Citrus Sinensis ID: 030129

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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-------170-------180--
Protein Sequence
MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIGQMRYIRRWKIKSLVEAEIKTHYWLLACTLLVDKKTSHALLRKSALSPMELQRRKLAEQKNTL
Secondary Structure (PSIPRED)
ccccccccccccccEEEEcccccEEcccccEEEEcccccccccccccccccccccccccccccccccccccccEEEEccccccccccccHHHHHcccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHcccccccHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEccccccEEcccccEEEcccEEcccccEEEccccccccccccccccccccccccccEEEEccccccccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHccHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mtdafcsdckkhtevvfdhsagdtvcsecglvleshsidetsewrtfanesgdndpvrvggptnplladgglstviakpngasgeflSSSLGrwqnrgsnpdrGLILAFKTIATMSDRIGQMRYIRRWKIKSLVEAEIKTHYWLLACTLLVDKKTSHALLRKSALSPMELQRRKLAEQKNTL
Flexible Loop (DISEMBL)
mtdafcsdcKKHTevvfdhsagdtVCSECGLVLESHSIDETSEWRTFanesgdndpvrVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIatmsdrigqmRYIRRWKIKSLVEAEIKTHYWLLACTLLVDKKTSHALlrksalspmelqrrklaeqkntl
Low Complexity Region (SEG)
MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIGQMRYIRRWKIKSLVEAEIKTHYWLLACTLLVDKKTSHALLRKSALSPMELQRRKLAEQKNTL
Disordered region (IsUnstruct)
****FCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDE***W**********************************************************RGLILAFKTIATMSDRIGQMRYIRRWKIKSLVEAEIKTHYWLLACTLLVDKKTSHAL***********************
Disordered Region (DISOPRED)
**DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDET************************LLADGGLSTVIAKP****************************AFKTIATMSDRIGQMRYIRRWKIKSLVEAEIKTHYWLLACTLLVDKKTSHALLRKSALSPMELQRRKLAEQ*N**
Disordered Region (DISEMBL)
********CKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIGQMRYIRRWKIKSLVEAEIKTHYWLLACTLLVDKKTSHALLRKSALSPMELQRR*********
Disordered Region (DISPRO)
****FCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANE******VRVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIGQMRYIRRWKIKSLVEAEIKTHYWLLACTLLVDKKTSHALLRKSALSPMELQRRKLAE*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIGQMRYIRRWKIKSLVEAEIKTHYWLLACTLLVDKKTSHALLRKSALSPMELQRRKLAEQKNTL
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	182	2.2.26 [Sep-21-2011]
Q9SS44	312	Transcription initiation	yes	no	0.692	0.403	0.888	2e-65
Q8W0W3	312	Transcription initiation	yes	no	0.692	0.403	0.841	3e-62
P48513	313	Transcription initiation	yes	no	0.692	0.402	0.866	5e-61
P48512	312	Transcription initiation	no	no	0.692	0.403	0.793	2e-56
P29052	315	Transcription initiation	yes	no	0.637	0.368	0.495	3e-24
Q5R886	316	Transcription initiation	yes	no	0.626	0.360	0.479	5e-23
Q4R3J5	316	Transcription initiation	N/A	no	0.626	0.360	0.479	5e-23
Q00403	316	Transcription initiation	yes	no	0.626	0.360	0.479	5e-23
Q2KIN8	316	Transcription initiation	yes	no	0.626	0.360	0.479	5e-23
P62916	316	Transcription initiation	yes	no	0.626	0.360	0.479	5e-23

>sp|Q9SS44|TF2B2_ARATH Transcription initiation factor IIB-2 OS=Arabidopsis thaliana GN=TFIIB2 PE=2 SV=1

 Score =  248 bits (632), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 112/126 (88%), Positives = 123/126 (97%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M+DAFCSDCK+HTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct: 1   MSDAFCSDCKRHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GPTNPLLADGGL+TVI+KPNG+SG+FLSSSLGRWQNRGSNPDRGLI+AFKTIATM+DR+G
Sbjct: 61  GPTNPLLADGGLTTVISKPNGSSGDFLSSSLGRWQNRGSNPDRGLIVAFKTIATMADRLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVATIK 126

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.
Arabidopsis thaliana (taxid: 3702)

>sp|Q8W0W3|TF2B_ORYSJ Transcription initiation factor IIB OS=Oryza sativa subsp. japonica GN=TFIIB PE=1 SV=1

 Score =  237 bits (605), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 106/126 (84%), Positives = 116/126 (92%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M+D+FC DCKKHTEV FDHSAGDTVC+ECGLVLE+HS+DETSEWRTFANES DNDPVRVG
Sbjct: 1   MSDSFCPDCKKHTEVAFDHSAGDTVCTECGLVLEAHSVDETSEWRTFANESSDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GPTNPLL DGGLSTVIAKPNGA GEFLSSSLGRWQNRGSNPDR LILAF+TIA M+DR+G
Sbjct: 61  GPTNPLLTDGGLSTVIAKPNGAQGEFLSSSLGRWQNRGSNPDRSLILAFRTIANMADRLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVATIK 126

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|P48513|TF2B_SOYBN Transcription initiation factor IIB OS=Glycine max GN=TFIIB1 PE=2 SV=1

 Score =  233 bits (594), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 110/127 (86%), Positives = 116/127 (91%), Gaps = 1/127 (0%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M+DAFCSDCK+ TEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDP RVG
Sbjct: 1   MSDAFCSDCKRQTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPNRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPN-GASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRI 119
           GP+NPLL DGGLSTVIAKPN G  GEFLSSSLGRWQNRGSNPDR LI AFKTIATMSDR+
Sbjct: 61  GPSNPLLTDGGLSTVIAKPNGGGGGEFLSSSLGRWQNRGSNPDRALIQAFKTIATMSDRL 120

Query: 120 GQMRYIR 126
           G +  I+
Sbjct: 121 GLVATIK 127

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Glycine max (taxid: 3847)

>sp|P48512|TF2B1_ARATH Transcription initiation factor IIB-1 OS=Arabidopsis thaliana GN=TFIIB1 PE=1 SV=1

 Score =  218 bits (555), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 100/126 (79%), Positives = 114/126 (90%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M+DA+C+DCKK TE+V DHSAGDT+CSECGLVLESHSIDETSEWRTFANES ++DP RVG
Sbjct: 1   MSDAYCTDCKKETELVVDHSAGDTLCSECGLVLESHSIDETSEWRTFANESSNSDPNRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GPTNPLLAD  L+TVIAKPNG+SG+FLSSSLGRWQNR SN DRGLI AFKTIATMS+R+G
Sbjct: 61  GPTNPLLADSALTTVIAKPNGSSGDFLSSSLGRWQNRNSNSDRGLIQAFKTIATMSERLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVATIK 126

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Arabidopsis thaliana (taxid: 3702)

>sp|P29052|TF2B_DROME Transcription initiation factor IIB OS=Drosophila melanogaster GN=TfIIB PE=2 SV=1

 Score =  111 bits (277), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 60/121 (49%), Positives = 76/121 (62%), Gaps = 5/121 (4%)

Query: 9   CKKHTE--VVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
           C  H E  ++ D+ AGD +CSECGLV+    ID  SEWRTF+NE    DP RVGGP NPL
Sbjct: 14  CYAHPESPLIEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPL 73

Query: 67  LADGGLSTVIAKPNGASGEFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQMRY 124
           L+ G LST+I  P   S  F +    ++QNR   S+ DR LI AFK I++M+DRI   + 
Sbjct: 74  LSGGDLSTIIG-PGTGSASFDAFGAPKYQNRRTMSSSDRSLISAFKEISSMADRINLPKT 132

Query: 125 I 125
           I
Sbjct: 133 I 133

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Drosophila melanogaster (taxid: 7227)

>sp|Q5R886|TF2B_PONAB Transcription initiation factor IIB OS=Pongo abelii GN=GTF2B PE=2 SV=1

 Score =  107 bits (267), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 59/123 (47%), Positives = 76/123 (61%), Gaps = 9/123 (7%)

Query: 9   CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
           C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+    DP RVG   NPL
Sbjct: 15  CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPL 74

Query: 67  LADGGLSTVIAKPNGASG--EFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQM 122
           L+DG LST+I K  GA+   EF +S   ++QNR   S+ DR ++ AFK I TM+DRI   
Sbjct: 75  LSDGDLSTMIGKGTGAASFDEFGNS---KYQNRRTMSSSDRAMMNAFKEITTMADRINLP 131

Query: 123 RYI 125
           R I
Sbjct: 132 RNI 134

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Pongo abelii (taxid: 9601)

>sp|Q4R3J5|TF2B_MACFA Transcription initiation factor IIB OS=Macaca fascicularis GN=GTF2B PE=2 SV=1

 Score =  107 bits (267), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 59/123 (47%), Positives = 76/123 (61%), Gaps = 9/123 (7%)

Query: 9   CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
           C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+    DP RVG   NPL
Sbjct: 15  CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPL 74

Query: 67  LADGGLSTVIAKPNGASG--EFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQM 122
           L+DG LST+I K  GA+   EF +S   ++QNR   S+ DR ++ AFK I TM+DRI   
Sbjct: 75  LSDGDLSTMIGKGTGAASFDEFGNS---KYQNRRTMSSSDRAMMNAFKEITTMADRINLP 131

Query: 123 RYI 125
           R I
Sbjct: 132 RNI 134

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Macaca fascicularis (taxid: 9541)

>sp|Q00403|TF2B_HUMAN Transcription initiation factor IIB OS=Homo sapiens GN=GTF2B PE=1 SV=1

 Score =  107 bits (267), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 59/123 (47%), Positives = 76/123 (61%), Gaps = 9/123 (7%)

Query: 9   CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
           C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+    DP RVG   NPL
Sbjct: 15  CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPL 74

Query: 67  LADGGLSTVIAKPNGASG--EFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQM 122
           L+DG LST+I K  GA+   EF +S   ++QNR   S+ DR ++ AFK I TM+DRI   
Sbjct: 75  LSDGDLSTMIGKGTGAASFDEFGNS---KYQNRRTMSSSDRAMMNAFKEITTMADRINLP 131

Query: 123 RYI 125
           R I
Sbjct: 132 RNI 134

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Homo sapiens (taxid: 9606)

>sp|Q2KIN8|TF2B_BOVIN Transcription initiation factor IIB OS=Bos taurus GN=GTF2B PE=2 SV=1

 Score =  107 bits (267), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 59/123 (47%), Positives = 76/123 (61%), Gaps = 9/123 (7%)

Query: 9   CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
           C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+    DP RVG   NPL
Sbjct: 15  CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPL 74

Query: 67  LADGGLSTVIAKPNGASG--EFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQM 122
           L+DG LST+I K  GA+   EF +S   ++QNR   S+ DR ++ AFK I TM+DRI   
Sbjct: 75  LSDGDLSTMIGKGTGAASFDEFGNS---KYQNRRTMSSSDRAMMNAFKEITTMADRINLP 131

Query: 123 RYI 125
           R I
Sbjct: 132 RNI 134

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Bos taurus (taxid: 9913)

>sp|P62916|TF2B_RAT Transcription initiation factor IIB OS=Rattus norvegicus GN=Gtf2b PE=2 SV=1

 Score =  107 bits (267), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 59/123 (47%), Positives = 76/123 (61%), Gaps = 9/123 (7%)

Query: 9   CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
           C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+    DP RVG   NPL
Sbjct: 15  CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPL 74

Query: 67  LADGGLSTVIAKPNGASG--EFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQM 122
           L+DG LST+I K  GA+   EF +S   ++QNR   S+ DR ++ AFK I TM+DRI   
Sbjct: 75  LSDGDLSTMIGKGTGAASFDEFGNS---KYQNRRTMSSSDRAMMNAFKEITTMADRINLP 131

Query: 123 RYI 125
           R I
Sbjct: 132 RNI 134

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Rattus norvegicus (taxid: 10116)

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	182
317106705	312	JHL06B08.6 [Jatropha curcas]	0.692	0.403	0.928	1e-64
255588003	312	transcription initiation factor iib, put	0.692	0.403	0.920	2e-64
224138070	312	predicted protein [Populus trichocarpa]	0.692	0.403	0.920	4e-64
449465789	312	PREDICTED: transcription initiation fact	0.692	0.403	0.912	4e-64
297829558	312	transcription initiation factor IIB-2 [A	0.692	0.403	0.888	1e-63
15228267	312	transcription initiation factor IIB-2 [A	0.692	0.403	0.888	1e-63
225441886	312	PREDICTED: transcription initiation fact	0.692	0.403	0.896	3e-63
225464249	312	PREDICTED: transcription initiation fact	0.692	0.403	0.896	4e-63
224090077	312	predicted protein [Populus trichocarpa]	0.692	0.403	0.904	9e-63
357509669	313	Transcription initiation factor IIB [Med	0.692	0.402	0.873	3e-61

>gi|317106705|dbj|BAJ53205.1| JHL06B08.6 [Jatropha curcas]

 Score =  251 bits (640), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 117/126 (92%), Positives = 121/126 (96%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M DAFCSDCK+ TEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct: 1   MGDAFCSDCKRQTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDR+G
Sbjct: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVATIK 126

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255588003|ref|XP_002534470.1| transcription initiation factor iib, putative [Ricinus communis] gi|223525233|gb|EEF27913.1| transcription initiation factor iib, putative [Ricinus communis]

 Score =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 116/126 (92%), Positives = 121/126 (96%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M DA+CSDCK+ TEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct: 1   MGDAYCSDCKRQTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDR+G
Sbjct: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVATIK 126

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224138070|ref|XP_002322722.1| predicted protein [Populus trichocarpa] gi|222867352|gb|EEF04483.1| predicted protein [Populus trichocarpa]

 Score =  249 bits (636), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 116/126 (92%), Positives = 120/126 (95%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M DAFCSDCK+HTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct: 1   MGDAFCSDCKRHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GPTNPLL DGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLI AFKTIATMSDR+G
Sbjct: 61  GPTNPLLTDGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLITAFKTIATMSDRLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVATIK 126

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449465789|ref|XP_004150610.1| PREDICTED: transcription initiation factor IIB-2-like [Cucumis sativus] gi|449529834|ref|XP_004171903.1| PREDICTED: transcription initiation factor IIB-2-like [Cucumis sativus]

 Score =  249 bits (635), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 115/126 (91%), Positives = 121/126 (96%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M+DAFCSDCK+ TEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct: 1   MSDAFCSDCKRQTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GPTNPLLADGGLSTVIAKPNG +GEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDR+G
Sbjct: 61  GPTNPLLADGGLSTVIAKPNGTTGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVATIK 126

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297829558|ref|XP_002882661.1| transcription initiation factor IIB-2 [Arabidopsis lyrata subsp. lyrata] gi|297328501|gb|EFH58920.1| transcription initiation factor IIB-2 [Arabidopsis lyrata subsp. lyrata]

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 112/126 (88%), Positives = 123/126 (97%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M+DAFCSDCK+HTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct: 1   MSDAFCSDCKRHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GPTNPLLADGGL+TVI+KPNG+SG+FLSSSLGRWQNRGSNPDRGLI+AFKTIATM+DR+G
Sbjct: 61  GPTNPLLADGGLTTVISKPNGSSGDFLSSSLGRWQNRGSNPDRGLIVAFKTIATMADRLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVATIK 126

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15228267|ref|NP_187644.1| transcription initiation factor IIB-2 [Arabidopsis thaliana] gi|21363045|sp|Q9SS44.1|TF2B2_ARATH RecName: Full=Transcription initiation factor IIB-2; AltName: Full=General transcription factor TFIIB-2; Short=AtTFIIB2 gi|6056193|gb|AAF02810.1|AC009400_6 transcription initiation factor IIB (TFIIB) [Arabidopsis thaliana] gi|15215784|gb|AAK91437.1| AT3g10330/F14P13_7 [Arabidopsis thaliana] gi|16974427|gb|AAL31139.1| AT3g10330/F14P13_7 [Arabidopsis thaliana] gi|21593436|gb|AAM65403.1| transcription initiation factor IIB (TFIIB) [Arabidopsis thaliana] gi|39545880|gb|AAR28003.1| TFIIB2 [Arabidopsis thaliana] gi|332641371|gb|AEE74892.1| transcription initiation factor IIB-2 [Arabidopsis thaliana]

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 112/126 (88%), Positives = 123/126 (97%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M+DAFCSDCK+HTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct: 1   MSDAFCSDCKRHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GPTNPLLADGGL+TVI+KPNG+SG+FLSSSLGRWQNRGSNPDRGLI+AFKTIATM+DR+G
Sbjct: 61  GPTNPLLADGGLTTVISKPNGSSGDFLSSSLGRWQNRGSNPDRGLIVAFKTIATMADRLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVATIK 126

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225441886|ref|XP_002284342.1| PREDICTED: transcription initiation factor IIB-2 [Vitis vinifera] gi|297739630|emb|CBI29812.3| unnamed protein product [Vitis vinifera]

 Score =  246 bits (627), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 113/126 (89%), Positives = 120/126 (95%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M DAFC+DCKK+TEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct: 1   MADAFCTDCKKNTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GP+NPLL DGGLSTVIAKPNG SG+FLSSSLGRWQNRGSNPDRGLILAFKTIATMSDR+G
Sbjct: 61  GPSNPLLTDGGLSTVIAKPNGVSGDFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVATIK 126

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225464249|ref|XP_002269045.1| PREDICTED: transcription initiation factor IIB-2 [Vitis vinifera] gi|296088031|emb|CBI35314.3| unnamed protein product [Vitis vinifera]

 Score =  246 bits (627), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 113/126 (89%), Positives = 120/126 (95%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M DAFC+DCKK+TEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct: 1   MADAFCTDCKKNTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GP+NPLL DGGLSTVIAKPNG SG+FLSSSLGRWQNRGSNPDRGLILAFKTIATMSDR+G
Sbjct: 61  GPSNPLLTDGGLSTVIAKPNGVSGDFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVATIK 126

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224090077|ref|XP_002308933.1| predicted protein [Populus trichocarpa] gi|222854909|gb|EEE92456.1| predicted protein [Populus trichocarpa]

 Score =  244 bits (624), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 114/126 (90%), Positives = 119/126 (94%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M DAFCSDCKKHTEVV DHSAGDTVCSECGLVLESHSIDETSEWR FANESGDNDPVRVG
Sbjct: 1   MGDAFCSDCKKHTEVVCDHSAGDTVCSECGLVLESHSIDETSEWRIFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GPTNPLL DGGLSTVIAKPNGASG+FLS+SLGRWQNRGSNPDRGLILAFKTIATMSDR+G
Sbjct: 61  GPTNPLLTDGGLSTVIAKPNGASGDFLSTSLGRWQNRGSNPDRGLILAFKTIATMSDRLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVATIK 126

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357509669|ref|XP_003625123.1| Transcription initiation factor IIB [Medicago truncatula] gi|355500138|gb|AES81341.1| Transcription initiation factor IIB [Medicago truncatula]

 Score =  239 bits (610), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 110/126 (87%), Positives = 119/126 (94%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M+DAFCSDCK+ TEVVFDHSAGD VCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct: 1   MSDAFCSDCKRATEVVFDHSAGDAVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
           GP+NPLL DGGLSTVIAKPNGASG+FLSSSLGRWQNRGSNPDRGLILAFKTI TM++R+G
Sbjct: 61  GPSNPLLTDGGLSTVIAKPNGASGDFLSSSLGRWQNRGSNPDRGLILAFKTIGTMAERLG 120

Query: 121 QMRYIR 126
            +  I+
Sbjct: 121 LVPTIK 126

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	182
TAIR|locus:2076259	312	AT3G10330 [Arabidopsis thalian	0.692	0.403	0.888	8.1e-60
TAIR|locus:2062703	312	TFIIB "transcription factor II	0.692	0.403	0.793	5.6e-52
TAIR|locus:2093852	336	pBRP2 "plant-specific TFIIB-re	0.653	0.354	0.476	4.2e-24
FB|FBgn0004915	315	TfIIB "Transcription factor II	0.604	0.349	0.513	1.1e-23
UNIPROTKB|F2Z4J6	316	LOC786656 "Uncharacterized pro	0.637	0.367	0.471	1.3e-22
UNIPROTKB|Q2KIN8	316	GTF2B "Transcription initiatio	0.637	0.367	0.471	1.3e-22
UNIPROTKB|E2RPG1	316	GTF2B "Uncharacterized protein	0.637	0.367	0.471	1.3e-22
UNIPROTKB|B1APE1	224	GTF2B "Transcription initiatio	0.637	0.517	0.471	1.3e-22
UNIPROTKB|Q00403	316	GTF2B "Transcription initiatio	0.637	0.367	0.471	1.3e-22
UNIPROTKB|F2Z5J6	316	GTF2B "Uncharacterized protein	0.637	0.367	0.471	1.3e-22

