ss_dssp             CSCHHHHHHHHHHHHTCGGGHHHHHHHHHHHHTSSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcCCCccceehhhhhHHHHHHHH
Confidence            34888899999999999999999999999999997  7899999999999977644

>1vdy_A Hypothetical protein (RAFL09-17-B18); structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Arabidopsis thaliana} PDB: 2dcp_A

Probab=90.16  E-value=0.59  Score=35.88  Aligned_cols=73  Identities=12%  Similarity=0.006  Sum_probs=58.7

Q ss_pred             HHHhhHHHh--hhhhcCCC-CCcHHHHHHHHHHHHHh-hHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhh
Q psy9417          56 VIGEWNQEL--LSINSTKP-PISKAKITGIVKLALKA-THYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARL  128 (161)
Q Consensus        56 vIDef~~eL--~sL~~~k~-~iSrskI~~LT~lA~en-ik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~  128 (161)
                      .|++|....  ..=+...+ |-++..+.+|+.+...+ .+.+..|+..|.+.+.+..|.+|+-+|=+||-+|++...
T Consensus         6 ~~~~~~~~~~V~~ATs~d~~~~pgylm~EIA~~T~~s~~~~~~eim~~L~kRL~~k~~~vk~KaL~lL~yL~~~Gs~   82 (140)
T 1vdy_A            6 SGESYWRSRMIDAVTSDEDKVAPVYKLEEICDLLRSSHVSIVKEFSEFILKRLDNKSPIVKQKALRLIKYAVGKSGS   82 (140)
T ss_dssp             SCTHHHHHHHHHHTTCSCSSCCCHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHTSSSHHHHHHHHHHHHHHTTTSCH
T ss_pred             HHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcchhHHHHHHHHHHHHhcCCCcceeehHHHHHHHHHHhCCH
Confidence            355666544  33333444 89999999999999886 466799999999999999999999999999999987753

>1x5b_A Signal transducing adaptor molecule 2; VHS domain, ubiquitin binding, STAM2, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2l0t_B

Probab=86.02  E-value=1.4  Score=34.00  Aligned_cols=72  Identities=14%  Similarity=0.070  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccH-HhhHHHHHHHHh
Q psy9417          76 KAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYA-PRFARNLYRTFG  149 (161)
Q Consensus        76 rskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~-~rF~~nl~~tf~  149 (161)
                      =+.|-.|.++.-..-...+..+..|.++|+...|.--+-+|-++|+.++|.|.++.  ...+ .+|...|..++.
T Consensus        33 w~~~leicD~I~~~~~~~keA~ral~krl~~~n~~vql~AL~LLd~~vkNcG~~Fh--~evas~~Fl~el~~l~~  105 (163)
T 1x5b_A           33 WSLIMDICDKVGSTPNGAKDCLKAIMKRVNHKVPHVALQALTLLGACVANCGKIFH--LEVCSRDFATEVRAVIK  105 (163)
T ss_dssp             HHHHHHHHHHHHHSSSHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHTCHHHH--HHHTSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhHHHH--HHHhhHHHHHHHHHHHc
Confidence            34455566555555567888899999999988888889999999999999987744  1111 456666655553

>1mhq_A ADP-ribosylation factor binding protein GGA2; super helix, protein transport; 2.20A {Homo sapiens} SCOP: a.118.9.2

Probab=81.51  E-value=2.4  Score=32.11  Aligned_cols=72  Identities=14%  Similarity=0.127  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHHHh
Q psy9417          77 AKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFG  149 (161)
Q Consensus        77 skI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~tf~  149 (161)
                      +.|-.|..+--......+..+..|-+.|+...|.-=+-+|-++|+.++|.|.+|. .-+=..+|...|..++.
T Consensus        20 ~~~leicD~I~~~~~~~k~a~rai~krl~~~n~~vql~AL~LLe~~vkNCG~~fh-~evas~~Fl~eL~kl~~   91 (148)
T 1mhq_A           20 SAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCMNHCGEKFH-SEVAKFRFLNELIKVLS   91 (148)
T ss_dssp             HHHHHHHHHHHHSSHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHH-HHHTSHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHcCCccHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHcCHHHH-HHHhhHHHHHHHHHHHc
Confidence            3455555555555566888899999999988899999999999999999998753 00111455555555443