TAIR|locus:2076259 AT3G10330 [Arabidopsis thaliana (taxid:3702)]

 Score = 613 (220.8 bits), Expect = 8.1e-60, P = 8.1e-60
 Identities = 112/126 (88%), Positives = 123/126 (97%)

Query:     1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
             M+DAFCSDCK+HTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct:     1 MSDAFCSDCKRHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query:    61 GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
             GPTNPLLADGGL+TVI+KPNG+SG+FLSSSLGRWQNRGSNPDRGLI+AFKTIATM+DR+G
Sbjct:    61 GPTNPLLADGGLTTVISKPNGSSGDFLSSSLGRWQNRGSNPDRGLIVAFKTIATMADRLG 120

Query:   121 QMRYIR 126
              +  I+
Sbjct:   121 LVATIK 126

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

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

GO:0006413 "translational initiation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

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

TAIR|locus:2062703 TFIIB "transcription factor IIB" [Arabidopsis thaliana (taxid:3702)]

 Score = 539 (194.8 bits), Expect = 5.6e-52, P = 5.6e-52
 Identities = 100/126 (79%), Positives = 114/126 (90%)

Query:     1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
             M+DA+C+DCKK TE+V DHSAGDT+CSECGLVLESHSIDETSEWRTFANES ++DP RVG
Sbjct:     1 MSDAYCTDCKKETELVVDHSAGDTLCSECGLVLESHSIDETSEWRTFANESSNSDPNRVG 60

Query:    61 GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIG 120
             GPTNPLLAD  L+TVIAKPNG+SG+FLSSSLGRWQNR SN DRGLI AFKTIATMS+R+G
Sbjct:    61 GPTNPLLADSALTTVIAKPNGSSGDFLSSSLGRWQNRNSNSDRGLIQAFKTIATMSERLG 120

Query:   121 QMRYIR 126
              +  I+
Sbjct:   121 LVATIK 126

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

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

GO:0006413 "translational initiation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

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

TAIR|locus:2093852 pBRP2 "plant-specific TFIIB-related protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 60/126 (47%), Positives = 78/126 (61%)

Query:     1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESG--DNDPVR 58
             M +  C DCK+ T +V DHS+GDT+CSECGLVLE+H I+ + EWRTFA++    D DP R
Sbjct:     1 MEEETCLDCKRPTIMVVDHSSGDTICSECGLVLEAHIIEYSQEWRTFASDDNHSDRDPNR 60

Query:    59 VGGPTNPLLADGGLSTVIAKPNGASGEFLS----SSLGRWQNRGSNPDRGLIL-AFKTIA 113
             VG  TNP L  G L T+I KP   +   LS    S+L R  N+  N +  LI  AF+ I 
Sbjct:    61 VGAATNPFLKSGDLVTIIEKPKETASSVLSKDDISTLFRAHNQVKNHEEDLIKQAFEEIQ 120

Query:   114 TMSDRI 119
              M+D +
Sbjct:   121 RMTDAL 126

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

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

GO:0006413 "translational initiation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046686 "response to cadmium ion" evidence=IEP

GO:0000769 "syncytium formation by mitosis without cytokinesis" evidence=IMP

GO:0009960 "endosperm development" evidence=IMP

GO:0010440 "stomatal lineage progression" evidence=RCA

FB|FBgn0004915 TfIIB "Transcription factor IIB" [Drosophila melanogaster (taxid:7227)]

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 59/115 (51%), Positives = 74/115 (64%)

Query:     9 CKKHTE--VVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
             C  H E  ++ D+ AGD +CSECGLV+    ID  SEWRTF+NE    DP RVGGP NPL
Sbjct:    14 CYAHPESPLIEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPL 73

Query:    67 LADGGLSTVIAKPNGASGEFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRI 119
             L+ G LST+I  P   S  F +    ++QNR   S+ DR LI AFK I++M+DRI
Sbjct:    74 LSGGDLSTIIG-PGTGSASFDAFGAPKYQNRRTMSSSDRSLISAFKEISSMADRI 127

GO:0005634 "nucleus" evidence=NAS;IDA

GO:0001174 "transcriptional start site selection at RNA polymerase II promoter" evidence=IDA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=NAS;IDA

GO:0008134 "transcription factor binding" evidence=IPI

GO:0051101 "regulation of DNA binding" evidence=IDA

GO:0005667 "transcription factor complex" evidence=ISS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

UNIPROTKB|F2Z4J6 LOC786656 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 57/121 (47%), Positives = 73/121 (60%)

Query:     9 CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
             C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+    DP RVG   NPL
Sbjct:    15 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPL 74

Query:    67 LADGGLSTVIAKPNGASGEFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQMRY 124
             L+DG LST+I K  GA+  F      ++QNR   S+ DR ++ AFK I TM+DRI   R 
Sbjct:    75 LSDGDLSTMIGKGTGAAS-FDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRN 133

Query:   125 I 125
             I
Sbjct:   134 I 134

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

UNIPROTKB|Q2KIN8 GTF2B "Transcription initiation factor IIB" [Bos taurus (taxid:9913)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 57/121 (47%), Positives = 73/121 (60%)

Query:     9 CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
             C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+    DP RVG   NPL
Sbjct:    15 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPL 74

Query:    67 LADGGLSTVIAKPNGASGEFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQMRY 124
             L+DG LST+I K  GA+  F      ++QNR   S+ DR ++ AFK I TM+DRI   R 
Sbjct:    75 LSDGDLSTMIGKGTGAAS-FDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRN 133

Query:   125 I 125
             I
Sbjct:   134 I 134

GO:0005634 "nucleus" evidence=IEA

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

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

UNIPROTKB|E2RPG1 GTF2B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 57/121 (47%), Positives = 73/121 (60%)

Query:     9 CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
             C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+    DP RVG   NPL
Sbjct:    15 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPL 74

Query:    67 LADGGLSTVIAKPNGASGEFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQMRY 124
             L+DG LST+I K  GA+  F      ++QNR   S+ DR ++ AFK I TM+DRI   R 
Sbjct:    75 LSDGDLSTMIGKGTGAAS-FDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRN 133

Query:   125 I 125
             I
Sbjct:   134 I 134

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

UNIPROTKB|B1APE1 GTF2B "Transcription initiation factor IIB" [Homo sapiens (taxid:9606)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 57/121 (47%), Positives = 73/121 (60%)

Query:     9 CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
             C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+    DP RVG   NPL
Sbjct:    14 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPL 73

Query:    67 LADGGLSTVIAKPNGASGEFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQMRY 124
             L+DG LST+I K  GA+  F      ++QNR   S+ DR ++ AFK I TM+DRI   R 
Sbjct:    74 LSDGDLSTMIGKGTGAAS-FDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRN 132

Query:   125 I 125
             I
Sbjct:   133 I 133

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

UNIPROTKB|Q00403 GTF2B "Transcription initiation factor IIB" [Homo sapiens (taxid:9606)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 57/121 (47%), Positives = 73/121 (60%)

Query:     9 CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
             C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+    DP RVG   NPL
Sbjct:    15 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPL 74

Query:    67 LADGGLSTVIAKPNGASGEFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQMRY 124
             L+DG LST+I K  GA+  F      ++QNR   S+ DR ++ AFK I TM+DRI   R 
Sbjct:    75 LSDGDLSTMIGKGTGAAS-FDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRN 133

Query:   125 I 125
             I
Sbjct:   134 I 134

GO:0008270 "zinc ion binding" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

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

GO:0019048 "virus-host interaction" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0046966 "thyroid hormone receptor binding" evidence=IPI

GO:0008134 "transcription factor binding" evidence=IPI

GO:0005654 "nucleoplasm" evidence=TAS

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

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

UNIPROTKB|F2Z5J6 GTF2B "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 57/121 (47%), Positives = 73/121 (60%)

Query:     9 CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPL 66
             C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+    DP RVG   NPL
Sbjct:    15 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPL 74

Query:    67 LADGGLSTVIAKPNGASGEFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQMRY 124
             L+DG LST+I K  GA+  F      ++QNR   S+ DR ++ AFK I TM+DRI   R 
Sbjct:    75 LSDGDLSTMIGKGTGAAS-FDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRN 133

Query:   125 I 125
             I
Sbjct:   134 I 134

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9SS44	TF2B2_ARATH	No assigned EC number	0.8888	0.6923	0.4038	yes	no
Q8W0W3	TF2B_ORYSJ	No assigned EC number	0.8412	0.6923	0.4038	yes	no
P48513	TF2B_SOYBN	No assigned EC number	0.8661	0.6923	0.4025	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	182
COG1405	285	COG1405, SUA7, Transcription initiation factor TFI	5e-22
PRK00423	310	PRK00423, tfb, transcription initiation factor IIB	4e-16
pfam08271	40	pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding	4e-12
TIGR04272	37	TIGR04272, cxxc_cxxc_Mbark, CxxC-x17-CxxC domain	0.002

>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]

 Score = 89.7 bits (223), Expect = 5e-22
 Identities = 39/118 (33%), Positives = 57/118 (48%), Gaps = 12/118 (10%)

Query: 6   CSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNP 65
           C +C   T ++ D+  G+ VC++CGLVLE   ID   EWR F     +    RVG P  P
Sbjct: 4   CPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAF----DERHERRVGAPLTP 58

Query: 66  LLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNP---DRGLILAFKTIATMSDRIG 120
            + D GLST+I   +          L +WQ R       +R LI A + +  ++  +G
Sbjct: 59  SIHDKGLSTIIGWGDKD----KMYRLRKWQIRIRVSSAKERNLITALEELERIASALG 112

Length = 285

>gnl|CDD|234758 PRK00423, tfb, transcription initiation factor IIB; Reviewed

 Score = 73.9 bits (182), Expect = 4e-16
 Identities = 41/132 (31%), Positives = 66/132 (50%), Gaps = 13/132 (9%)

Query: 6   CSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNP 65
           C +C    ++++D+  G+ VC++CGLV+E + ID+  EWR F  E       RVG P   
Sbjct: 14  CPECG-SDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTY 71

Query: 66  LLADGGLSTVIAKPN-GASGEFLSSS-------LGRWQNR---GSNPDRGLILAFKTIAT 114
            + D GLST I   N  + G+ +S         L +WQ R    +  +R L  A   +  
Sbjct: 72  TIHDKGLSTDIDWRNKDSYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDR 131

Query: 115 MSDRIGQMRYIR 126
           ++ ++G  R +R
Sbjct: 132 IASQLGLPRSVR 143

Length = 310

>gnl|CDD|203895 pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding

 Score = 57.7 bits (140), Expect = 4e-12
 Identities = 22/39 (56%), Positives = 28/39 (71%), Gaps = 1/39 (2%)

Query: 6  CSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEW 44
          C +C   TE+VFD+  G+ VC+ECGLVLE + IDE  EW
Sbjct: 3  CPNCG-STEIVFDYERGEYVCTECGLVLEDNIIDEGPEW 40

The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure. Length = 40

>gnl|CDD|211995 TIGR04272, cxxc_cxxc_Mbark, CxxC-x17-CxxC domain

 Score = 34.1 bits (79), Expect = 0.002
 Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 1/30 (3%)

Query: 1  MTDAFCSDCKKHTEVVFDHSAGDTV-CSEC 29
          M +A C++C + T+V F  +    V C EC
Sbjct: 3  MYEAVCAECGQETQVPFKPTGDRPVYCREC 32

This domain, with a pair of CXXC motifs separated by 17 amino acids, is a candidate zinc finger domain based on these motifs. Some proteins have two copies of the domain, while others are fused to another probable zinc-binding domain, described by pfam13451. Length = 37

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	182
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	100.0
KOG1597	308	consensus Transcription initiation factor TFIIB [T	100.0
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	100.0
KOG1598	521	consensus Transcription initiation factor TFIIIB,	99.85
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	99.7
PF00382	71	TFIIB: Transcription factor TFIIB repeat; InterPro	99.55
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	99.04
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	98.83
KOG1597	308	consensus Transcription initiation factor TFIIB [T	98.56
cd00043	88	CYCLIN Cyclin box fold. Protein binding domain fun	98.37
smart00385	83	CYCLIN domain present in cyclins, TFIIB and Retino	98.32
PF11781	36	RRN7: RNA polymerase I-specific transcription init	97.16
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	97.05
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	96.74
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	96.73
PHA00626	59	hypothetical protein	96.71
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	96.66
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	96.55
PF01857	135	RB_B: Retinoblastoma-associated protein B domain;	96.48
COG5333	297	CCL1 Cdk activating kinase (CAK)/RNA polymerase II	96.46
PLN00209	86	ribosomal protein S27; Provisional	96.25
KOG1598	521	consensus Transcription initiation factor TFIIIB,	96.25
PTZ00083	85	40S ribosomal protein S27; Provisional	96.16
PRK00420	112	hypothetical protein; Validated	96.16
TIGR00569	305	ccl1 cyclin ccl1. University).	96.14
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	96.07
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	95.96
PF13248	26	zf-ribbon_3: zinc-ribbon domain	95.86
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	95.83
PRK00432	50	30S ribosomal protein S27ae; Validated	95.79
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	95.7
smart00778	37	Prim_Zn_Ribbon Zinc-binding domain of primase-heli	95.61
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	95.52
PRK11827	60	hypothetical protein; Provisional	95.27
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	95.0
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	94.96
PF00134	127	Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR	94.95
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	94.87
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	94.84
KOG0794	264	consensus CDK8 kinase-activating protein cyclin C	94.77
KOG0834	323	consensus CDK9 kinase-activating protein cyclin T	94.69
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	94.58
smart00661	52	RPOL9 RNA polymerase subunit 9.	94.53
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	94.52
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	94.46
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	94.42
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	94.41
PF03966	68	Trm112p: Trm112p-like protein; InterPro: IPR005651	94.39
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	93.87
COG2835	60	Uncharacterized conserved protein [Function unknow	93.75
PF08273	40	Prim_Zn_Ribbon: Zinc-binding domain of primase-hel	93.68
TIGR00244	147	transcriptional regulator NrdR. Members of this al	93.64
PRK10220	111	hypothetical protein; Provisional	92.94
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	92.92
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	92.54
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	92.45
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	91.85
PF01780	90	Ribosomal_L37ae: Ribosomal L37ae protein family; I	91.78
KOG1779	84	consensus 40s ribosomal protein S27 [Translation,	91.46
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	91.33
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	91.28
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	90.79
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	90.43
PRK12495	226	hypothetical protein; Provisional	90.32
PTZ00255	90	60S ribosomal protein L37a; Provisional	90.12
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	90.12
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	90.09
COG2824	112	PhnA Uncharacterized Zn-ribbon-containing protein	89.93
COG4888	104	Uncharacterized Zn ribbon-containing protein [Gene	89.83
PRK14892	99	putative transcription elongation factor Elf1; Pro	89.53
COG1327	156	Predicted transcriptional regulator, consists of a	89.07
KOG0835	367	consensus Cyclin L [General function prediction on	88.99
TIGR00280	91	L37a ribosomal protein L37a. This model finds euka	88.99
TIGR00686	109	phnA alkylphosphonate utilization operon protein P	88.53
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	88.44
PF05129	81	Elf1: Transcription elongation factor Elf1 like; I	88.14
PRK03976	90	rpl37ae 50S ribosomal protein L37Ae; Reviewed	87.99
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	87.98
COG4640	465	Predicted membrane protein [Function unknown]	87.77
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	87.33
PRK09710	64	lar restriction alleviation and modification prote	87.26
PRK05978	148	hypothetical protein; Provisional	87.19
PF02984	118	Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR	87.18
PRK09678	72	DNA-binding transcriptional regulator; Provisional	86.91
PF12773	50	DZR: Double zinc ribbon	86.76
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	86.71
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	86.65
KOG0835	367	consensus Cyclin L [General function prediction on	86.45
PRK06266	178	transcription initiation factor E subunit alpha; V	85.41
PRK08402	355	replication factor A; Reviewed	85.4
PF14255	52	Cys_rich_CPXG: Cysteine-rich CPXCG	85.24
PF11672	102	DUF3268: Protein of unknown function (DUF3268); In	85.21
PRK02935	110	hypothetical protein; Provisional	85.11
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	85.0
PF15616	131	TerY-C: TerY-C metal binding domain	83.84
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	83.79
KOG2496	325	consensus Cdk activating kinase (CAK)/RNA polymera	83.51
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	82.92
PF08646	146	Rep_fac-A_C: Replication factor-A C terminal domai	82.8
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	82.7
COG3478	68	Predicted nucleic-acid-binding protein containing	82.34
COG5349	126	Uncharacterized protein conserved in bacteria [Fun	82.08
PF06827	30	zf-FPG_IleRS: Zinc finger found in FPG and IleRS;	82.07
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	81.74
cd04476	166	RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds cor	81.71
KOG4164	497	consensus Cyclin ik3-1/CABLES [Cell cycle control,	81.58
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	81.37
PRK13130	56	H/ACA RNA-protein complex component Nop10p; Review	81.34
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	81.06
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	81.01
PHA02942	383	putative transposase; Provisional	80.98
PRK00241	256	nudC NADH pyrophosphatase; Reviewed	80.91
KOG2906	105	consensus RNA polymerase III subunit C11 [Transcri	80.65
PRK12286	57	rpmF 50S ribosomal protein L32; Reviewed	80.47
COG3877	122	Uncharacterized protein conserved in bacteria [Fun	80.44
PRK12366	637	replication factor A; Reviewed	80.16
COG1326	201	Uncharacterized archaeal Zn-finger protein [Genera	80.11

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=100.00  E-value=9.1e-47  Score=320.66  Aligned_cols=176  Identities=27%  Similarity=0.471  Sum_probs=158.2

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccccccccccCCCCCCCCccccCCCCccccCCCCceEEecCC-C
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPN-G   81 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~sr~G~~~~~~~~~~gl~T~i~~~~-~   81 (182)
                      ...||+||+ +++++|+.+|++||++||+||+|++||+|||||+|++|+ .++++|+|+|.++++||.||+|.|+++. +
T Consensus        11 ~~~Cp~Cg~-~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~-~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~   88 (310)
T PRK00423         11 KLVCPECGS-DKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNKD   88 (310)
T ss_pred             CCcCcCCCC-CCeeEECCCCeEeecccCCcccccccccCCCccCCCccc-cCCccccCCCCCccccCCCCceEeecCCcc
Confidence            357999998 789999999999999999999999999999999999985 5699999999999999999999999643 3


Q ss_pred             CCCcccc-------ccccccccCC---CCchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHH
Q 030129           82 ASGEFLS-------SSLGRWQNRG---SNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWL  144 (182)
Q Consensus        82 ~~~~~l~-------~~l~~~q~~~---~~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~  144 (182)
                      +.|+.++       .+|++||++.   ++.||+|..||++|.++|+.|+||+.++|+  .||+++.++  +   ++++++
T Consensus        89 ~~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~  168 (310)
T PRK00423         89 SYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVV  168 (310)
T ss_pred             cccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHH
Confidence            3455444       2588999875   678999999999999999999999999999  999999887  3   999999


Q ss_pred             HHHHHHHHhhCC-----HHHHHhcCCCceeeeceeeehhcc
Q 030129          145 LACTLLVDKKTS-----HALLRKSALSPMELQRRKLAEQKN  180 (182)
Q Consensus       145 AAclY~acr~~~-----~eia~~~~v~~~~i~r~~~~~~~~  180 (182)
                      |||||+|||+++     +||++++++++++||+.|..+.|.
T Consensus       169 AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~  209 (310)
T PRK00423        169 AAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRE  209 (310)
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            999999999995     999999999999999998877653

>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]

Probab=100.00  E-value=7.9e-44  Score=293.60  Aligned_cols=169  Identities=49%  Similarity=0.738  Sum_probs=155.4

Q ss_pred             CCCCCCCCCCc-eeEeCCCCceEeCCCceeeeCCCcccccccccccCCCCCCCCccccCCCCccccCCCCceEEecCCCC
Q 030129            4 AFCSDCKKHTE-VVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGA   82 (182)
Q Consensus         4 ~~Cp~Cg~~~~-iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~sr~G~~~~~~~~~~gl~T~i~~~~~~   82 (182)
                      ++||+|+..+. +|+|+.+|+++|..||+|+++++||+++|||+|++++++.||+|||+|.||++.+.+|+|.|+++.+.
T Consensus         1 ~~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~Id~~sEwrtfsnd~~~~DPsrvG~~sNPlL~~g~L~T~I~~g~g~   80 (308)
T KOG1597|consen    1 MTCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRIIDEGSEWRTFSNDDSDADPSRVGASSNPLLDGGDLSTFISKGTGT   80 (308)
T ss_pred             CCCCCCCCCCCCeeeeccCCceecccCCeeeccccccccccccccccCCCCCCccccCCCCCCCCCCCCcceeeecCCCC
Confidence            46999998777 99999999999999999999999999999999999988899999999999999999999999988766


Q ss_pred             CCccccccccccccC--CCCchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHh
Q 030129           83 SGEFLSSSLGRWQNR--GSNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDK  153 (182)
Q Consensus        83 ~~~~l~~~l~~~q~~--~~~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr  153 (182)
                      .+..++ .|.++|++  +++.|+.|..||+.|..|++.|+||..|.++  +||+++.+.  +   +.++++|||||+|||
T Consensus        81 ~s~~~s-~l~~~Q~~~sm~~~d~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACR  159 (308)
T KOG1597|consen   81 SSSFAS-SLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACR  159 (308)
T ss_pred             CHHHHH-HHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHH
Confidence            554433 48889984  5789999999999999999999999999999  999999976  4   999999999999999


Q ss_pred             hCC-----HHHHHhcCCCceeeece
Q 030129          154 KTS-----HALLRKSALSPMELQRR  173 (182)
Q Consensus       154 ~~~-----~eia~~~~v~~~~i~r~  173 (182)
                      +.+     +||+.+++|+.+||||.
T Consensus       160 q~~~pRT~kEI~~~anv~kKEIgr~  184 (308)
T KOG1597|consen  160 QEDVPRTFKEISAVANVSKKEIGRC  184 (308)
T ss_pred             hcCCCchHHHHHHHHcCCHHHHHHH
Confidence            985     99999999999999993

>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]

Probab=100.00  E-value=3.9e-40  Score=275.88  Aligned_cols=169  Identities=28%  Similarity=0.496  Sum_probs=150.6

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccccccccccCCCCCCCCccccCCCCccccCCCCceEEecCCCC
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGA   82 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~sr~G~~~~~~~~~~gl~T~i~~~~~~   82 (182)
                      ++.||+||+ ++++.|++.|++||.+||+|++|..||.|||||+| ++  ...+ |+|+|.++.+||.|++|.|+++...
T Consensus         1 ~~~CpeCg~-~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f-~e--~~~~-r~g~P~t~~~~d~~l~t~i~~~~~~   75 (285)
T COG1405           1 VMSCPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAF-DE--RHER-RVGAPLTPSIHDKGLSTIIGWGDKD   75 (285)
T ss_pred             CCCCCCCCC-ccceeeccCCeEEeccCCEEeccccccCCCCcccc-cc--cccc-cccCCCccccCccchhhhcccchhH
Confidence            367999998 69999999999999999999999999999999999 33  2234 9999999999999999999975422


Q ss_pred             CCccccccccccccCC---CCchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHH
Q 030129           83 SGEFLSSSLGRWQNRG---SNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVD  152 (182)
Q Consensus        83 ~~~~l~~~l~~~q~~~---~~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~ac  152 (182)
                          ...+|++||.+.   +++||+|..|+.+|.++++.|+||..+.|.  .||+++.++ +    +.++++|||||+||
T Consensus        76 ----~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~ac  151 (285)
T COG1405          76 ----KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAAC  151 (285)
T ss_pred             ----HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHH
Confidence                235789999754   479999999999999999999999999999  999999998 5    89999999999999


Q ss_pred             hhCC-----HHHHHhcCCCceeeeceeeehhcc
Q 030129          153 KKTS-----HALLRKSALSPMELQRRKLAEQKN  180 (182)
Q Consensus       153 r~~~-----~eia~~~~v~~~~i~r~~~~~~~~  180 (182)
                      |+++     .||++++++++++|||+|....++
T Consensus       152 R~~~~prtl~eIa~a~~V~~kei~rtyr~~~~~  184 (285)
T COG1405         152 RINGVPRTLDEIAKALGVSKKEIGRTYRLLVRE  184 (285)
T ss_pred             HHcCCCccHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            9984     999999999999999999866554

>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]

Probab=99.85  E-value=1.3e-21  Score=172.89  Aligned_cols=137  Identities=18%  Similarity=0.298  Sum_probs=114.4

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccccccccccCCCCCCCCccccCCCCccccCCCCceEEecCCCCC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGAS   83 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~sr~G~~~~~~~~~~gl~T~i~~~~~~~   83 (182)
                      +.|++||+ +++..|+.+|+.+|+.||.|+|+++|..+.   +|.+.           +         .|+.|+....+.
T Consensus         1 ~~C~~C~~-s~fe~d~a~g~~~C~~CG~v~E~~~ivsev---~F~e~-----------~---------~G~~v~~~~~g~   56 (521)
T KOG1598|consen    1 MVCKNCGG-SNFERDEATGNLYCTACGTVLEYNNIVAEV---TFVEG-----------A---------QGQFVRVGQSGA   56 (521)
T ss_pred             CcCCCCCC-CCcccccccCCceeccccceeeccceeEEe---eeecc-----------c---------ceeEEeccccCC
Confidence            47999998 799999999999999999999999998754   56532           1         134554322111


Q ss_pred             CccccccccccccCCCCchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC
Q 030129           84 GEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus        84 ~~~l~~~l~~~q~~~~~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~  156 (182)
                      +.           ..+++++++++|.+.|..++.+|+|+. +++.  .+|++|.++ |    +...|+|||+|++||+++
T Consensus        57 ~~-----------s~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~  124 (521)
T KOG1598|consen   57 GS-----------SLESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEK  124 (521)
T ss_pred             cc-----------chHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhC
Confidence            10           126789999999999999999999999 7777  999999998 7    899999999999999984


Q ss_pred             -----HHHHHhcCCCceeeeceeee
Q 030129          157 -----HALLRKSALSPMELQRRKLA  176 (182)
Q Consensus       157 -----~eia~~~~v~~~~i~r~~~~  176 (182)
                           .|+++++.|+++.||++||.
T Consensus       125 t~hlliDfS~~Lqv~Vy~LG~~~l~  149 (521)
T KOG1598|consen  125 TDHLLIDFSSYLQVSVYDLGSNFLE  149 (521)
T ss_pred             CceEEEEeccceEEehhhhhHHHHH
Confidence                 89999999999999999874

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.70  E-value=8.4e-18  Score=103.23  Aligned_cols=43  Identities=51%  Similarity=1.076  Sum_probs=38.7

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccccccccc
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTF   47 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f   47 (182)
                      ++||+||+ +.+++|+.+|++||+.||+||+|+.|++++|||+|
T Consensus         1 m~Cp~Cg~-~~~~~D~~~g~~vC~~CG~Vl~e~~i~~~~e~r~f   43 (43)
T PF08271_consen    1 MKCPNCGS-KEIVFDPERGELVCPNCGLVLEENIIDEGPEWREF   43 (43)
T ss_dssp             ESBTTTSS-SEEEEETTTTEEEETTT-BBEE-TTBSCCCSCCHC
T ss_pred             CCCcCCcC-CceEEcCCCCeEECCCCCCEeecccccCCcccccC
Confidence            47999998 56999999999999999999999999999999987

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=99.55  E-value=1e-14  Score=98.45  Aligned_cols=59  Identities=14%  Similarity=0.253  Sum_probs=52.2

Q ss_pred             HHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceee
Q 030129          112 IATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMEL  170 (182)
Q Consensus       112 I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i  170 (182)
                      |++||+.|+||+.+.+.  +||+++.+. +    +|.+++|||||+|||+++     +||+++++|+++||
T Consensus         1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI   71 (71)
T PF00382_consen    1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI   71 (71)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred             ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence            78999999999999999  999999887 4    899999999999999985     99999999999876

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=99.04  E-value=3.3e-10  Score=96.66  Aligned_cols=72  Identities=6%  Similarity=0.095  Sum_probs=64.5

Q ss_pred             HHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeeeceee
Q 030129          108 AFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQRRKL  175 (182)
Q Consensus       108 a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~r~~~  175 (182)
                      +.++|.++|+.|+||..+.+.  +|++++.+. +    +|.++||||||+||+.++     +|||++++|++.||.++|-
T Consensus       219 p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~yk  298 (310)
T PRK00423        219 PIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYK  298 (310)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHH
Confidence            568999999999999999888  999999876 4    999999999999999974     9999999999999998885


Q ss_pred             ehhc
Q 030129          176 AEQK  179 (182)
Q Consensus       176 ~~~~  179 (182)
                      -..+
T Consensus       299 el~~  302 (310)
T PRK00423        299 ELAE  302 (310)
T ss_pred             HHHH
Confidence            5443

>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]

Probab=98.83  E-value=6.2e-09  Score=87.80  Aligned_cols=69  Identities=12%  Similarity=0.157  Sum_probs=63.0

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeeece
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQRR  173 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~r~  173 (182)
                      .+..++|++||+.||||+.+...  +|.+++.+. +    +|..+||||||+|++.++     +|||.+++|++.||-.+
T Consensus       192 ~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnr  271 (285)
T COG1405         192 VDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNR  271 (285)
T ss_pred             CCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHH
Confidence            35678999999999999988777  999999887 4    999999999999999985     99999999999999988


Q ss_pred             e
Q 030129          174 K  174 (182)
Q Consensus       174 ~  174 (182)
                      |
T Consensus       272 y  272 (285)
T COG1405         272 Y  272 (285)
T ss_pred             H
Confidence            8

>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]

Probab=98.56  E-value=8.3e-08  Score=80.30  Aligned_cols=69  Identities=9%  Similarity=0.102  Sum_probs=62.5

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhC-----CHHHHHhcCCCceeeece
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKT-----SHALLRKSALSPMELQRR  173 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~-----~~eia~~~~v~~~~i~r~  173 (182)
                      ..+-++|.++|+.|+||..+.+.  ++.+++.+. +    +|.+||||.||++++..     .+||.+++||.+.||-..
T Consensus       201 ~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~s  280 (308)
T KOG1597|consen  201 ISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNS  280 (308)
T ss_pred             hhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHH
Confidence            34678999999999999999988  999999887 4    99999999999999987     399999999999999877


Q ss_pred             e
Q 030129          174 K  174 (182)
Q Consensus       174 ~  174 (182)
                      |
T Consensus       281 Y  281 (308)
T KOG1597|consen  281 Y  281 (308)
T ss_pred             H
Confidence            6

>cd00043 CYCLIN Cyclin box fold

Probab=98.37  E-value=1e-06  Score=59.43  Aligned_cols=68  Identities=10%  Similarity=0.109  Sum_probs=58.2

Q ss_pred             HHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC-----HHHHHhcCC-Cceeeece
Q 030129          107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS-----HALLRKSAL-SPMELQRR  173 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~-----~eia~~~~v-~~~~i~r~  173 (182)
                      .+++.|.+++..++++..+...  .+++++...  +   ++..+++||||+||+..+     .|+...++. +..+|.+.
T Consensus         4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~   83 (88)
T cd00043           4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILRM   83 (88)
T ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHHH
Confidence            5789999999999999998888  888888665  3   999999999999999873     889999888 87777654


Q ss_pred             e
Q 030129          174 K  174 (182)
Q Consensus       174 ~  174 (182)
                      +
T Consensus        84 e   84 (88)
T cd00043          84 E   84 (88)
T ss_pred             H
Confidence            3

Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.

>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma

Probab=98.32  E-value=1.2e-06  Score=58.51  Aligned_cols=64  Identities=9%  Similarity=0.050  Sum_probs=54.4

Q ss_pred             HHHHHHHHhCChHHHHHH--HHHHHHHh-c-c---CHHHHHHHHHHHHHhhCC-----HHHHHhcCC-Cceeeecee
Q 030129          111 TIATMSDRIGQMRYIRRW--KIKSLVEA-E-I---KTHYWLLACTLLVDKKTS-----HALLRKSAL-SPMELQRRK  174 (182)
Q Consensus       111 ~I~~i~~~L~L~~~v~~~--~i~k~a~~-~-l---~~~~v~AAclY~acr~~~-----~eia~~~~v-~~~~i~r~~  174 (182)
                      .|.+++..+++|+.+...  .+++++.. . +   ++..++|||||+||+..+     .++...++. ++.+|.+.+
T Consensus         2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~   78 (83)
T smart00385        2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRME   78 (83)
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHH
Confidence            578999999999998888  88888866 3 3   999999999999999884     888998988 877776543

A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.

>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[]

Probab=97.16  E-value=0.00034  Score=41.04  Aligned_cols=27  Identities=30%  Similarity=0.554  Sum_probs=23.2

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      .|+.|++ .  .+....|.++|..||.|++
T Consensus        10 ~C~~C~~-~--~~~~~dG~~yC~~cG~~~E   36 (36)
T PF11781_consen   10 PCPVCGS-R--WFYSDDGFYYCDRCGHQSE   36 (36)
T ss_pred             cCCCCCC-e--EeEccCCEEEhhhCceEcC
Confidence            4999997 2  6778999999999999974

>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors []

Probab=97.05  E-value=0.00075  Score=38.81  Aligned_cols=31  Identities=23%  Similarity=0.451  Sum_probs=25.6

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      |....|+.|+.  +.++..+.+..+|.+||.+.
T Consensus         1 ~~~~~C~~C~~--~~i~~~~~~~~~C~~Cg~~~   31 (33)
T PF08792_consen    1 SNLKKCSKCGG--NGIVNKEDDYEVCIFCGSSF   31 (33)
T ss_pred             CCceEcCCCCC--CeEEEecCCeEEcccCCcEe
Confidence            56678999997  35566789999999999985

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=96.74  E-value=0.00084  Score=43.54  Aligned_cols=30  Identities=37%  Similarity=0.780  Sum_probs=27.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      .+||.|+. ..+|+++.+-...|..||.+|.
T Consensus        12 VkCp~C~n-~q~vFsha~t~V~C~~Cg~~L~   41 (59)
T PRK00415         12 VKCPDCGN-EQVVFSHASTVVRCLVCGKTLA   41 (59)
T ss_pred             EECCCCCC-eEEEEecCCcEEECcccCCCcc
Confidence            57999997 7899999999999999999985

>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]

Probab=96.73  E-value=0.0011  Score=43.75  Aligned_cols=31  Identities=35%  Similarity=0.778  Sum_probs=28.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      .+||.|+. ..+++++.+-...|..||.+|-+
T Consensus        20 VkCpdC~N-~q~vFshast~V~C~~CG~~l~~   50 (67)
T COG2051          20 VKCPDCGN-EQVVFSHASTVVTCLICGTTLAE   50 (67)
T ss_pred             EECCCCCC-EEEEeccCceEEEecccccEEEe
Confidence            47999997 78999999999999999999953

>PHA00626 hypothetical protein

Probab=96.71  E-value=0.0015  Score=41.80  Aligned_cols=31  Identities=23%  Similarity=0.549  Sum_probs=23.2

Q ss_pred             CCCCCCCCCCceeEe----CCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFD----HSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D----~~~G~~vC~~CG~Vl~e   35 (182)
                      |.||.||+ .+|+..    -.+..+.|.+||.-...
T Consensus         1 m~CP~CGS-~~Ivrcg~cr~~snrYkCkdCGY~ft~   35 (59)
T PHA00626          1 MSCPKCGS-GNIAKEKTMRGWSDDYVCCDCGYNDSK   35 (59)
T ss_pred             CCCCCCCC-ceeeeeceecccCcceEcCCCCCeech
Confidence            46999998 556542    23689999999998643

>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.66  E-value=0.00081  Score=43.08  Aligned_cols=30  Identities=33%  Similarity=0.722  Sum_probs=22.8

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      .+||.|+. ..+|+++++-...|..||.+|-
T Consensus         8 VkCp~C~~-~q~vFSha~t~V~C~~Cg~~L~   37 (55)
T PF01667_consen    8 VKCPGCYN-IQTVFSHAQTVVKCVVCGTVLA   37 (55)
T ss_dssp             EE-TTT-S-EEEEETT-SS-EE-SSSTSEEE
T ss_pred             EECCCCCC-eeEEEecCCeEEEcccCCCEec
Confidence            57999997 6899999999999999999995

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=96.55  E-value=0.0026  Score=36.79  Aligned_cols=28  Identities=25%  Similarity=0.666  Sum_probs=15.6

Q ss_pred             CCCCCCCCCCceeEeC----CCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDH----SAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~----~~G~~vC~~CG~Vl   33 (182)
                      .+||.||..  +....    +.-..||+.||.|-
T Consensus         1 kfC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~Ih   32 (34)
T PF14803_consen    1 KFCPQCGGP--LERRIPEGDDRERLVCPACGFIH   32 (34)
T ss_dssp             -B-TTT--B---EEE--TT-SS-EEEETTTTEEE
T ss_pred             CccccccCh--hhhhcCCCCCccceECCCCCCEE
Confidence            379999973  44433    34449999999983

>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation

Probab=96.48  E-value=0.013  Score=44.38  Aligned_cols=53  Identities=11%  Similarity=0.046  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc---c----CHHHHHHHHHHHHHhhCC
Q 030129          104 GLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE---I----KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       104 ~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~---l----~~~~v~AAclY~acr~~~  156 (182)
                      .+.-|...|..+|++|+|++.+.+.  .+|+.+..+   |    ..+.++..|+|+.||.+.
T Consensus        10 vy~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~   71 (135)
T PF01857_consen   10 VYKLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSK   71 (135)
T ss_dssp             HHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhc
Confidence            3455899999999999999998777  888877543   3    899999999999999884

They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.

>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=96.46  E-value=0.0037  Score=53.01  Aligned_cols=59  Identities=15%  Similarity=0.125  Sum_probs=48.9

Q ss_pred             hHHH-HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC--HHHH
Q 030129          102 DRGL-ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS--HALL  160 (182)
Q Consensus       102 er~L-~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~--~eia  160 (182)
                      +.+| ..++..|..+|.+|+||..+..+  .+|++..-.  +   ++..++++|||+||+.+.  .+|.
T Consensus        41 e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~  109 (297)
T COG5333          41 ELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDIS  109 (297)
T ss_pred             hhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhh
Confidence            4444 45789999999999999999999  788887554  3   999999999999999886  5553

>PLN00209 ribosomal protein S27; Provisional

Probab=96.25  E-value=0.0029  Score=43.97  Aligned_cols=31  Identities=35%  Similarity=0.657  Sum_probs=28.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      .+||.|+. ..+|+.+++-...|..||.+|.+
T Consensus        37 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~   67 (86)
T PLN00209         37 VKCQGCFN-ITTVFSHSQTVVVCGSCQTVLCQ   67 (86)
T ss_pred             EECCCCCC-eeEEEecCceEEEccccCCEeec
Confidence            57999997 68999999999999999999953

>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]

Probab=96.25  E-value=0.0013  Score=59.30  Aligned_cols=70  Identities=11%  Similarity=0.022  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHH--hc--c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceee
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVE--AE--I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMEL  170 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~--~~--l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i  170 (182)
                      ..-.-+|.++++.|-..+.-.+.  .-++++.  ++  +    +|..++.||||+|||.++     .||+.++.|++.||
T Consensus       164 vDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl  243 (521)
T KOG1598|consen  164 VDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTL  243 (521)
T ss_pred             cCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHH
Confidence            34445666777666443322222  2222322  22  2    999999999999999996     89999999999999


Q ss_pred             eceee
Q 030129          171 QRRKL  175 (182)
Q Consensus       171 ~r~~~  175 (182)
                      .++|.
T Consensus       244 ~kRl~  248 (521)
T KOG1598|consen  244 SKRLK  248 (521)
T ss_pred             HHHHH
Confidence            88763

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=96.16  E-value=0.0035  Score=43.42  Aligned_cols=31  Identities=26%  Similarity=0.618  Sum_probs=28.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      .+||.|+. ..+|+++++-...|..||.+|-+
T Consensus        36 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~   66 (85)
T PTZ00083         36 VKCPGCSQ-ITTVFSHAQTVVLCGGCSSQLCQ   66 (85)
T ss_pred             EECCCCCC-eeEEEecCceEEEccccCCEeec
Confidence            57999997 68999999999999999999953

>PRK00420 hypothetical protein; Validated

Probab=96.16  E-value=0.0043  Score=45.50  Aligned_cols=31  Identities=29%  Similarity=0.600  Sum_probs=23.9

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      |-...||.||.  ++ +-...|..+|..||.++.
T Consensus        21 ml~~~CP~Cg~--pL-f~lk~g~~~Cp~Cg~~~~   51 (112)
T PRK00420         21 MLSKHCPVCGL--PL-FELKDGEVVCPVHGKVYI   51 (112)
T ss_pred             HccCCCCCCCC--cc-eecCCCceECCCCCCeee
Confidence            34467999996  33 444899999999999874

>TIGR00569 ccl1 cyclin ccl1

Probab=96.14  E-value=0.018  Score=49.26  Aligned_cols=55  Identities=11%  Similarity=0.054  Sum_probs=46.2

Q ss_pred             hHHH-HHHHHHHHHHHHHhC--ChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC
Q 030129          102 DRGL-ILAFKTIATMSDRIG--QMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       102 er~L-~~a~~~I~~i~~~L~--L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~  156 (182)
                      |+.| ...-..|.++|..|+  ||+.++-+  .+|++..-.  +   .+..|++||||+||+.+.
T Consensus        52 E~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE  116 (305)
T TIGR00569        52 ELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE  116 (305)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccc
Confidence            5555 347789999999999  99999888  888887554  3   999999999999999873

University).