>3ldz_A STAM-1, signal transducing adapter molecule 1; ubiquitin-binding, cytoplasm, UBL conjugation, endosome, membrane, protein transport, SH3 domain; 2.60A {Homo sapiens} SCOP: a.118.9.0

Probab=80.92  E-value=2.1  Score=31.98  Aligned_cols=73  Identities=14%  Similarity=0.136  Sum_probs=52.0

Q ss_pred             cHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHHH
Q psy9417          75 SKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTF  148 (161)
Q Consensus        75 SrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~tf  148 (161)
                      .=+.|-.+.++.-......+..+.+|.+++....|.--+-+|-++|+.++|.|.++. .-+=..+|...|..++
T Consensus        22 dw~~ileicD~I~~~~~~~k~a~rai~Krl~~~n~~~ql~AL~LLe~~vkNcG~~f~-~evas~~Fl~el~~l~   94 (140)
T 3ldz_A           22 DWGLILDICDKVGQSRTGPKDCLRSIMRRVNHKDPHVAMQALTLLGACVSNCGKIFH-LEVCSRDFASEVSNVL   94 (140)
T ss_dssp             CHHHHHHHHHHHTTSTTHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHH-HHHSSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCcCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhcCHHHH-HHHhhHHHHHHHHHHh
Confidence            334566666665555566888899999999888888889999999999999998754 0011145666555554

---

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	161
d1szaa_	144	a.118.9.4 (A:) PCF11 protein {Baker's yeast (Sacch	6e-12
d1szaa_	144	a.118.9.4 (A:) PCF11 protein {Baker's yeast (Sacch	8e-04

>d1szaa_ a.118.9.4 (A:) PCF11 protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 144

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: RPR domain (SMART 00582 )
domain: PCF11 protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 57.8 bits (139), Expect = 6e-12
 Identities = 26/106 (24%), Positives = 44/106 (41%), Gaps = 10/106 (9%)

Query: 56  VIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPG 115
           ++ ++N  L  +     PI    IT + KLA +     +Y V ++E  I KC  + KL  
Sbjct: 8   IVKDFNSILEELTFNSRPI----ITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYA 63

Query: 116 LYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
            Y +D+I             Y   F+RNL+  +   +   D   + 
Sbjct: 64  FYALDSICKNVG------SPYTIYFSRNLFNLYKRTYLLVDNTTRT 103

>d1szaa_ a.118.9.4 (A:) PCF11 protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 144

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: RPR domain (SMART 00582 )
domain: PCF11 protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 35.4 bits (81), Expect = 8e-04
 Identities = 15/46 (32%), Positives = 23/46 (50%)

Query: 12 ISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 57
           S+  IT + KLA +     +Y V ++E  I KC  + KL   Y +
Sbjct: 22 NSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYAL 67

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	161
d1szaa_	144	PCF11 protein {Baker's yeast (Saccharomyces cerevi	99.84
d1szaa_	144	PCF11 protein {Baker's yeast (Saccharomyces cerevi	98.92
d1dvpa1	145	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	81.72

>d1szaa_ a.118.9.4 (A:) PCF11 protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: RPR domain (SMART 00582 )
domain: PCF11 protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.84  E-value=1.2e-21  Score=148.96  Aligned_cols=94  Identities=27%  Similarity=0.405  Sum_probs=86.9

Q ss_pred             hHHHHHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcc
Q psy9417          53 GLYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKY  132 (161)
Q Consensus        53 ~lyvIDef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~  132 (161)
                      +-.++++|+..|++|++    +||++|++||.+|++|.+++++||++|++++++|+|++||+.||++|||++|++++   
T Consensus         5 ~~~~~~~f~~~L~~L~~----ns~~~I~~Lt~~a~~~~~~a~~Iv~~i~~~i~~~~~~~KL~~LYLiddI~~n~~~~---   77 (144)
T d1szaa_           5 TEVIVKDFNSILEELTF----NSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNVGSP---   77 (144)
T ss_dssp             HHHHHHHHHHHHTTCSS----CCHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTCTT---
T ss_pred             HHHHHHHHHHHHHHHhh----ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcccchhhhhhHHHHHHHhHHH---
Confidence            34688999999999964    79999999999999999999999999999999999999999999999999999876   