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

Probab=96.07  E-value=0.005  Score=37.77  Aligned_cols=31  Identities=29%  Similarity=0.682  Sum_probs=25.2

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      |-...||.||.  .+.+|+..+...|..||.-+
T Consensus         1 ~~~y~C~~CG~--~~~~~~~~~~~~Cp~CG~~~   31 (46)
T PRK00398          1 MAEYKCARCGR--EVELDEYGTGVRCPYCGYRI   31 (46)
T ss_pred             CCEEECCCCCC--EEEECCCCCceECCCCCCeE
Confidence            55678999996  57778777799999999754

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=95.96  E-value=0.0043  Score=46.56  Aligned_cols=29  Identities=24%  Similarity=0.704  Sum_probs=21.8

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEeCCCc-eee
Q 030129            1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECG-LVL   33 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG-~Vl   33 (182)
                      |-...||.||.  ++. - .+|+++|..|| .+.
T Consensus        26 ML~~hCp~Cg~--PLF-~-KdG~v~CPvC~~~~~   55 (131)
T COG1645          26 MLAKHCPKCGT--PLF-R-KDGEVFCPVCGYREV   55 (131)
T ss_pred             HHHhhCcccCC--cce-e-eCCeEECCCCCceEE
Confidence            33457999996  343 3 89999999999 554

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=95.86  E-value=0.0046  Score=33.48  Aligned_cols=22  Identities=27%  Similarity=0.967  Sum_probs=17.4

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGL   31 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~   31 (182)
                      +.||+||. . +    +.+..+|..||.
T Consensus         3 ~~Cp~Cg~-~-~----~~~~~fC~~CG~   24 (26)
T PF13248_consen    3 MFCPNCGA-E-I----DPDAKFCPNCGA   24 (26)
T ss_pred             CCCcccCC-c-C----CcccccChhhCC
Confidence            67999996 2 2    356899999996

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=95.83  E-value=0.01  Score=34.50  Aligned_cols=31  Identities=19%  Similarity=0.484  Sum_probs=18.5

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      +..||+||+ -=+......+...|..||++.+
T Consensus         1 m~FCp~C~n-lL~p~~~~~~~~~C~~C~Y~~~   31 (35)
T PF02150_consen    1 MRFCPECGN-LLYPKEDKEKRVACRTCGYEEP   31 (35)
T ss_dssp             --BETTTTS-BEEEEEETTTTEEESSSS-EEE
T ss_pred             CeeCCCCCc-cceEcCCCccCcCCCCCCCccC
Confidence            358999996 2222233444457999999964

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=95.79  E-value=0.0078  Score=37.83  Aligned_cols=28  Identities=25%  Similarity=0.707  Sum_probs=21.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ...||.||+ . +..++ .+...|..||+..
T Consensus        20 ~~fCP~Cg~-~-~m~~~-~~r~~C~~Cgyt~   47 (50)
T PRK00432         20 NKFCPRCGS-G-FMAEH-LDRWHCGKCGYTE   47 (50)
T ss_pred             cCcCcCCCc-c-hhecc-CCcEECCCcCCEE
Confidence            357999997 4 55554 4899999999874

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=95.70  E-value=0.0047  Score=32.54  Aligned_cols=22  Identities=27%  Similarity=0.963  Sum_probs=16.6

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGLV   32 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V   32 (182)
                      +||+||.  .+    ..+..+|..||.-
T Consensus         1 ~Cp~CG~--~~----~~~~~fC~~CG~~   22 (23)
T PF13240_consen    1 YCPNCGA--EI----EDDAKFCPNCGTP   22 (23)
T ss_pred             CCcccCC--CC----CCcCcchhhhCCc
Confidence            5999997  22    2467889999974

>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase

Probab=95.61  E-value=0.013  Score=34.56  Aligned_cols=29  Identities=31%  Similarity=0.720  Sum_probs=22.2

Q ss_pred             CCCCCCCCCCCceeEeC--CCCceEeCCCce
Q 030129            3 DAFCSDCKKHTEVVFDH--SAGDTVCSECGL   31 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~--~~G~~vC~~CG~   31 (182)
                      +..||.||+...+-+|.  .+|..+|..||.
T Consensus         3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~   33 (37)
T smart00778        3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA   33 (37)
T ss_pred             ccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence            46799999865555555  458999999974

This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=95.52  E-value=0.011  Score=37.73  Aligned_cols=30  Identities=33%  Similarity=0.720  Sum_probs=21.5

Q ss_pred             CCCCCCCCCCceeEeCCCCc-eEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGD-TVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~-~vC~~CG~Vl~   34 (182)
                      -.||.||.. --+.|...|+ +.|..||.-++
T Consensus         3 ~~CP~CG~~-iev~~~~~GeiV~Cp~CGaele   33 (54)
T TIGR01206         3 FECPDCGAE-IELENPELGELVICDECGAELE   33 (54)
T ss_pred             cCCCCCCCE-EecCCCccCCEEeCCCCCCEEE
Confidence            479999973 2233445576 67999999985

This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.

>PRK11827 hypothetical protein; Provisional

Probab=95.27  E-value=0.017  Score=37.73  Aligned_cols=28  Identities=14%  Similarity=0.494  Sum_probs=24.1

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ..||.|++  .+..|....+++|..||++.
T Consensus         9 LaCP~ckg--~L~~~~~~~~Lic~~~~laY   36 (60)
T PRK11827          9 IACPVCNG--KLWYNQEKQELICKLDNLAF   36 (60)
T ss_pred             eECCCCCC--cCeEcCCCCeEECCccCeec
Confidence            46999986  57888888899999999985

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=95.00  E-value=0.016  Score=33.91  Aligned_cols=29  Identities=28%  Similarity=0.653  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCceeEeC-----CCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDH-----SAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~-----~~G~~vC~~CG~Vl~   34 (182)
                      ..||+|+..  +.++.     ..+...|..||.++.
T Consensus         3 ~~CP~C~~~--~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         3 IQCPNCKTS--FRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             EECCCCCCE--EEeCHHHcCCCCCEEECCCCCCEEE
Confidence            569999972  33342     345799999999874

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues

Probab=94.96  E-value=0.032  Score=31.31  Aligned_cols=27  Identities=26%  Similarity=0.439  Sum_probs=14.5

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      -+||.|++. ....  +...+||.+||.-+
T Consensus         3 p~Cp~C~se-~~y~--D~~~~vCp~C~~ew   29 (30)
T PF08274_consen    3 PKCPLCGSE-YTYE--DGELLVCPECGHEW   29 (30)
T ss_dssp             ---TTT------EE---SSSEEETTTTEEE
T ss_pred             CCCCCCCCc-ceec--cCCEEeCCcccccC
Confidence            479999983 3333  46779999999754

The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.

>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=94.95  E-value=0.11  Score=37.56  Aligned_cols=52  Identities=15%  Similarity=0.128  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhC
Q 030129          104 GLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKT  155 (182)
Q Consensus       104 ~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~  155 (182)
                      ......+.|..++..++++..+.-.  .++.+....  +   ++..+++||+|+||+.+
T Consensus        30 ~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~   88 (127)
T PF00134_consen   30 MRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKME   88 (127)
T ss_dssp             HHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhh
Confidence            3466889999999999999988777  777777665  3   88999999999999987

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....

>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]

Probab=94.87  E-value=0.027  Score=39.26  Aligned_cols=29  Identities=28%  Similarity=0.563  Sum_probs=25.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      -.||.|++ + .+....+|-..|..||.++.
T Consensus        36 ~~Cp~C~~-~-~VkR~a~GIW~C~kCg~~fA   64 (89)
T COG1997          36 HVCPFCGR-T-TVKRIATGIWKCRKCGAKFA   64 (89)
T ss_pred             CcCCCCCC-c-ceeeeccCeEEcCCCCCeec
Confidence            46999998 4 67888999999999999863

>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]

Probab=94.84  E-value=0.019  Score=35.82  Aligned_cols=27  Identities=30%  Similarity=0.768  Sum_probs=22.7

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV   32 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V   32 (182)
                      ..||.||. ..++.|+.. .+.|..||+.
T Consensus        20 ~~CPrCG~-gvfmA~H~d-R~~CGkCgyT   46 (51)
T COG1998          20 RFCPRCGP-GVFMADHKD-RWACGKCGYT   46 (51)
T ss_pred             ccCCCCCC-cchhhhcCc-eeEeccccce
Confidence            57999995 677888766 8999999987

>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]

Probab=94.77  E-value=0.067  Score=44.00  Aligned_cols=49  Identities=10%  Similarity=0.046  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-----cCHHHHHHHHHHHHHhhC
Q 030129          107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-----IKTHYWLLACTLLVDKKT  155 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-----l~~~~v~AAclY~acr~~  155 (182)
                      -..+.|..++..|+|.+.|+-+  .++|+..-+     +.|..+|+-|||+||+.+
T Consensus        43 ~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvE   98 (264)
T KOG0794|consen   43 FMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVE   98 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhh
Confidence            3568899999999999999888  555665443     399999999999999976

>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]

Probab=94.69  E-value=0.091  Score=45.31  Aligned_cols=51  Identities=14%  Similarity=-0.031  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~  156 (182)
                      .++...|.+++.+|++|..-+..  .+|-+..-.  |   .+..+|+||||+|++.+.
T Consensus        40 ~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEe   97 (323)
T KOG0834|consen   40 QEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEE   97 (323)
T ss_pred             HHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhccc
Confidence            67999999999999999876555  666665433  4   778999999999999883

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains

Probab=94.58  E-value=0.062  Score=30.31  Aligned_cols=29  Identities=21%  Similarity=0.460  Sum_probs=16.8

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ..+|+.||+  ........-..+|..||...
T Consensus         3 ~rfC~~CG~--~t~~~~~g~~r~C~~Cg~~~   31 (32)
T PF09297_consen    3 HRFCGRCGA--PTKPAPGGWARRCPSCGHEH   31 (32)
T ss_dssp             TSB-TTT----BEEE-SSSS-EEESSSS-EE
T ss_pred             CcccCcCCc--cccCCCCcCEeECCCCcCEe
Confidence            578999997  33445555669999999863

; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=94.53  E-value=0.038  Score=34.29  Aligned_cols=28  Identities=25%  Similarity=0.687  Sum_probs=19.1

Q ss_pred             CCCCCCCCCceeEeCC-C-CceEeCCCceeee
Q 030129            5 FCSDCKKHTEVVFDHS-A-GDTVCSECGLVLE   34 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~-~-G~~vC~~CG~Vl~   34 (182)
                      +||.||+ - +..... . ..++|..||.+..
T Consensus         2 FCp~Cg~-~-l~~~~~~~~~~~vC~~Cg~~~~   31 (52)
T smart00661        2 FCPKCGN-M-LIPKEGKEKRRFVCRKCGYEEP   31 (52)
T ss_pred             CCCCCCC-c-cccccCCCCCEEECCcCCCeEE
Confidence            7999996 2 222222 2 3799999998854

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=94.52  E-value=0.031  Score=43.22  Aligned_cols=30  Identities=27%  Similarity=0.576  Sum_probs=20.5

Q ss_pred             CCCCCCCCCCceeEeCC---CCc-----eEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHS---AGD-----TVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~---~G~-----~vC~~CG~Vl   33 (182)
                      |+||+||+....+.|..   .|.     .-|++||.-+
T Consensus         1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f   38 (154)
T PRK00464          1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF   38 (154)
T ss_pred             CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence            57999997432566653   454     4599999765

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=94.46  E-value=0.019  Score=31.15  Aligned_cols=24  Identities=29%  Similarity=0.833  Sum_probs=18.3

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      .||+|+..  |    ......|..||.++.
T Consensus         2 ~CP~C~~~--V----~~~~~~Cp~CG~~F~   25 (26)
T PF10571_consen    2 TCPECGAE--V----PESAKFCPHCGYDFE   25 (26)
T ss_pred             cCCCCcCC--c----hhhcCcCCCCCCCCc
Confidence            69999972  2    245689999999863

Several members are annotated as putative helicases.

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=94.42  E-value=0.024  Score=41.30  Aligned_cols=31  Identities=23%  Similarity=0.664  Sum_probs=25.5

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH   36 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~   36 (182)
                      ...||.||..   .+|-..--+||..||.++.-.
T Consensus         9 KR~Cp~CG~k---FYDLnk~PivCP~CG~~~~~~   39 (108)
T PF09538_consen    9 KRTCPSCGAK---FYDLNKDPIVCPKCGTEFPPE   39 (108)
T ss_pred             cccCCCCcch---hccCCCCCccCCCCCCccCcc
Confidence            4679999972   589888889999999998644

The function of members of this family is unknown.

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=94.41  E-value=0.041  Score=33.12  Aligned_cols=27  Identities=33%  Similarity=0.849  Sum_probs=20.5

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEeCCCc
Q 030129            1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECG   30 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG   30 (182)
                      |-...||.|+.  .+.. ..+|.++|..|+
T Consensus        15 ML~~~Cp~C~~--PL~~-~k~g~~~Cv~C~   41 (41)
T PF06677_consen   15 MLDEHCPDCGT--PLMR-DKDGKIYCVSCG   41 (41)
T ss_pred             HhcCccCCCCC--eeEE-ecCCCEECCCCC
Confidence            34568999974  4544 578999999996

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function

Probab=94.39  E-value=0.058  Score=35.77  Aligned_cols=17  Identities=29%  Similarity=0.788  Sum_probs=15.6

Q ss_pred             EeCCCCceEeCCCceee
Q 030129           17 FDHSAGDTVCSECGLVL   33 (182)
Q Consensus        17 ~D~~~G~~vC~~CG~Vl   33 (182)
                      ++..+|.++|.+||.+.
T Consensus        47 ~~i~eg~L~Cp~c~r~Y   63 (68)
T PF03966_consen   47 VEIVEGELICPECGREY   63 (68)
T ss_dssp             EETTTTEEEETTTTEEE
T ss_pred             ccccCCEEEcCCCCCEE
Confidence            68899999999999986

The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=93.87  E-value=0.076  Score=34.15  Aligned_cols=28  Identities=25%  Similarity=0.656  Sum_probs=20.2

Q ss_pred             CCCCCCCCCCCceeEeCCCC-------ceEeCCCce
Q 030129            3 DAFCSDCKKHTEVVFDHSAG-------DTVCSECGL   31 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G-------~~vC~~CG~   31 (182)
                      ..-||.||+ ..+.+....+       .+.|.+||.
T Consensus         3 LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga   37 (61)
T PF14354_consen    3 LKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA   37 (61)
T ss_pred             CcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence            356999987 5666665544       256999999

>COG2835 Uncharacterized conserved protein [Function unknown]

Probab=93.75  E-value=0.056  Score=35.15  Aligned_cols=30  Identities=27%  Similarity=0.669  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ...-||.|++  .+.+|.+.++++|..|++..
T Consensus         7 eiLaCP~~kg--~L~~~~~~~~L~c~~~~~aY   36 (60)
T COG2835           7 EILACPVCKG--PLVYDEEKQELICPRCKLAY   36 (60)
T ss_pred             eeeeccCcCC--cceEeccCCEEEecccCcee
Confidence            3456999997  48999999999999999985

>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4

Probab=93.68  E-value=0.065  Score=32.09  Aligned_cols=29  Identities=28%  Similarity=0.634  Sum_probs=16.4

Q ss_pred             CCCCCCCCCCcee-EeC--CCCceEeCCCcee
Q 030129            4 AFCSDCKKHTEVV-FDH--SAGDTVCSECGLV   32 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv-~D~--~~G~~vC~~CG~V   32 (182)
                      ..||.|++...+- ++.  .+|..+|..|+-+
T Consensus         4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~~   35 (40)
T PF08273_consen    4 GPCPICGGKDRFRIFDDKDGRGTWICRQCGGD   35 (40)
T ss_dssp             E--TTTT-TTTEEEETT----S-EEETTTTBE
T ss_pred             CCCCCCcCccccccCcCcccCCCEECCCCCCc
Confidence            4699999865554 443  4699999999434

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.

>TIGR00244 transcriptional regulator NrdR

Probab=93.64  E-value=0.072  Score=40.81  Aligned_cols=30  Identities=30%  Similarity=0.742  Sum_probs=22.8

Q ss_pred             CCCCCCCCCCceeEeC---CCCceE-----eCCCceee
Q 030129            4 AFCSDCKKHTEVVFDH---SAGDTV-----CSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~---~~G~~v-----C~~CG~Vl   33 (182)
                      |+||.|+....-|.|+   +.|..|     |..||.=+
T Consensus         1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF   38 (147)
T TIGR00244         1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF   38 (147)
T ss_pred             CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence            6799999866667786   667655     99998754

Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.

>PRK10220 hypothetical protein; Provisional

Probab=92.94  E-value=0.09  Score=38.19  Aligned_cols=30  Identities=23%  Similarity=0.523  Sum_probs=21.8

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      |+.-.||.|.+ .-.-.  +...+||.+||.--
T Consensus         1 m~lP~CP~C~s-eytY~--d~~~~vCpeC~hEW   30 (111)
T PRK10220          1 MSLPHCPKCNS-EYTYE--DNGMYICPECAHEW   30 (111)
T ss_pred             CCCCcCCCCCC-cceEc--CCCeEECCcccCcC
Confidence            77889999997 33223  34569999999643

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=92.92  E-value=0.067  Score=39.97  Aligned_cols=31  Identities=13%  Similarity=0.288  Sum_probs=25.8

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH   36 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~   36 (182)
                      ...||.||..   .+|-..--++|..||.++...
T Consensus         9 Kr~Cp~cg~k---FYDLnk~p~vcP~cg~~~~~~   39 (129)
T TIGR02300         9 KRICPNTGSK---FYDLNRRPAVSPYTGEQFPPE   39 (129)
T ss_pred             cccCCCcCcc---ccccCCCCccCCCcCCccCcc
Confidence            4679999972   589888899999999998644

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=92.54  E-value=0.08  Score=33.39  Aligned_cols=31  Identities=23%  Similarity=0.283  Sum_probs=20.1

Q ss_pred             CCCCCCCCCCceeE---eC--CCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVF---DH--SAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~---D~--~~G~~vC~~CG~Vl~   34 (182)
                      ..||.||+....+.   +.  ..|...|..||....
T Consensus         2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~   37 (53)
T TIGR03655         2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP   37 (53)
T ss_pred             CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence            46999998433132   32  334457999999864

Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=92.45  E-value=0.08  Score=37.81  Aligned_cols=28  Identities=32%  Similarity=0.739  Sum_probs=21.5

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      ..||.||+  .+  .+..+.++|..||.+.+.
T Consensus         1 ~fC~~Cg~--~l--~~~~~~~~C~~C~~~~~~   28 (104)
T TIGR01384         1 KFCPKCGS--LM--TPKNGVYVCPSCGYEKEK   28 (104)
T ss_pred             CCCcccCc--cc--ccCCCeEECcCCCCcccc
Confidence            37999996  22  456789999999998653

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=91.85  E-value=0.16  Score=37.23  Aligned_cols=25  Identities=32%  Similarity=0.679  Sum_probs=20.0

Q ss_pred             CCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129            6 CSDCKKHTEVVFDHSAGDTVCSECGLVLESH   36 (182)
Q Consensus         6 Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~   36 (182)
                      ||.||+ .-.|+     .+-|.+||+.|+-+
T Consensus         1 CPvCg~-~l~vt-----~l~C~~C~t~i~G~   25 (113)
T PF09862_consen    1 CPVCGG-ELVVT-----RLKCPSCGTEIEGE   25 (113)
T ss_pred             CCCCCC-ceEEE-----EEEcCCCCCEEEee
Confidence            999997 44454     59999999999644

>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=91.78  E-value=0.13  Score=36.19  Aligned_cols=29  Identities=31%  Similarity=0.524  Sum_probs=24.8

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ..||.||+ .. +.....|-.-|..||.++.
T Consensus        36 y~Cp~Cgk-~~-vkR~a~GIW~C~~C~~~~A   64 (90)
T PF01780_consen   36 YTCPFCGK-TS-VKRVATGIWKCKKCGKKFA   64 (90)
T ss_dssp             BEESSSSS-SE-EEEEETTEEEETTTTEEEE
T ss_pred             CcCCCCCC-ce-eEEeeeEEeecCCCCCEEe
Confidence            46999997 44 6788999999999999984

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....

>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]

Probab=91.46  E-value=0.11  Score=35.47  Aligned_cols=29  Identities=34%  Similarity=0.751  Sum_probs=26.1

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      .+||.|-. ...++.++...++|.+|+.|+
T Consensus        35 VkC~gc~~-iT~vfSHaqtvVvc~~c~~il   63 (84)
T KOG1779|consen   35 VKCPGCFK-ITTVFSHAQTVVVCEGCSTIL   63 (84)
T ss_pred             EEcCCceE-EEEEeecCceEEEcCCCceEE
Confidence            57999986 567899999999999999997

>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

Probab=91.33  E-value=0.15  Score=37.33  Aligned_cols=34  Identities=29%  Similarity=0.579  Sum_probs=23.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH   36 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~   36 (182)
                      +..||.||+---.-.|...+.++|..||...+-.
T Consensus         2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~   35 (113)
T COG1594           2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS   35 (113)
T ss_pred             ccccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence            5789999972111123356789999999987644

>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins

Probab=91.28  E-value=0.18  Score=33.17  Aligned_cols=29  Identities=21%  Similarity=0.576  Sum_probs=21.2

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ..||.||.. . ..+.......|..||...+
T Consensus        29 q~C~~CG~~-~-~~~~~~r~~~C~~Cg~~~~   57 (69)
T PF07282_consen   29 QTCPRCGHR-N-KKRRSGRVFTCPNCGFEMD   57 (69)
T ss_pred             cCccCcccc-c-ccccccceEEcCCCCCEEC
Confidence            569999963 2 2245667899999999864

More information about these proteins can be found at Protein of the Month: Transposase [].

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=90.79  E-value=0.12  Score=30.23  Aligned_cols=28  Identities=21%  Similarity=0.665  Sum_probs=20.5

Q ss_pred             CCCCCCCCCCceeEeC-----CCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDH-----SAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~-----~~G~~vC~~CG~Vl   33 (182)
                      ..||+|+..  ..+++     ..+..-|..||.++
T Consensus         3 i~CP~C~~~--f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    3 ITCPNCQTR--FRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EECCCCCce--EEcCHHHcccCCcEEECCCCCcEe
Confidence            469999963  33332     46779999999986

>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc

Probab=90.43  E-value=0.31  Score=29.70  Aligned_cols=27  Identities=22%  Similarity=0.469  Sum_probs=20.2

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGL   31 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~   31 (182)
                      ..||.||+ ..+..-...+..-|.+|+.
T Consensus        19 ~~CP~Cg~-~~~~~~~~~~~~~C~~C~~   45 (46)
T PF12760_consen   19 FVCPHCGS-TKHYRLKTRGRYRCKACRK   45 (46)
T ss_pred             CCCCCCCC-eeeEEeCCCCeEECCCCCC
Confidence            46999998 4544444569999999974

It may be a zinc-binding beta ribbon domain that could bind DNA.

>PRK12495 hypothetical protein; Provisional

Probab=90.32  E-value=0.19  Score=40.93  Aligned_cols=31  Identities=29%  Similarity=0.812  Sum_probs=24.8

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129            1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      |....|+.||. + | + -..|.++|..|+.++.+
T Consensus        40 msa~hC~~CG~-P-I-p-a~pG~~~Cp~CQ~~~~~   70 (226)
T PRK12495         40 MTNAHCDECGD-P-I-F-RHDGQEFCPTCQQPVTE   70 (226)
T ss_pred             cchhhcccccC-c-c-c-CCCCeeECCCCCCcccc
Confidence            56678999997 3 3 3 45899999999999875

>PTZ00255 60S ribosomal protein L37a; Provisional

Probab=90.12  E-value=0.26  Score=34.75  Aligned_cols=29  Identities=28%  Similarity=0.528  Sum_probs=24.3

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ..||.||+ .. +.....|-..|..||.++.
T Consensus        37 y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~A   65 (90)
T PTZ00255         37 YFCPFCGK-HA-VKRQAVGIWRCKGCKKTVA   65 (90)
T ss_pred             ccCCCCCC-Cc-eeeeeeEEEEcCCCCCEEe
Confidence            57999997 44 5677889999999999984

>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2

Probab=90.12  E-value=0.054  Score=31.63  Aligned_cols=29  Identities=28%  Similarity=0.718  Sum_probs=20.3

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      .||.||..-++.+++..-+.+|..||.-|
T Consensus         3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L   31 (36)
T PF05191_consen    3 ICPKCGRIYHIEFNPPKVEGVCDNCGGEL   31 (36)
T ss_dssp             EETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred             CcCCCCCccccccCCCCCCCccCCCCCee
Confidence            58888875566777777778888888754

7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=90.09  E-value=0.15  Score=29.83  Aligned_cols=30  Identities=33%  Similarity=0.545  Sum_probs=19.2

Q ss_pred             CCCCCCCCCCceeEeCC-CCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHS-AGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~-~G~~vC~~CG~Vl   33 (182)
                      .+|++||..-++..... .....|..||.-+
T Consensus         6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~   36 (41)
T smart00834        6 YRCEDCGHTFEVLQKISDDPLATCPECGGDV   36 (41)
T ss_pred             EEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence            47999996323333322 4567899999843

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]

Probab=89.93  E-value=0.3  Score=35.39  Aligned_cols=33  Identities=24%  Similarity=0.697  Sum_probs=24.2

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129            1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH   36 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~   36 (182)
                      |+...||.|.+  +.+++ +.+.++|.+|+.--.+.
T Consensus         1 ~~lp~cp~c~s--EytYe-d~~~~~cpec~~ew~~~   33 (112)
T COG2824           1 MSLPPCPKCNS--EYTYE-DGGQLICPECAHEWNEN   33 (112)
T ss_pred             CCCCCCCccCC--ceEEe-cCceEeCchhccccccc
Confidence            56778999996  45554 45589999999765433

>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]

Probab=89.83  E-value=0.21  Score=35.83  Aligned_cols=29  Identities=34%  Similarity=0.865  Sum_probs=22.2

Q ss_pred             CCCCCCCCCcee---EeC--CCCceEeCCCceeee
Q 030129            5 FCSDCKKHTEVV---FDH--SAGDTVCSECGLVLE   34 (182)
Q Consensus         5 ~Cp~Cg~~~~iv---~D~--~~G~~vC~~CG~Vl~   34 (182)
                      .||.||. ..++   ++-  .-|..+|..||+-.+
T Consensus        24 tCp~Cgh-e~vs~ctvkk~~~~g~~~Cg~CGls~e   57 (104)
T COG4888          24 TCPRCGH-EKVSSCTVKKTVNIGTAVCGNCGLSFE   57 (104)
T ss_pred             ecCccCC-eeeeEEEEEecCceeEEEcccCcceEE
Confidence            5999997 4444   443  668899999999875

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=89.53  E-value=0.19  Score=36.10  Aligned_cols=30  Identities=27%  Similarity=0.612  Sum_probs=22.3

Q ss_pred             CCCCCCCCCCce--eEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEV--VFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~i--v~D~~~G~~vC~~CG~Vl~   34 (182)
                      ..||+||. ..+  -.|...+..+|..||...+
T Consensus        22 f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y~~   53 (99)
T PRK14892         22 FECPRCGK-VSISVKIKKNIAIITCGNCGLYTE   53 (99)
T ss_pred             eECCCCCC-eEeeeecCCCcceEECCCCCCccC
Confidence            35999995 332  2455778899999999865

>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]

Probab=89.07  E-value=0.28  Score=37.73  Aligned_cols=30  Identities=30%  Similarity=0.635  Sum_probs=20.5

Q ss_pred             CCCCCCCCCCceeEeC---CCCc-----eEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDH---SAGD-----TVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~---~~G~-----~vC~~CG~Vl   33 (182)
                      |+||.|+....-|.|+   +.|.     -.|.+||.=+
T Consensus         1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RF   38 (156)
T COG1327           1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERF   38 (156)
T ss_pred             CCCCCCCCCCCeeeecccccccchhhhhhccccccccc
Confidence            6799999855556675   4454     3588888643

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=88.99  E-value=0.86  Score=39.39  Aligned_cols=49  Identities=10%  Similarity=0.053  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHhCChHHH-HHHHHHHHHHhc-----c---CHHHHHHHHHHHHHhhC
Q 030129          107 LAFKTIATMSDRIGQMRYI-RRWKIKSLVEAE-----I---KTHYWLLACTLLVDKKT  155 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~~v-~~~~i~k~a~~~-----l---~~~~v~AAclY~acr~~  155 (182)
                      ...+.|-.+-..|+||++. +.+..+.-+.+.     +   +++.||+||+|+|.|..
T Consensus       140 hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~  197 (367)
T KOG0835|consen  140 HPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNL  197 (367)
T ss_pred             ccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhh
Confidence            3446677888888998876 222333333333     2   99999999999999976

>TIGR00280 L37a ribosomal protein L37a

Probab=88.99  E-value=0.31  Score=34.36  Aligned_cols=29  Identities=31%  Similarity=0.565  Sum_probs=24.5

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ..||.|+. .. +.....|-..|..||.++.
T Consensus        36 y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~A   64 (91)
T TIGR00280        36 YVCPFCGK-KT-VKRGSTGIWTCRKCGAKFA   64 (91)
T ss_pred             ccCCCCCC-Cc-eEEEeeEEEEcCCCCCEEe
Confidence            57999997 44 5677999999999999974

This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.

>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA

Probab=88.53  E-value=0.43  Score=34.68  Aligned_cols=28  Identities=18%  Similarity=0.496  Sum_probs=19.7

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      -.||.|++ .-.-.|  ...+||.+||.--.
T Consensus         3 p~CP~C~s-eytY~d--g~~~iCpeC~~EW~   30 (109)
T TIGR00686         3 PPCPKCNS-EYTYHD--GTQLICPSCLYEWN   30 (109)
T ss_pred             CcCCcCCC-cceEec--CCeeECcccccccc
Confidence            46999997 333333  44699999998654

The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=88.44  E-value=0.31  Score=31.64  Aligned_cols=26  Identities=31%  Similarity=0.754  Sum_probs=12.7

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGLV   32 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V   32 (182)
                      .|..||.  .|-.+..--...|.+||.+
T Consensus        11 ~CtSCg~--~i~p~e~~v~F~CPnCGe~   36 (61)
T COG2888          11 VCTSCGR--EIAPGETAVKFPCPNCGEV   36 (61)
T ss_pred             eeccCCC--EeccCCceeEeeCCCCCce
Confidence            5666664  2222322233567777743

>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines

Probab=88.14  E-value=0.22  Score=34.33  Aligned_cols=32  Identities=25%  Similarity=0.564  Sum_probs=17.6

Q ss_pred             CCCCCCCCCce--eEeC--CCCceEeCCCceeeeCC
Q 030129            5 FCSDCKKHTEV--VFDH--SAGDTVCSECGLVLESH   36 (182)
Q Consensus         5 ~Cp~Cg~~~~i--v~D~--~~G~~vC~~CG~Vl~e~   36 (182)
                      .||.|+....+  ..|.  ..|.+.|..||...+-.
T Consensus        24 ~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~   59 (81)
T PF05129_consen   24 DCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK   59 (81)
T ss_dssp             --TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred             cCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence            59999943333  3344  46789999999998643

; PDB: 1WII_A.

>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed

Probab=87.99  E-value=0.39  Score=33.82  Aligned_cols=29  Identities=24%  Similarity=0.559  Sum_probs=24.3

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ..||.|++ .. +.....|-.-|..||.++.
T Consensus        37 y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~A   65 (90)
T PRK03976         37 HVCPVCGR-PK-VKRVGTGIWECRKCGAKFA   65 (90)
T ss_pred             ccCCCCCC-Cc-eEEEEEEEEEcCCCCCEEe
Confidence            57999986 44 5677899999999999985

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=87.98  E-value=0.43  Score=29.07  Aligned_cols=27  Identities=30%  Similarity=0.720  Sum_probs=19.3

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ..|.+||.  ++..+ ..+.+-|.+||.=|
T Consensus         3 Y~C~~Cg~--~~~~~-~~~~irC~~CG~rI   29 (44)
T smart00659        3 YICGECGR--ENEIK-SKDVVRCRECGYRI   29 (44)
T ss_pred             EECCCCCC--EeecC-CCCceECCCCCceE
Confidence            46999997  33333 56779999999644

present in RNA polymerase I, II and III

>COG4640 Predicted membrane protein [Function unknown]

Probab=87.77  E-value=0.28  Score=43.31  Aligned_cols=28  Identities=29%  Similarity=0.800  Sum_probs=20.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH   36 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~   36 (182)
                      |..||.||+. .     .+++.-|+.||.-+..+
T Consensus         1 M~fC~kcG~q-k-----~Ed~~qC~qCG~~~t~~   28 (465)
T COG4640           1 MKFCPKCGSQ-K-----AEDDVQCTQCGHKFTSR   28 (465)
T ss_pred             CCcccccccc-c-----ccccccccccCCcCCch
Confidence            4689999973 2     35677799999876533

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=87.33  E-value=0.62  Score=27.68  Aligned_cols=27  Identities=30%  Similarity=0.596  Sum_probs=18.5

Q ss_pred             CCCCCCCCCceeEe------CC---CCceEeCCCcee
Q 030129            5 FCSDCKKHTEVVFD------HS---AGDTVCSECGLV   32 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D------~~---~G~~vC~~CG~V   32 (182)
                      .||.||. .+.++-      .+   +-.++|.+||..
T Consensus         2 ~Cp~C~~-~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~   37 (40)
T smart00440        2 PCPKCGN-REATFFQLQTRSADEPMTVFYVCTKCGHR   37 (40)
T ss_pred             cCCCCCC-CeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence            6999997 455431      12   336899999965

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=87.26  E-value=0.63  Score=30.67  Aligned_cols=28  Identities=21%  Similarity=0.398  Sum_probs=18.8

Q ss_pred             CCCCCCCCCCceeEeCCCCc--eEeCCCcee
Q 030129            4 AFCSDCKKHTEVVFDHSAGD--TVCSECGLV   32 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~--~vC~~CG~V   32 (182)
                      ..||.||.. .+..-...|-  .+|..||..
T Consensus         7 KPCPFCG~~-~~~v~~~~g~~~v~C~~CgA~   36 (64)
T PRK09710          7 KPCPFCGCP-SVTVKAISGYYRAKCNGCESR   36 (64)
T ss_pred             cCCCCCCCc-eeEEEecCceEEEEcCCCCcC
Confidence            469999984 3333333443  689999985

>PRK05978 hypothetical protein; Provisional

Probab=87.19  E-value=0.42  Score=36.74  Aligned_cols=32  Identities=19%  Similarity=0.445  Sum_probs=21.4

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH   36 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~   36 (182)
                      .+||.||. ..+..-+-.=..-|..||+-++-.
T Consensus        34 grCP~CG~-G~LF~g~Lkv~~~C~~CG~~~~~~   65 (148)
T PRK05978         34 GRCPACGE-GKLFRAFLKPVDHCAACGEDFTHH   65 (148)
T ss_pred             CcCCCCCC-CcccccccccCCCccccCCccccC
Confidence            47999997 555332233346799999987533

>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=87.18  E-value=1.5  Score=30.86  Aligned_cols=66  Identities=12%  Similarity=0.082  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHhCChHHHHHH--HHHHHH-Hhc-c---CHHHHHHHHHHHHHhhCC------HHHHHhcCCCceeeece
Q 030129          108 AFKTIATMSDRIGQMRYIRRW--KIKSLV-EAE-I---KTHYWLLACTLLVDKKTS------HALLRKSALSPMELQRR  173 (182)
Q Consensus       108 a~~~I~~i~~~L~L~~~v~~~--~i~k~a-~~~-l---~~~~v~AAclY~acr~~~------~eia~~~~v~~~~i~r~  173 (182)
                      .+..|+.+....+....+...  .+...+ .+. |   +|..+||||+|+|.+..+      ..+...++++..+|-..
T Consensus         3 p~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c   81 (118)
T PF02984_consen    3 PYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKEC   81 (118)
T ss_dssp             HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHH
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHH
Confidence            456777774444444455555  444554 333 3   999999999999998742      45666777766665443

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=86.91  E-value=0.79  Score=30.96  Aligned_cols=31  Identities=13%  Similarity=0.308  Sum_probs=21.8

Q ss_pred             CCCCCCCCCCCceeEeC-------CCCceEeC--CCceeee
Q 030129            3 DAFCSDCKKHTEVVFDH-------SAGDTVCS--ECGLVLE   34 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~-------~~G~~vC~--~CG~Vl~   34 (182)
                      ++.||.||. ...|.+.       .+=...|+  +||..+-
T Consensus         1 mm~CP~Cg~-~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~   40 (72)
T PRK09678          1 MFHCPLCQH-AAHARTSRYITDTTKERYHQCQNVNCSATFI   40 (72)
T ss_pred             CccCCCCCC-ccEEEEChhcChhhheeeeecCCCCCCCEEE
Confidence            478999998 4566664       22236788  8998764

>PF12773 DZR: Double zinc ribbon

Probab=86.76  E-value=0.36  Score=29.65  Aligned_cols=11  Identities=27%  Similarity=0.863  Sum_probs=5.6

Q ss_pred             ceEeCCCceee
Q 030129           23 DTVCSECGLVL   33 (182)
Q Consensus        23 ~~vC~~CG~Vl   33 (182)
                      ..+|..||..+
T Consensus        29 ~~~C~~Cg~~~   39 (50)
T PF12773_consen   29 KKICPNCGAEN   39 (50)
T ss_pred             CCCCcCCcCCC
Confidence            44555555543

>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.71  E-value=0.72  Score=25.30  Aligned_cols=22  Identities=23%  Similarity=0.540  Sum_probs=11.8

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCC
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSE   28 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~   28 (182)
                      .||.||+  .++...+.-.+.|.+
T Consensus         1 ~CP~C~s--~l~~~~~ev~~~C~N   22 (28)
T PF03119_consen    1 TCPVCGS--KLVREEGEVDIRCPN   22 (28)
T ss_dssp             B-TTT----BEEE-CCTTCEEE--
T ss_pred             CcCCCCC--EeEcCCCCEeEECCC
Confidence            5999996  566666666788864

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.