Q ss_pred             cCccHHhhHHHHHHHHhhhhcCCC
Q psy9417         133 KDVYAPRFARNLYRTFGYVFQCPD  156 (161)
Q Consensus       133 kd~Y~~rF~~nl~~tf~~~~~c~~  156 (161)
                         |.+.|++.|.++|.++|.+.+
T Consensus        78 ---y~~~f~~~l~~~f~~~y~~~~   98 (144)
T d1szaa_          78 ---YTIYFSRNLFNLYKRTYLLVD   98 (144)
T ss_dssp             ---HHHHHHTTHHHHHHHHHTTSC
T ss_pred             ---HHHHHHHHHHHHHHHHHHcCC
Confidence               779999999999999996544

>d1szaa_ a.118.9.4 (A:) PCF11 protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: RPR domain (SMART 00582 )
domain: PCF11 protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.92  E-value=3.6e-10  Score=84.83  Aligned_cols=99  Identities=23%  Similarity=0.344  Sum_probs=80.2

Q ss_pred             chHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHH------------hh----hhhcCCCCCc
Q psy9417          12 ISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQE------------LL----SINSTKPPIS   75 (161)
Q Consensus        12 ~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~e------------L~----sL~~~k~~iS   75 (161)
                      .||.+|+.+|.-|+.+.+++++||+.+++.|.+|.|+.|++.||++|+....            |.    +.....+.--
T Consensus        22 ns~~~I~~Lt~~a~~~~~~a~~Iv~~i~~~i~~~~~~~KL~~LYLiddI~~n~~~~y~~~f~~~l~~~f~~~y~~~~~~~  101 (144)
T d1szaa_          22 NSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNTT  101 (144)
T ss_dssp             CCHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTCTTHHHHHHTTHHHHHHHHHTTSCHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcccchhhhhhHHHHHHHhHHHHHHHHHHHHHHHHHHHHHcCCHHH
Confidence            4899999999999999999999999999999999999999999999996542            22    2222233456


Q ss_pred             HHHHHHHHHHHHHhh-----HHHHHHHHHHHHHHhhcCCC
Q psy9417          76 KAKITGIVKLALKAT-----HYYKYVVQSVEKFIWKCKSQ  110 (161)
Q Consensus        76 rskI~~LT~lA~eni-----k~~k~IV~~Ie~~I~k~~p~  110 (161)
                      |.+|..|.+++.+.-     =+-+.+++.|++++.++.+.
T Consensus       102 r~kl~rll~iW~~r~~~~~~vFp~~~l~~ie~~L~~a~~~  141 (144)
T d1szaa_         102 RTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLIKASAA  141 (144)
T ss_dssp             HHHHHHHHHHHSSGGGCSSCSSCHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHHHhccCCCCcCCCCHHHHHHHHHHHHHhHhh
Confidence            888888888888754     26678888888888887654

>d1dvpa1 a.118.9.2 (A:1-145) Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: VHS domain
domain: Hrs
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=81.72  E-value=0.65  Score=33.09  Aligned_cols=55  Identities=13%  Similarity=0.071  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhc
Q psy9417          77 AKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFK  131 (161)
Q Consensus        77 skI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~  131 (161)
                      +-|-.+.++.-.+-...+..++.|-+.++.-.|.--+-+|-++|+.++|.|.++.
T Consensus        24 ~~il~icD~I~~~~~~~k~a~ral~krl~~~n~~v~l~aL~LLd~~vkNcG~~f~   78 (145)
T d1dvpa1          24 PSILLICDEINQKDVTPKNAFAAIKKKMNSPNPHSSCYSLLVLESIVKNCGAPVH   78 (145)
T ss_dssp             HHHHHHHHHHHTTSSCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSHHHHH
T ss_pred             HHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHccchHHH
Confidence            3455555555545455888899999999988899999999999999999998765