>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.65  E-value=0.78  Score=27.05  Aligned_cols=27  Identities=33%  Similarity=0.607  Sum_probs=15.1

Q ss_pred             CCCCCCCCCceeEe-C-----C---CCceEeCCCcee
Q 030129            5 FCSDCKKHTEVVFD-H-----S---AGDTVCSECGLV   32 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D-~-----~---~G~~vC~~CG~V   32 (182)
                      .||.||.. +.++- .     +   +-.++|.+||..
T Consensus         2 ~Cp~Cg~~-~a~~~~~Q~rsaDE~~T~fy~C~~C~~~   37 (39)
T PF01096_consen    2 KCPKCGHN-EAVFFQIQTRSADEPMTLFYVCCNCGHR   37 (39)
T ss_dssp             --SSS-SS-EEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred             CCcCCCCC-eEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence            69999974 44332 1     2   224889999975

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=86.45  E-value=3.4  Score=35.81  Aligned_cols=55  Identities=15%  Similarity=0.087  Sum_probs=44.4

Q ss_pred             chHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHH-Hhc-c---CHHHHHHHHHHHHHhhC
Q 030129          101 PDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLV-EAE-I---KTHYWLLACTLLVDKKT  155 (182)
Q Consensus       101 ~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a-~~~-l---~~~~v~AAclY~acr~~  155 (182)
                      .+--..-+-..|++-+=-|+||+...-+  -||... ... |   ..+.++.|||.+|++.+
T Consensus        19 e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiE   80 (367)
T KOG0835|consen   19 EEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIE   80 (367)
T ss_pred             HHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhc
Confidence            3444466899999999999999987666  566554 555 5   89999999999999987

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=85.41  E-value=0.2  Score=39.59  Aligned_cols=29  Identities=31%  Similarity=0.796  Sum_probs=20.8

Q ss_pred             CCCCCCCCCceeE-eCCCCceEeCCCceeeeC
Q 030129            5 FCSDCKKHTEVVF-DHSAGDTVCSECGLVLES   35 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~-D~~~G~~vC~~CG~Vl~e   35 (182)
                      .||.|+.  ...+ |.-+....|..||.++.+
T Consensus       119 ~Cp~C~~--rytf~eA~~~~F~Cp~Cg~~L~~  148 (178)
T PRK06266        119 FCPNCHI--RFTFDEAMEYGFRCPQCGEMLEE  148 (178)
T ss_pred             ECCCCCc--EEeHHHHhhcCCcCCCCCCCCee
Confidence            5999986  2333 334567899999999864

>PRK08402 replication factor A; Reviewed

Probab=85.40  E-value=0.63  Score=40.71  Aligned_cols=27  Identities=30%  Similarity=0.767  Sum_probs=22.1

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV   32 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V   32 (182)
                      ..||.|++  .++.|...|...|..||.|
T Consensus       213 ~aCp~CnK--kv~~~~~~~~~~Ce~~~~v  239 (355)
T PRK08402        213 DACPECRR--KVDYDPATDTWICPEHGEV  239 (355)
T ss_pred             ecCCCCCe--EEEEecCCCCEeCCCCCCc
Confidence            36999986  4555888899999999975

>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG

Probab=85.24  E-value=0.67  Score=29.30  Aligned_cols=29  Identities=34%  Similarity=0.696  Sum_probs=21.4

Q ss_pred             CCCCCCCCCceeEeCCCCc----eEeCCCceee
Q 030129            5 FCSDCKKHTEVVFDHSAGD----TVCSECGLVL   33 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~----~vC~~CG~Vl   33 (182)
                      .||+||....+..|.+.|+    -=|.-|-.=+
T Consensus         2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI   34 (52)
T PF14255_consen    2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPI   34 (52)
T ss_pred             CCCCCCCeeEEEEecCCCCeeEEeehhhcCCcc
Confidence            6999998778888998886    2366666543

>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150

Probab=85.21  E-value=0.95  Score=32.63  Aligned_cols=31  Identities=23%  Similarity=0.518  Sum_probs=20.3

Q ss_pred             CCCCCCCCCCCceeEe------CC--C-Cc-eEeCCCceeee
Q 030129            3 DAFCSDCKKHTEVVFD------HS--A-GD-TVCSECGLVLE   34 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D------~~--~-G~-~vC~~CG~Vl~   34 (182)
                      ...||+||. ..+..+      ..  . .. ++|+.|+.-+.
T Consensus         2 p~~CpYCg~-~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG   42 (102)
T PF11672_consen    2 PIICPYCGG-PAELVDGSEIYGHRYDDGPYLYVCTPCDAYVG   42 (102)
T ss_pred             CcccCCCCC-eeEEcccchhcCccCCCCceeEECCCCCceee
Confidence            468999998 344444      11  2 22 78999988775

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK02935 hypothetical protein; Provisional

Probab=85.11  E-value=0.64  Score=33.63  Aligned_cols=38  Identities=26%  Similarity=0.581  Sum_probs=24.4

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCccccccccccc
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFA   48 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~   48 (182)
                      ..||+|++.+.+.=+    ...|-.|+.-+.   +|.+.|-..|+
T Consensus        71 V~CP~C~K~TKmLGr----vD~CM~C~~PLT---Ld~~legkefd  108 (110)
T PRK02935         71 VICPSCEKPTKMLGR----VDACMHCNQPLT---LDRSLEGKEFD  108 (110)
T ss_pred             eECCCCCchhhhccc----eeecCcCCCcCC---cCccccccCcC
Confidence            469999986554322    358999998874   45444433444

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=85.00  E-value=0.56  Score=26.64  Aligned_cols=24  Identities=29%  Similarity=0.715  Sum_probs=15.9

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCce
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGL   31 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~   31 (182)
                      .|.+||..   +.+.....+-|..||.
T Consensus         2 ~C~~Cg~~---~~~~~~~~irC~~CG~   25 (32)
T PF03604_consen    2 ICGECGAE---VELKPGDPIRCPECGH   25 (32)
T ss_dssp             BESSSSSS---E-BSTSSTSSBSSSS-
T ss_pred             CCCcCCCe---eEcCCCCcEECCcCCC
Confidence            58899862   2244556688999985

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>PF15616 TerY-C: TerY-C metal binding domain

Probab=83.84  E-value=0.71  Score=34.77  Aligned_cols=9  Identities=22%  Similarity=0.733  Sum_probs=6.9

Q ss_pred             CCCCCCCCC
Q 030129            4 AFCSDCKKH   12 (182)
Q Consensus         4 ~~Cp~Cg~~   12 (182)
                      --||+||..
T Consensus        78 PgCP~CGn~   86 (131)
T PF15616_consen   78 PGCPHCGNQ   86 (131)
T ss_pred             CCCCCCcCh
Confidence            459999973

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=83.79  E-value=0.5  Score=43.70  Aligned_cols=43  Identities=21%  Similarity=0.596  Sum_probs=28.8

Q ss_pred             CCCCCCCCCCcee-----E----eCCCCceEeCCCceeeeCCC---ccccccccc
Q 030129            4 AFCSDCKKHTEVV-----F----DHSAGDTVCSECGLVLESHS---IDETSEWRT   46 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv-----~----D~~~G~~vC~~CG~Vl~e~~---id~~~ewr~   46 (182)
                      ..||+||....+.     .    ++.+-.++|..||..++|+-   +...-+|+.
T Consensus       201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~  255 (557)
T PF05876_consen  201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVA  255 (557)
T ss_pred             ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEe
Confidence            4699999643332     2    24566799999999998753   223457764

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]

Probab=83.51  E-value=3.1  Score=35.69  Aligned_cols=45  Identities=7%  Similarity=0.060  Sum_probs=35.2

Q ss_pred             CChHHHHHH--HHHHHHH-hc--c--CHHHHHHHHHHHHHhhCC-----HHHHHhcC
Q 030129          120 GQMRYIRRW--KIKSLVE-AE--I--KTHYWLLACTLLVDKKTS-----HALLRKSA  164 (182)
Q Consensus       120 ~L~~~v~~~--~i~k~a~-~~--l--~~~~v~AAclY~acr~~~-----~eia~~~~  164 (182)
                      .||..|+-+  .+|+++. ..  .  +|..|+++|+|+||+...     .+|+.-..
T Consensus        73 ~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~  129 (325)
T KOG2496|consen   73 NLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN  129 (325)
T ss_pred             CCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc
Confidence            789999888  8899884 33  2  999999999999999763     45555443

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=82.92  E-value=0.62  Score=28.85  Aligned_cols=28  Identities=29%  Similarity=0.567  Sum_probs=16.4

Q ss_pred             CCCCCCCCCCceeEe-CCCCceEeCCCce
Q 030129            4 AFCSDCKKHTEVVFD-HSAGDTVCSECGL   31 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D-~~~G~~vC~~CG~   31 (182)
                      .+|++||..-++... .+.....|..||.
T Consensus         6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~   34 (52)
T TIGR02605         6 YRCTACGHRFEVLQKMSDDPLATCPECGG   34 (52)
T ss_pred             EEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence            468888852232221 1235567888886

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

>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing

Probab=82.80  E-value=1.4  Score=33.20  Aligned_cols=27  Identities=30%  Similarity=0.740  Sum_probs=19.4

Q ss_pred             CCC--CCCCCCceeEeCCCCceEeCCCceeee
Q 030129            5 FCS--DCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         5 ~Cp--~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      .||  .|++  .+..+ ..|.+.|..||..++
T Consensus        20 aC~~~~C~k--Kv~~~-~~~~y~C~~C~~~~~   48 (146)
T PF08646_consen   20 ACPNEKCNK--KVTEN-GDGSYRCEKCNKTVE   48 (146)
T ss_dssp             E-TSTTTS---B-EEE-TTTEEEETTTTEEES
T ss_pred             CCCCccCCC--EeecC-CCcEEECCCCCCcCC
Confidence            499  9997  35555 779999999999873

It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=82.70  E-value=0.57  Score=27.20  Aligned_cols=29  Identities=31%  Similarity=0.722  Sum_probs=19.2

Q ss_pred             CCCCCCCCCCceeEe----CCCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFD----HSAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D----~~~G~~vC~~CG~Vl   33 (182)
                      ..||+|+..-. |-|    .....+-|+.||.++
T Consensus         3 i~Cp~C~~~y~-i~d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    3 ITCPNCQAKYE-IDDEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             EECCCCCCEEe-CCHHHCCCCCcEEECCCCCCEe
Confidence            46999996322 222    244568899999875

>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]

Probab=82.34  E-value=0.99  Score=29.78  Aligned_cols=13  Identities=23%  Similarity=0.445  Sum_probs=9.0

Q ss_pred             CCCCCCCCCceeEe
Q 030129            5 FCSDCKKHTEVVFD   18 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D   18 (182)
                      +||.||. ++..++
T Consensus         6 kCpKCgn-~~~~ek   18 (68)
T COG3478           6 KCPKCGN-TNYEEK   18 (68)
T ss_pred             cCCCcCC-cchhhc
Confidence            4999997 455444

>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=82.08  E-value=0.67  Score=34.37  Aligned_cols=36  Identities=22%  Similarity=0.483  Sum_probs=23.0

Q ss_pred             CCCCCCCCCceeEe-CCCCceEeCCCceeeeCCCccccc
Q 030129            5 FCSDCKKHTEVVFD-HSAGDTVCSECGLVLESHSIDETS   42 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D-~~~G~~vC~~CG~Vl~e~~id~~~   42 (182)
                      .||+||. ..+ +| .-.=--.|..||.=+..+--|++|
T Consensus        23 rCP~CGe-GrL-F~gFLK~~p~C~aCG~dyg~~~a~DgP   59 (126)
T COG5349          23 RCPRCGE-GRL-FRGFLKVVPACEACGLDYGFADADDGP   59 (126)
T ss_pred             CCCCCCC-chh-hhhhcccCchhhhccccccCCcccCCC
Confidence            6999996 443 33 222336899999887655444444

>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=82.07  E-value=0.83  Score=25.11  Aligned_cols=28  Identities=18%  Similarity=0.372  Sum_probs=15.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGL   31 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~   31 (182)
                      .+||.|+....-+.....+..+|..|=-
T Consensus         2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq~   29 (30)
T PF06827_consen    2 EKCPRCWNYIEDIGINGRSTYLCPRCQK   29 (30)
T ss_dssp             SB-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred             CcCccCCCcceEeEecCCCCeECcCCcC
Confidence            4799999743334445677799998843

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....

>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ]

Probab=81.74  E-value=0.37  Score=30.28  Aligned_cols=32  Identities=16%  Similarity=0.359  Sum_probs=22.8

Q ss_pred             CCCCCCCCCCCCCcee-EeCCCCceEeCCCceee
Q 030129            1 MTDAFCSDCKKHTEVV-FDHSAGDTVCSECGLVL   33 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv-~D~~~G~~vC~~CG~Vl   33 (182)
                      |....|++|++- =.. -+....++-|..||.+-
T Consensus         2 ~~eiRC~~Cnkl-La~~g~~~~leIKCpRC~tiN   34 (51)
T PF10122_consen    2 LKEIRCGHCNKL-LAKAGEVIELEIKCPRCKTIN   34 (51)
T ss_pred             CcceeccchhHH-HhhhcCccEEEEECCCCCccc
Confidence            356789999862 111 24566889999999995

>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70)

Probab=81.71  E-value=1.1  Score=34.44  Aligned_cols=26  Identities=27%  Similarity=0.760  Sum_probs=20.0

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      .||.|++  .+ .+...|.+.|..|+..+
T Consensus        36 aC~~C~k--kv-~~~~~~~~~C~~C~~~~   61 (166)
T cd04476          36 ACPGCNK--KV-VEEGNGTYRCEKCNKSV   61 (166)
T ss_pred             cccccCc--cc-EeCCCCcEECCCCCCcC
Confidence            5999997  23 34444899999999886

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun

>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]

Probab=81.58  E-value=3.6  Score=36.60  Aligned_cols=48  Identities=15%  Similarity=0.083  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHhCChHHHHHH--HHHHH-HHhc-c---CHHHHHHHHHHHHHhhC
Q 030129          108 AFKTIATMSDRIGQMRYIRRW--KIKSL-VEAE-I---KTHYWLLACTLLVDKKT  155 (182)
Q Consensus       108 a~~~I~~i~~~L~L~~~v~~~--~i~k~-a~~~-l---~~~~v~AAclY~acr~~  155 (182)
                      ..+++.++....+|....+-+  -+|.+ +.+. +   +....|.|||.+|.+.+
T Consensus       385 lKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmn  439 (497)
T KOG4164|consen  385 LKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMN  439 (497)
T ss_pred             HHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhh
Confidence            445666666666776544444  55554 4666 4   88999999999999987

>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

Probab=81.37  E-value=0.56  Score=29.30  Aligned_cols=28  Identities=29%  Similarity=0.669  Sum_probs=21.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ..|-.||+  .+..|.....+-|+.||.=|
T Consensus         7 Y~C~~Cg~--~~~~~~~~~~irCp~Cg~rI   34 (49)
T COG1996           7 YKCARCGR--EVELDQETRGIRCPYCGSRI   34 (49)
T ss_pred             EEhhhcCC--eeehhhccCceeCCCCCcEE
Confidence            46999996  34446688889999999643

>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed

Probab=81.34  E-value=0.75  Score=29.55  Aligned_cols=24  Identities=21%  Similarity=0.522  Sum_probs=18.3

Q ss_pred             CCCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      .+.+|+.||. ..+       ..+|..||...
T Consensus         4 ~mr~C~~Cgv-YTL-------k~~CP~CG~~t   27 (56)
T PRK13130          4 KIRKCPKCGV-YTL-------KEICPVCGGKT   27 (56)
T ss_pred             cceECCCCCC-EEc-------cccCcCCCCCC
Confidence            3568999996 333       57999999775

>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins

Probab=81.06  E-value=1.6  Score=28.74  Aligned_cols=9  Identities=33%  Similarity=1.147  Sum_probs=7.7

Q ss_pred             eEeCCCcee
Q 030129           24 TVCSECGLV   32 (182)
Q Consensus        24 ~vC~~CG~V   32 (182)
                      ++|++||..
T Consensus        37 v~C~~CGYT   45 (64)
T PF09855_consen   37 VSCTNCGYT   45 (64)
T ss_pred             EECCCCCCE
Confidence            689999987

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=81.01  E-value=1.3  Score=25.10  Aligned_cols=23  Identities=30%  Similarity=0.807  Sum_probs=14.1

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCce
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGL   31 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~   31 (182)
                      .|+.||-    ++|.......|..||.
T Consensus         3 ~C~~CGy----~y~~~~~~~~CP~Cg~   25 (33)
T cd00350           3 VCPVCGY----IYDGEEAPWVCPVCGA   25 (33)
T ss_pred             ECCCCCC----EECCCcCCCcCcCCCC
Confidence            4777763    3455556667777765

The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PHA02942 putative transposase; Provisional

Probab=80.98  E-value=1.2  Score=39.30  Aligned_cols=28  Identities=18%  Similarity=0.480  Sum_probs=20.5

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ..||.||.. .  .+.......|..||.+.+
T Consensus       326 q~Cs~CG~~-~--~~l~~r~f~C~~CG~~~d  353 (383)
T PHA02942        326 VSCPKCGHK-M--VEIAHRYFHCPSCGYEND  353 (383)
T ss_pred             ccCCCCCCc-c--CcCCCCEEECCCCCCEeC
Confidence            569999962 2  244456799999999974

>PRK00241 nudC NADH pyrophosphatase; Reviewed

Probab=80.91  E-value=1.3  Score=36.99  Aligned_cols=29  Identities=17%  Similarity=0.450  Sum_probs=20.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ..+||.||+.  +......-...|..||.+.
T Consensus        99 ~~fC~~CG~~--~~~~~~~~~~~C~~c~~~~  127 (256)
T PRK00241         99 HRFCGYCGHP--MHPSKTEWAMLCPHCRERY  127 (256)
T ss_pred             CccccccCCC--CeecCCceeEECCCCCCEE
Confidence            4689999973  3334444558899999765

>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]

Probab=80.65  E-value=1.4  Score=31.49  Aligned_cols=31  Identities=23%  Similarity=0.515  Sum_probs=20.5

Q ss_pred             CCCCCCCCCCCceeEeCC-CCceEeCCCceeee
Q 030129            3 DAFCSDCKKHTEVVFDHS-AGDTVCSECGLVLE   34 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~-~G~~vC~~CG~Vl~   34 (182)
                      +..||.||+ .-+|+--+ -....|..|++|..
T Consensus         1 m~FCP~Cgn-~Live~g~~~~rf~C~tCpY~~~   32 (105)
T KOG2906|consen    1 MLFCPTCGN-MLIVESGESCNRFSCRTCPYVFP   32 (105)
T ss_pred             CcccCCCCC-EEEEecCCeEeeEEcCCCCceee
Confidence            358999996 32332222 25578999999964

>PRK12286 rpmF 50S ribosomal protein L32; Reviewed

Probab=80.47  E-value=0.9  Score=29.23  Aligned_cols=26  Identities=23%  Similarity=0.646  Sum_probs=17.4

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH   36 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~   36 (182)
                      ..||+||. ..      .--.+|..||+--+..
T Consensus        28 ~~C~~CG~-~~------~~H~vC~~CG~Y~gr~   53 (57)
T PRK12286         28 VECPNCGE-PK------LPHRVCPSCGYYKGRE   53 (57)
T ss_pred             eECCCCCC-cc------CCeEECCCCCcCCCEE
Confidence            46999996 22      1248999999765433

>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.44  E-value=1.5  Score=31.84  Aligned_cols=27  Identities=22%  Similarity=0.589  Sum_probs=21.9

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH   36 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~   36 (182)
                      ..||.||. ..||+     ++-|..|++-+.-+
T Consensus         7 ~~cPvcg~-~~iVT-----eL~c~~~etTVrg~   33 (122)
T COG3877           7 NRCPVCGR-KLIVT-----ELKCSNCETTVRGN   33 (122)
T ss_pred             CCCCcccc-cceeE-----EEecCCCCceEecc
Confidence            47999998 56776     59999999998644

>PRK12366 replication factor A; Reviewed

Probab=80.16  E-value=1.1  Score=42.18  Aligned_cols=25  Identities=36%  Similarity=0.954  Sum_probs=19.7

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV   32 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V   32 (182)
                      ..||.|++  .++ + ..|.+.|..||.+
T Consensus       533 ~aCp~Cnk--Kv~-~-~~g~~~C~~c~~~  557 (637)
T PRK12366        533 YLCPNCRK--RVE-E-VDGEYICEFCGEV  557 (637)
T ss_pred             ecccccCe--EeE-c-CCCcEECCCCCCC
Confidence            36999986  333 3 5799999999988

>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]

Probab=80.11  E-value=0.68  Score=37.06  Aligned_cols=31  Identities=32%  Similarity=0.587  Sum_probs=19.8

Q ss_pred             CCCCCCCCCCce--eEeCCCC---ceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEV--VFDHSAG---DTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~i--v~D~~~G---~~vC~~CG~Vl~e   35 (182)
                      +.||.|+. .++  .+=-..|   .+-|.+||+|-.+
T Consensus         7 ~~Cp~Cg~-eev~hEVik~~g~~~lvrC~eCG~V~~~   42 (201)
T COG1326           7 IECPSCGS-EEVSHEVIKERGREPLVRCEECGTVHPA   42 (201)
T ss_pred             EECCCCCc-chhhHHHHHhcCCceEEEccCCCcEeec
Confidence            46999994 333  1111223   4789999999855

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	182
3k7a_M	345	Crystal Structure Of An Rna Polymerase Ii-Tfiib Com		5e-13
1dl6_A	58	Solution Structure Of Human Tfiib N-Terminal Domain		7e-07
1rly_A	60	Rdc-Derived Models Of The Zinc Ribbon Domain Of Hum		1e-06
3k1f_M	197	Crystal Structure Of Rna Polymerase Ii In Complex W		3e-06
1pft_A	50	N-Terminal Domain Of Tfiib, Nmr Length = 50		8e-05

>pdb|3K7A|M Chain M, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex Length = 345

Iteration: 1
 Score = 70.5 bits (171), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 46/117 (39%), Positives = 61/117 (52%), Gaps = 7/117 (5%)
Query: 6   CSDCKKHT-EVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANE--SGDNDPVRVGGP 62
           C +CK +  ++V   S GD VC+ CGLVL    +D  SEWRTF+N+  +GD DP RVG  
Sbjct: 24  CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGD-DPSRVGEA 82
Query: 63  TNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSD 117
           +NPLL    LST I K       F +  L + Q +      D  +  AF  I  + D
Sbjct: 83  SNPLLDGNNLSTRIGKGETTDMRF-TKELNKAQGKNVMDKKDNEVQAAFAKITMLCD 138

>pdb|1DL6|A Chain A, Solution Structure Of Human Tfiib N-Terminal Domain Length = 58

Iteration: 1
 Score = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 28/44 (63%), Gaps = 2/44 (4%)
Query: 9  CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANE 50
          C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+
Sbjct: 14 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 57

>pdb|1RLY|A Chain A, Rdc-Derived Models Of The Zinc Ribbon Domain Of Human General Transcription Tfiib (Zinc Bound Structures) Length = 60

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 21/44 (47%), Positives = 28/44 (63%), Gaps = 2/44 (4%)
Query: 9  CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANE 50
          C  H + +   D+ AGD +C ECGLV+    ID  SEWRTF+N+
Sbjct: 15 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 58

>pdb|3K1F|M Chain M, Crystal Structure Of Rna Polymerase Ii In Complex With Tfiib Length = 197

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 29/45 (64%), Gaps = 1/45 (2%)
Query: 6  CSDCKKHT-EVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFAN 49
          C +CK +  ++V   S GD VC+ CGLVL    +D  SEWRTF+N
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSN 68

>pdb|1PFT|A Chain A, N-Terminal Domain Of Tfiib, Nmr Length = 50

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 6  CSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTF 47
          C  C+   E+++D   G+ VC++CG V+E + ID   EWR F
Sbjct: 8  CPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAF 48

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	182
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	2e-28
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	1e-27
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	2e-16
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	2e-15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-07

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197

 Score =  103 bits (258), Expect = 2e-28
 Identities = 22/45 (48%), Positives = 29/45 (64%), Gaps = 1/45 (2%)

Query: 6  CSDCKKH-TEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFAN 49
          C +CK +  ++V   S GD VC+ CGLVL    +D  SEWRTF+N
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSN 68

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae} Length = 345

 Score =  105 bits (261), Expect = 1e-27
 Identities = 44/119 (36%), Positives = 59/119 (49%), Gaps = 5/119 (4%)

Query: 6   CSDCKKH-TEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANE-SGDNDPVRVGGPT 63
           C +CK +  ++V   S GD VC+ CGLVL    +D  SEWRTF+N+    +DP RVG  +
Sbjct: 24  CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEAS 83

Query: 64  NPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNP--DRGLILAFKTIATMSDRIG 120
           NPLL    LST I K       F +  L + Q +      D  +  AF  I  + D   
Sbjct: 84  NPLLDGNNLSTRIGKGETTDMRF-TKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAE 141

>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A Length = 58

 Score = 68.8 bits (168), Expect = 2e-16
 Identities = 21/45 (46%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 6  CSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANE 50
          C +      +V D+ AGD +C ECGLV+    ID  SEWRTF+N+
Sbjct: 14 CPNHPD-AILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 57

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1 Length = 50

 Score = 66.0 bits (161), Expect = 2e-15
 Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 6  CSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTF 47
          C  C+   E+++D   G+ VC++CG V+E + ID   EWR F
Sbjct: 8  CPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAF 48

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 47.5 bits (112), Expect = 6e-07
 Identities = 38/199 (19%), Positives = 59/199 (29%), Gaps = 58/199 (29%)

Query: 3   DAFCSDCKKHTEV------VFDHSAGDTVCSECGLVLESHSI----DETSE-WRTFANES 51
           +AF   CK    +      V D  +  T      + L+ HS+    DE       + +  
Sbjct: 260 NAFNLSCK--ILLTTRFKQVTDFLSAATTTH---ISLDHHSMTLTPDEVKSLLLKYLDCR 314

Query: 52  GDNDPVRVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQN-RGSNPDRGLILAFK 110
             + P  V   TNP      LS +         E +   L  W N +  N D+       
Sbjct: 315 PQDLPREVLT-TNPRR----LSII--------AESIRDGLATWDNWKHVNCDK-----LT 356

Query: 111 TIATMSDRIGQMRYIRRWKIKSLVEAEIKTHYWLLACTLLVDKKTSHALL-----RKSAL 165
           TI   S             +  L  AE +  +  L+            LL          
Sbjct: 357 TIIESS-------------LNVLEPAEYRKMFDRLS-VFPPSAHIPTILLSLIWFDVIKS 402

Query: 166 SPM----ELQRRKLAEQKN 180
             M    +L +  L E++ 
Sbjct: 403 DVMVVVNKLHKYSLVEKQP 421

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	182
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	100.0
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	100.0
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	99.84
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	99.79
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	99.67
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	99.56
1c9b_A	207	General transcription factor IIB; protein-DNA comp	99.4
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	98.95
1c9b_A	207	General transcription factor IIB; protein-DNA comp	98.79
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	98.57
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	98.37
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	97.97
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	97.36
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	97.33
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	97.29
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	97.25
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	97.12
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	96.85
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	96.77
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	96.76
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	96.75
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	96.71
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	96.59
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	96.58
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	96.57
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	96.51
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	96.37
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	96.2
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	96.17
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	96.12
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	95.98
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	95.83
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	95.77
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	95.71
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	95.53
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	95.12
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	95.08
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	94.99
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	94.58
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	94.4
3m03_A	95	ORC6, origin recognition complex subunit 6; helix	94.31
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	94.06
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	93.99
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	93.97
2akl_A	138	PHNA-like protein PA0128; two domains, Zn binding	93.44
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	93.44
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	93.42
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	93.14
1nui_A	255	DNA primase/helicase; zinc-biding domain, toprim f	92.7
2k5r_A	97	Uncharacterized protein XF2673; solution structure	92.63
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	92.55
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	92.28
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	92.19
3j21_i	83	50S ribosomal protein L37AE; archaea, archaeal, KI	91.55
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	91.2
3cc2_Z	116	50S ribosomal protein L37AE, 50S ribosomal protein	91.2
1ffk_W	73	Ribosomal protein L37AE; ribosome assembly, RNA-RN	90.98
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	90.98
4rxn_A	54	Rubredoxin; electron transfer(iron-sulfur protein)	90.92
1e8j_A	52	Rubredoxin; iron-sulfur-protein, zinc-substitution	90.59
4a17_Y	103	RPL37A, 60S ribosomal protein L32; eukaryotic ribo	90.49
3iz5_m	92	60S ribosomal protein L43 (L37AE); eukaryotic ribo	90.43
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	90.33
4ell_A	411	Retinoblastoma-associated protein; cyclin fold, tu	90.21
3jyw_9	72	60S ribosomal protein L43; eukaryotic ribosome, RA	90.08
3izc_m	92	60S ribosomal protein RPL43 (L37AE); eukaryotic ri	89.9
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	89.8
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	89.6
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	89.58
3h4c_A	260	Transcription factor TFIIB-like; cyclin, transcrip	89.14
2r7g_A	347	PP110, retinoblastoma-associated protein, P105-RB,	88.64
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	88.56
3ga8_A	78	HTH-type transcriptional regulator MQSA (YGIT/B30;	88.27
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	88.22
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	88.03
1k81_A	36	EIF-2-beta, probable translation initiation factor	87.94
3u50_C	172	Telomerase-associated protein 82; TEB1, processivi	87.17
4elj_A	656	Retinoblastoma-associated protein; cyclin fold, tu	85.87
1dxg_A	36	Desulforedoxin; non-heme iron protein, rubredoxin	85.73
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	85.7
2qdj_A	304	Retinoblastoma-associated protein; cyclin fold, cy	85.29
2v3b_B	55	Rubredoxin 2, rubredoxin; alkane degradation, iron	85.0
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	83.54
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	83.49
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	83.37
1dx8_A	70	Rubredoxin; electron transport, zinc-substitution;	83.03
2kn9_A	81	Rubredoxin; metalloprotein, ssgcid, structural gen	82.06
2apo_B	60	Ribosome biogenesis protein NOP10; protein-protein	81.14
1gnf_A	46	Transcription factor GATA-1; zinc finger, transcri	80.93
1tfi_A	50	Transcriptional elongation factor SII; transcripti	80.72

>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M

Probab=100.00  E-value=6e-48  Score=330.90  Aligned_cols=176  Identities=27%  Similarity=0.445  Sum_probs=157.5

Q ss_pred             CCCCCCCCC-CCceeEeCCCCceEeCCCceeeeCCCcccccccccccCCC-CCCCCccccCCCCccccCCCCceEEecCC
Q 030129            3 DAFCSDCKK-HTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANES-GDNDPVRVGGPTNPLLADGGLSTVIAKPN   80 (182)
Q Consensus         3 ~~~Cp~Cg~-~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~-~~~~~sr~G~~~~~~~~~~gl~T~i~~~~   80 (182)
                      ..+||+||+ .+++++|+.+|++||++||+||+|++||+|||||+|++++ ++.|++|+|+|.||++||.||+|.|++++
T Consensus        21 ~~~Cp~C~~~~~~lv~D~~~G~~vC~~CGlVl~e~~iD~g~EWR~f~~d~~~~~d~sRvG~~~~~~~~~~glsT~I~~~~  100 (345)
T 4bbr_M           21 VLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEASNPLLDGNNLSTRIGKGE  100 (345)
T ss_dssp             -CCCSSCCCSSCCEEEEGGGTEEEETTTCBEEESCCBCHHHHHTTTSCSCSSSCCSSCCEEEECHHHHCSCCCCEEECCS
T ss_pred             CCcCCCCCCCCCceeEECCCCcEEeCCCCCCccCcccccCccccCCCcccccCCCcCCCCCCCCccccCCCcceeecCCC
Confidence            357999996 4689999999999999999999999999999999999864 46789999999999999999999999765


Q ss_pred             CCCCccccccccccccCC--CCchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHH
Q 030129           81 GASGEFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLV  151 (182)
Q Consensus        81 ~~~~~~l~~~l~~~q~~~--~~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~a  151 (182)
                      ++.+ ....+|++||+++  +++||+|..||++|.+||++|+||+.++++  .||+++.++ +    +.++++|||||+|
T Consensus       101 ~~~~-~~~~~L~r~q~r~~~~~~er~L~~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~a~~~~~~rGrs~e~vaAAclYiA  179 (345)
T 4bbr_M          101 TTDM-RFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIG  179 (345)
T ss_dssp             SCCH-HHHHHHHHHHHHTCCCCSSSSTTHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCTTTTTCCHHHHHHHHHHHH
T ss_pred             Ccch-hhHHHHHHHHHhhhcChHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHH
Confidence            4331 1234688999864  789999999999999999999999999999  999999887 4    8999999999999


Q ss_pred             HhhCC-----HHHHHhcCCCceeeeceeeehhc
Q 030129          152 DKKTS-----HALLRKSALSPMELQRRKLAEQK  179 (182)
Q Consensus       152 cr~~~-----~eia~~~~v~~~~i~r~~~~~~~  179 (182)
                      ||+++     +||+++++|++++|||.|...++
T Consensus       180 CR~~~~prtl~eI~~~~~v~~keigr~~k~l~~  212 (345)
T 4bbr_M          180 CRRAEVARTFKEIQSLIHVKTKEFGKTLNIMKN  212 (345)
T ss_dssp             HHHTCCBCCHHHHHHHHTCCTTHHHHHHHHHHH
T ss_pred             HHhcCCCccHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            99995     99999999999999999988765

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}

Probab=100.00  E-value=3e-44  Score=307.91  Aligned_cols=174  Identities=28%  Similarity=0.444  Sum_probs=144.8

Q ss_pred             CCCCCCCCCCC-ceeEeCCCCceEeCCCceeeeCCCcccccccccccCCC-CCCCCccccCCCCccccCCCCceEEecC-
Q 030129            3 DAFCSDCKKHT-EVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANES-GDNDPVRVGGPTNPLLADGGLSTVIAKP-   79 (182)
Q Consensus         3 ~~~Cp~Cg~~~-~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~-~~~~~sr~G~~~~~~~~~~gl~T~i~~~-   79 (182)
                      .++||+||+.+ ++++|+.+|++||++||+|++|++||++||||+|++++ ++.+++|+|+|.+|++|+.|++|.|+++ 
T Consensus        21 ~~~Cp~Cg~~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~EwR~F~~~~~~~~~~srvG~~~~~~~~~~~l~T~I~~~~  100 (345)
T 3k7a_M           21 VLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEASNPLLDGNNLSTRIGKGE  100 (345)
T ss_dssp             CCCCSTTCCSCCCCCCCSSSCSCCCSSSCCCCCCCCCCTTCCCCCC--------------CCCCCSSSCCCCCCCCCCTT
T ss_pred             CCcCcCCCCCCCceEEECCCCCEecCCCCeEcccccccCCccccccccccccCCCCCccCCCCCccccCCCCceeeccCC
Confidence            46799999832 69999999999999999999999999999999999853 3568999999999999999999999875 


Q ss_pred             -CCCCCccccccccccccC--CCCchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHH
Q 030129           80 -NGASGEFLSSSLGRWQNR--GSNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTL  149 (182)
Q Consensus        80 -~~~~~~~l~~~l~~~q~~--~~~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY  149 (182)
                       +++.|   ..+|++||++  .+++||+|.+|++.|.++++.|+||+.++++  .||+++.++  +   +.+.++|||||
T Consensus       101 ~~~~~~---~r~l~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~~~~~~~~kgr~~~~vaaAcly  177 (345)
T 3k7a_M          101 TTDMRF---TKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASIL  177 (345)
T ss_dssp             SCCHHH---HHHHHHHHHHHTTSSCCTTHHHHHHHHHHHHHHTTCCHHHHTHHHHHHHHHSSSCSSCCCCSHHHHTTTTT
T ss_pred             CCCchh---hhhhhhhcccccCCHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCcHHHHHHHHHH
Confidence             33333   2358899875  4899999999999999999999999999999  999999887  4   89999999999


Q ss_pred             HHHhhCC-----HHHHHhcCCCceeeeceeeehhc
Q 030129          150 LVDKKTS-----HALLRKSALSPMELQRRKLAEQK  179 (182)
Q Consensus       150 ~acr~~~-----~eia~~~~v~~~~i~r~~~~~~~  179 (182)
                      +|||+++     +||++++++++++||+.|..+.+
T Consensus       178 iAcR~e~~prtl~ei~~~~~v~~keIgr~~~~l~~  212 (345)
T 3k7a_M          178 IGCRRAEVARTFKEIQSLIHVKTKEFGKTLNIMKN  212 (345)
T ss_dssp             TTSBTTBSSCCHHHHHHSSSCCSHHHHHHHHHHHH
T ss_pred             HHHHHcCCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            9999984     99999999999999999987665

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae}

Probab=99.84  E-value=5.8e-22  Score=152.56  Aligned_cols=66  Identities=33%  Similarity=0.617  Sum_probs=58.5

Q ss_pred             CCCCCCCCCC-CceeEeCCCCceEeCCCceeeeCCCcccccccccccCCC-CCCCCccccCCCCcccc
Q 030129            3 DAFCSDCKKH-TEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANES-GDNDPVRVGGPTNPLLA   68 (182)
Q Consensus         3 ~~~Cp~Cg~~-~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~-~~~~~sr~G~~~~~~~~   68 (182)
                      ..+||+|++. +++++|+++|++||.+||+||+|++||.|||||+|++++ ++.+++|+|+|.++...
T Consensus        21 ~~~CPECGs~~t~IV~D~erGE~VCsdCGLVLEEriID~GPEWRAFsnDD~~~dDpSRVGAPs~~~~~   88 (197)
T 3k1f_M           21 VLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNXXXXXXXXXXXXXXXXXXXX   88 (197)
T ss_dssp             CCCCTTTCCSSCCEEEEGGGTEEEETTTCBBCCCCCBCHHHHHHHHHCCCTTTTCSCCCBCCBCCHHH
T ss_pred             CeECcCCCCcCCeEEEeCCCCEEEEcCCCCCcCCceeECCCCCcCcCCcccccccccccccccccccc
Confidence            4579999972 479999999999999999999999999999999999864 36789999999987664

>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A

Probab=99.79  E-value=6.1e-20  Score=118.71  Aligned_cols=47  Identities=45%  Similarity=0.834  Sum_probs=43.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccccccccccCC
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANE   50 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~   50 (182)
                      .+.||+|++ ..+++|+++|++||.+||+|++|++||.|||||+|+++
T Consensus        11 ~~~Cp~C~~-~~lv~D~~~ge~vC~~CGlVl~e~~iD~gpEWR~F~~~   57 (58)
T 1dl6_A           11 RVTCPNHPD-AILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND   57 (58)
T ss_dssp             CCSBTTBSS-SCCEECSSSCCEECTTTCCEECCSCCCCCCSCCCSCCC
T ss_pred             cccCcCCCC-CceeEeCCCCeEEeCCCCCEEeccccccCCcccccCCC
Confidence            357999998 57999999999999999999999999999999999975

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=99.67  E-value=4.6e-17  Score=102.09  Aligned_cols=44  Identities=39%  Similarity=0.989  Sum_probs=41.7

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCccccccccccc
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFA   48 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~   48 (182)
                      ..||.|++ ..+++|+++|++||..||+|++++.||.+||||+|+
T Consensus         6 ~~CP~C~~-~~l~~d~~~gelvC~~CG~v~~e~~id~~~ewr~f~   49 (50)
T 1pft_A            6 KVCPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAFD   49 (50)
T ss_dssp             CSCTTTSC-CCEEEETTTTEEEESSSCCBCCCCCCCCCSSSSCCC
T ss_pred             EeCcCCCC-cceEEcCCCCeEECcccCCcccccccccCCcccccC
Confidence            57999997 589999999999999999999999999999999997

>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B*

Probab=99.56  E-value=2.5e-15  Score=118.65  Aligned_cols=81  Identities=10%  Similarity=0.153  Sum_probs=70.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCC
Q 030129           99 SNPDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALS  166 (182)
Q Consensus        99 ~~~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~  166 (182)
                      +++||+|.+|++.|.++|++|+||+.+.+.  .+|+++.++ +    ++..++|||||+|||+++     +||+++++++
T Consensus         3 ~~~er~l~~a~~~I~~~~~~L~L~~~v~~~A~~l~~~~~~~~~~~gr~~~~vaaAclylAcr~~~~p~~l~di~~~~~v~   82 (200)
T 1ais_B            3 DAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVD   82 (200)
T ss_dssp             -----CHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTTTTTTCCHHHHHHHHHHHHHHHHTCCCCHHHHHHHTTSC
T ss_pred             ChHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCC
Confidence            578999999999999999999999999999  999999887 3    999999999999999984     9999999999


Q ss_pred             ceeeeceeeehhc
Q 030129          167 PMELQRRKLAEQK  179 (182)
Q Consensus       167 ~~~i~r~~~~~~~  179 (182)
                      +++||+.|....+
T Consensus        83 ~~~i~~~~~~l~~   95 (200)
T 1ais_B           83 KKEIGRSYRFIAR   95 (200)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999876554

>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A*

Probab=99.40  E-value=2.9e-13  Score=107.36  Aligned_cols=79  Identities=27%  Similarity=0.294  Sum_probs=72.3

Q ss_pred             chHHHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCce
Q 030129          101 PDRGLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS-----HALLRKSALSPM  168 (182)
Q Consensus       101 ~er~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~-----~eia~~~~v~~~  168 (182)
                      +||+|.+|++.|.++|.+|+||+.+.++  .+|+++.++  +   ++..++|||||+|||.++     +||+.+++++++
T Consensus         1 ~er~l~~a~~~I~~~~~~L~L~~~v~~~A~~~~~r~~~~~~~~~~~~~~v~aaclylAcK~ee~p~~l~di~~~~~~~~~   80 (207)
T 1c9b_A            1 SDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKK   80 (207)
T ss_dssp             CGGGHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTCSTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHTSSSCHH
T ss_pred             CchHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHH
Confidence            4899999999999999999999999999  999999876  4   999999999999999984     999999999999


Q ss_pred             eeeceeeehhc
Q 030129          169 ELQRRKLAEQK  179 (182)
Q Consensus       169 ~i~r~~~~~~~  179 (182)
                      +|++.|..+-+
T Consensus        81 ~i~~~~~~ll~   91 (207)
T 1c9b_A           81 EIGRCFKLILK   91 (207)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99998876543

>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B*

Probab=98.95  E-value=5.9e-10  Score=87.59  Aligned_cols=72  Identities=10%  Similarity=0.108  Sum_probs=63.7

Q ss_pred             HHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeeecee
Q 030129          107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQRRK  174 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~r~~  174 (182)
                      ....+|.++++.|+|++.+.+.  .|++.+.+. +    +|..+||||||+||+..+     +||+++++|++.||.++|
T Consensus       107 ~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~~~~gr~P~~iAaAaly~A~~~~~~~~t~~ei~~~~~vs~~ti~~~~  186 (200)
T 1ais_B          107 KPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNRY  186 (200)
T ss_dssp             CGGGGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence            3668999999999999998888  999999876 3    999999999999999984     899999999999999887


Q ss_pred             eehh
Q 030129          175 LAEQ  178 (182)
Q Consensus       175 ~~~~  178 (182)
                      -...
T Consensus       187 ~~l~  190 (200)
T 1ais_B          187 KELV  190 (200)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A*

Probab=98.79  E-value=6.1e-09  Score=82.25  Aligned_cols=72  Identities=3%  Similarity=-0.027  Sum_probs=63.3

Q ss_pred             HHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeeecee
Q 030129          107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQRRK  174 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~r~~  174 (182)
                      ..+++|.++++.|++++.+.+.  .+++.+.+. +    +|..+||||||+||+..+     .||+++++|++.||.++|
T Consensus       101 ~p~~~l~r~~~~l~l~~~~~~~A~~i~~~~~~~~l~~g~~P~~IAaAaiylA~~~~~~~~~~~~i~~~~~v~~~tI~~~~  180 (207)
T 1c9b_A          101 TTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSY  180 (207)
T ss_dssp             CTHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHHHTSSSCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence            4678999999999999988777  999988766 2    999999999999999874     799999999999999987


Q ss_pred             eehh
Q 030129          175 LAEQ  178 (182)
Q Consensus       175 ~~~~  178 (182)
                      -...
T Consensus       181 ~~l~  184 (207)
T 1c9b_A          181 RLIY  184 (207)
T ss_dssp             HHHG
T ss_pred             HHHH
Confidence            5543

>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M

Probab=98.57  E-value=6.8e-09  Score=88.60  Aligned_cols=71  Identities=4%  Similarity=-0.112  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeeece
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQRR  173 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~r~  173 (182)
                      .....+|.++|+.|+|+..+...  +|.+.+.+. +    +|..|||||||+||+.++     +|||++++|++.||..+
T Consensus       233 ~~p~~~i~Rf~s~L~l~~~v~~~A~~i~~~~~~~~i~~GR~P~~IAAAaIylAa~l~g~~~t~~eIa~v~~Vse~TIr~r  312 (345)
T 4bbr_M          233 AQNLTYIPRFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSG  312 (345)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcccccCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHH
Confidence            35667999999999999988777  888888776 4    999999999999999884     89999999999999998


Q ss_pred             eee
Q 030129          174 KLA  176 (182)
Q Consensus       174 ~~~  176 (182)
                      |--
T Consensus       313 yke  315 (345)
T 4bbr_M          313 YKI  315 (345)
T ss_dssp             ---
T ss_pred             HHH
Confidence            843

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}

Probab=98.37  E-value=4.6e-08  Score=83.30  Aligned_cols=69  Identities=4%  Similarity=-0.107  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeeecee
Q 030129          107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQRRK  174 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~r~~  174 (182)
                      ....+|.++|+.|+|+..+...  .|.+.+.+. +    +|..|||||||+|++..+     +||+++++|++.||..+|
T Consensus       234 ~p~~~i~Rf~~~L~l~~~v~~~A~~i~~~~~~~~l~~Gr~P~~IAaAaIylAa~~~~~~~t~~eIa~~~~Vse~TIr~~y  313 (345)
T 3k7a_M          234 QNLTYIPRFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSGY  313 (345)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhchhcCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3467788999999999888777  888888665 3    999999999999999873     899999999999999876


Q ss_pred             e
Q 030129          175 L  175 (182)
Q Consensus       175 ~  175 (182)
                      -
T Consensus       314 k  314 (345)
T 3k7a_M          314 K  314 (345)
T ss_dssp             -
T ss_pred             H
Confidence            4

>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe}

Probab=97.97  E-value=1.3e-05  Score=64.16  Aligned_cols=71  Identities=14%  Similarity=0.168  Sum_probs=58.2

Q ss_pred             HHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c----CHHHHHHHHHHHHHhhCC-----HHHHHhc--------
Q 030129          105 LILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I----KTHYWLLACTLLVDKKTS-----HALLRKS--------  163 (182)
Q Consensus       105 L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l----~~~~v~AAclY~acr~~~-----~eia~~~--------  163 (182)
                      ...+.+.|.+++..|+||+.+...  .+|++....  +    ++..+++||||+|||.+.     +||+.++        
T Consensus        28 R~~~~~~i~~v~~~l~L~~~t~~~A~~~~~Rf~~~~~~~~~~~~~lv~~acL~lA~K~Ee~~~~l~d~~~~~~~~~~~~~  107 (235)
T 1zp2_A           28 TIYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKGFSLEALVATCIYLSCKVEECPVHIRTICNEANDLWSLKV  107 (235)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCSCCCCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHTTCCCSS
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccccCHHHHHHHHHHHHhccccCcccHHHHHHHHHHHccchh
Confidence            567999999999999999999988  999998765  3    689999999999999883     7777655        


Q ss_pred             CCCceeeeceee
Q 030129          164 ALSPMELQRRKL  175 (182)
Q Consensus       164 ~v~~~~i~r~~~  175 (182)
                      ..+.++|++..+
T Consensus       108 ~~~~~~I~~~E~  119 (235)
T 1zp2_A          108 KLSRSNISEIEF  119 (235)
T ss_dssp             CCCHHHHHHHHH
T ss_pred             hccHHHHHHHHH
Confidence            456666665543

>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B*

Probab=97.36  E-value=0.00054  Score=55.32  Aligned_cols=58  Identities=10%  Similarity=0.040  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC-----HHHHHhc
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS-----HALLRKS  163 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~-----~eia~~~  163 (182)
                      ..+.+.|.+++..|+||+.+...  .+|++....  +   ++..+++||||+||+.+.     .||..++
T Consensus        32 ~~~~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~qlv~~acL~lA~K~EE~p~~l~d~~~~~  101 (257)
T 2ivx_A           32 QQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVA  101 (257)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhCChhhhCHHHHHHHHHHHHhccccCCcCHHHHHHHH
Confidence            45899999999999999999888  999998765  4   999999999999999884     6776544

>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1

Probab=97.33  E-value=0.00076  Score=54.33  Aligned_cols=57  Identities=11%  Similarity=-0.020  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC-----HHHHHh
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS-----HALLRK  162 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~-----~eia~~  162 (182)
                      ..+.+.|.+++..|+||+.+...  .+|++....  +   ++..+++||||+||+.+.     +||..+
T Consensus        42 ~~~~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~qlv~~acL~lA~K~eE~~~~l~d~~~~  110 (258)
T 2i53_A           42 REGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKT  110 (258)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCChhhcCHHHHHHHHHHHHHccccccccHHHHHHH
Confidence            46899999999999999999888  999998765  4   899999999999999883     666654

>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A

Probab=97.29  E-value=0.00088  Score=56.24  Aligned_cols=64  Identities=11%  Similarity=0.054  Sum_probs=52.7

Q ss_pred             chHHHHH-HHHHHHHHHHHhC--ChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC-----HHHHHhcC
Q 030129          101 PDRGLIL-AFKTIATMSDRIG--QMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS-----HALLRKSA  164 (182)
Q Consensus       101 ~er~L~~-a~~~I~~i~~~L~--L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~-----~eia~~~~  164 (182)
                      .|+.+.. +.+.|.+++..|+  ||+.+...  .+|++....  +   ++..|++||||+||+.+.     .||+.++.
T Consensus        52 eE~~lr~~~~~~I~ev~~~l~~~Lp~~t~~tA~~~~~RF~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~d~v~~~~  130 (323)
T 1jkw_A           52 EEMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLR  130 (323)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHGGGSS
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhhCChhhcCHHHHHHHHHHHHHhhhcCCCCHHHHHHHhc
Confidence            3566644 6799999999999  99999888  999998765  4   999999999999999884     56665543

>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens}

Probab=97.25  E-value=0.0009  Score=55.12  Aligned_cols=55  Identities=13%  Similarity=0.096  Sum_probs=47.6

Q ss_pred             chHHH-HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhC
Q 030129          101 PDRGL-ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKT  155 (182)
Q Consensus       101 ~er~L-~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~  155 (182)
                      .++.+ ..+.+.|.+++..|+||+.+...  .+|++....  +   ++..|++||||+||+.+
T Consensus        38 ~e~~~R~~~~~~I~~v~~~l~L~~~t~~tA~~~~~RF~~~~s~~~~~~~lva~acLfLA~K~E  100 (285)
T 3rgf_B           38 EYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVE  100 (285)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHSCTTTSCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhCCchhcCHHHHHHHHHHHHHhhh
Confidence            34444 45899999999999999999888  899998765  4   99999999999999987

>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C

Probab=97.12  E-value=0.00073  Score=57.58  Aligned_cols=57  Identities=11%  Similarity=-0.003  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC-----HHHHHh
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS-----HALLRK  162 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~-----~eia~~  162 (182)
                      ..+.+.|.+++..|+||+.+...  .+|++....  +   ++..|++||||+||+.+.     +||..+
T Consensus        39 ~~~v~wI~ev~~~l~L~~~t~~tAv~~~dRFl~~~sv~~~~~qlva~acLfLA~K~EE~p~~l~d~v~v  107 (358)
T 2pk2_A           39 QQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEEQPKKLEHVIKV  107 (358)
T ss_dssp             HHHHHHHHHHHTTTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHTT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHhhccCCCCHHHHHHH
Confidence            45899999999999999999888  899998765  4   999999999999999884     566544

>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}

Probab=96.85  E-value=0.0012  Score=43.46  Aligned_cols=31  Identities=23%  Similarity=0.501  Sum_probs=26.5

Q ss_pred             CCCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ....||.|++  .+.++...|.++|..||++..
T Consensus         7 ~iL~CP~ck~--~L~~~~~~~~LiC~~cg~~YP   37 (70)
T 2js4_A            7 DILVCPVCKG--RLEFQRAQAELVCNADRLAFP   37 (70)
T ss_dssp             CCCBCTTTCC--BEEEETTTTEEEETTTTEEEE
T ss_pred             hheECCCCCC--cCEEeCCCCEEEcCCCCceec
Confidence            3457999996  688898999999999999864

>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4

Probab=96.77  E-value=0.00058  Score=44.23  Aligned_cols=30  Identities=33%  Similarity=0.801  Sum_probs=27.7

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      .+||.|+. ..+|+++++-...|..||.+|-
T Consensus         8 VKCp~C~n-iq~VFShA~tvV~C~~Cg~~L~   37 (66)
T 1qxf_A            8 VKCPDCEH-EQVIFDHPSTIVKCIICGRTVA   37 (66)
T ss_dssp             EECTTTCC-EEEEESSCSSCEECSSSCCEEE
T ss_pred             EECCCCCC-ceEEEecCceEEEcccCCCEEe
Confidence            57999997 6899999999999999999995

>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}

Probab=96.76  E-value=0.0014  Score=42.89  Aligned_cols=31  Identities=10%  Similarity=0.165  Sum_probs=26.3

Q ss_pred             CCCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ....||.|++  .+.++...|.++|..||++..
T Consensus         7 ~iL~CP~ck~--~L~~~~~~~~LiC~~cg~~YP   37 (68)
T 2jr6_A            7 DILVCPVTKG--RLEYHQDKQELWSRQAKLAYP   37 (68)
T ss_dssp             CCCBCSSSCC--BCEEETTTTEEEETTTTEEEE
T ss_pred             hheECCCCCC--cCeEeCCCCEEEcCCCCcEec
Confidence            3457999996  688898999999999999863

>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1

Probab=96.75  E-value=0.0015  Score=42.67  Aligned_cols=30  Identities=17%  Similarity=0.082  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ...||.|++  .+.++..+|.++|..||+...
T Consensus        10 iL~CP~ck~--~L~~~~~~g~LvC~~c~~~YP   39 (67)
T 2jny_A           10 VLACPKDKG--PLRYLESEQLLVNERLNLAYR   39 (67)
T ss_dssp             CCBCTTTCC--BCEEETTTTEEEETTTTEEEE
T ss_pred             HhCCCCCCC--cCeEeCCCCEEEcCCCCcccc
Confidence            357999996  688899999999999999863

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=96.71  E-value=0.00079  Score=45.83  Aligned_cols=30  Identities=23%  Similarity=0.502  Sum_probs=26.4

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      ..||.||+  +.++++..|...|..||.++.-
T Consensus        28 y~Cp~CG~--~~v~r~atGiW~C~~Cg~~~ag   57 (83)
T 1vq8_Z           28 HACPNCGE--DRVDRQGTGIWQCSYCDYKFTG   57 (83)
T ss_dssp             EECSSSCC--EEEEEEETTEEEETTTCCEEEC
T ss_pred             CcCCCCCC--cceeccCCCeEECCCCCCEecC
Confidence            46999996  5789999999999999999753

>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1

Probab=96.59  E-value=0.0015  Score=42.95  Aligned_cols=30  Identities=17%  Similarity=0.327  Sum_probs=25.6

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ...||.|++  .+.++...|.++|..||++..
T Consensus         8 iL~CP~ck~--~L~~~~~~~~LiC~~cg~~YP   37 (69)
T 2pk7_A            8 ILACPICKG--PLKLSADKTELISKGAGLAYP   37 (69)
T ss_dssp             TCCCTTTCC--CCEECTTSSEEEETTTTEEEE
T ss_pred             heeCCCCCC--cCeEeCCCCEEEcCCCCcEec
Confidence            357999996  578888899999999999864

>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1

Probab=96.58  E-value=0.0018  Score=42.44  Aligned_cols=29  Identities=31%  Similarity=0.644  Sum_probs=25.4

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ..||.|++  .+.++...|.++|..||++..
T Consensus         9 L~CP~ck~--~L~~~~~~~~LiC~~cg~~YP   37 (68)
T 2hf1_A            9 LVCPLCKG--PLVFDKSKDELICKGDRLAFP   37 (68)
T ss_dssp             CBCTTTCC--BCEEETTTTEEEETTTTEEEE
T ss_pred             eECCCCCC--cCeEeCCCCEEEcCCCCcEec
Confidence            57999996  688888999999999999863

>3j20_W 30S ribosomal protein S27E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=96.57  E-value=0.0012  Score=42.36  Aligned_cols=30  Identities=37%  Similarity=0.777  Sum_probs=27.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      .+||.|+. ..+|+++.+-...|..||.+|-
T Consensus        16 VkCp~C~~-~q~VFSha~t~V~C~~Cgt~L~   45 (63)
T 3j20_W           16 VKCIDCGN-EQIVFSHPATKVRCLICGATLV   45 (63)
T ss_dssp             EECSSSCC-EEEEESSCSSCEECSSSCCEEE
T ss_pred             EECCCCCC-eeEEEecCCeEEEccCcCCEEe
Confidence            47999997 6899999999999999999995

>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B*

Probab=96.51  E-value=0.0063  Score=49.51  Aligned_cols=70  Identities=3%  Similarity=0.029  Sum_probs=55.7

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC------HHHHHhcC--CCceee
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS------HALLRKSA--LSPMEL  170 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~------~eia~~~~--v~~~~i  170 (182)
                      ....+.|.+++..++|++.+...  .++++....  +   +...+++||||+||+.+.      .||...++  .+..+|
T Consensus        39 ~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfl~~~~v~~~~lqlv~~acL~iA~K~eE~~~p~~~d~~~~~~~~~~~~eI  118 (269)
T 2b9r_A           39 AILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQNNSVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQI  118 (269)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHTTSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTCSSSCHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcCCCCcHHHhhHHHHHHHHHHHhcccccCccHHHHHHHhcCCCCHHHH
Confidence            45788999999999999888777  888888776  4   899999999999999862      67777664  466666


Q ss_pred             eceee
Q 030129          171 QRRKL  175 (182)
Q Consensus       171 ~r~~~  175 (182)
                      .+..+
T Consensus       119 ~~mE~  123 (269)
T 2b9r_A          119 RQMEM  123 (269)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55433

>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6

Probab=96.37  E-value=0.0013  Score=44.23  Aligned_cols=31  Identities=19%  Similarity=0.755  Sum_probs=27.9

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      .+||.|+. ..+|+++++-...|..||.||-+
T Consensus        33 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~   63 (81)
T 2xzm_6           33 VKCAQCQN-IQMIFSNAQSTIICEKCSAILCK   63 (81)
T ss_dssp             EECSSSCC-EEEEETTCSSCEECSSSCCEEEE
T ss_pred             eECCCCCC-eeEEEecCccEEEccCCCCEEee
Confidence            47999997 68999999999999999999953

>3u5c_b RP61, YS20, 40S ribosomal protein S27-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_X 3u5g_b

Probab=96.20  E-value=0.0015  Score=44.03  Aligned_cols=31  Identities=26%  Similarity=0.675  Sum_probs=28.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      .+||.|+. ..+|+.+++-.+.|..||.||-+
T Consensus        35 VkCp~C~~-~q~VFSha~t~V~C~~Cg~~L~~   65 (82)
T 3u5c_b           35 VKCPGCLN-ITTVFSHAQTAVTCESCSTILCT   65 (82)
T ss_dssp             EECTTSCS-CEEEESBCSSCCCCSSSCCCCEE
T ss_pred             EECCCCCC-eeEEEecCCeEEEccccCCEEec
Confidence            47999997 78999999999999999999953

>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ...

Probab=96.17  E-value=0.011  Score=47.69  Aligned_cols=69  Identities=9%  Similarity=0.014  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC------HHHHHhcC--CCcee
Q 030129          105 LILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS------HALLRKSA--LSPME  169 (182)
Q Consensus       105 L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~------~eia~~~~--v~~~~  169 (182)
                      -..+.+.|-+++..++|+..+.-.  .++++....  +   +...+++||||+||+.+.      .||..+.+  .+..+
T Consensus        39 R~~lvdwl~~v~~~~~l~~~tl~lAv~~lDRfls~~~v~~~~lqlv~~acl~iA~K~ee~~~~~~~d~~~i~~~~~~~~~  118 (260)
T 2cch_B           39 RAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQ  118 (260)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTSSSCHHH
T ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccCCCCHHHHhHHHHHHHHHHHHhcccCCCCHHHHHHHHcCCcCHHH
Confidence            356889999999999999887777  888887665  4   889999999999999873      67776654  45555


Q ss_pred             eece
Q 030129          170 LQRR  173 (182)
Q Consensus       170 i~r~  173 (182)
                      |.+.
T Consensus       119 i~~m  122 (260)
T 2cch_B          119 VLRM  122 (260)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5554

>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B*

Probab=96.12  E-value=0.006  Score=49.62  Aligned_cols=69  Identities=10%  Similarity=-0.116  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHHHhCChHHHHHH--HHHHHHHh-c-c---CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeeecee
Q 030129          107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEA-E-I---KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQRRK  174 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~-~-l---~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~r~~  174 (182)
                      ..++.|.+++..++++..+...  .+...+.. . +   +|..+||||||+|++..+     .+++.++|+++.+|-..+
T Consensus       137 tp~~fl~~~~~~~~~~~~~~~~a~~l~e~sl~~~~~~~~~Ps~iAaAai~lA~~~l~~~~w~~~l~~~tg~~~~~l~~~~  216 (269)
T 2b9r_A          137 LPLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFPPSQIAAGAFSLALKILDNGEWTPTLQHYLSYTEESLLPVM  216 (269)
T ss_dssp             CHHHHHHHHHHSSCCCHHHHHHHHHHHHHGGGCGGGSSSCTTHHHHHHHHHHHHHHTCCCSCTTHHHHSCCCSSTTTTHH
T ss_pred             CHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhhhcCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHCCCHHHHHHHH
Confidence            3567889999999988776655  55565543 2 3   999999999999998753     788999999998887654


Q ss_pred             e
Q 030129          175 L  175 (182)
Q Consensus       175 ~  175 (182)
                      -
T Consensus       217 ~  217 (269)
T 2b9r_A          217 Q  217 (269)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens}

Probab=95.98  E-value=0.013  Score=48.11  Aligned_cols=65  Identities=9%  Similarity=0.142  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHhCChHHHHHH--HHHHHHHhc---c--CHHHHHHHHHHHHHhhCC---HHHHHhcCCCceeeec
Q 030129          108 AFKTIATMSDRIGQMRYIRRW--KIKSLVEAE---I--KTHYWLLACTLLVDKKTS---HALLRKSALSPMELQR  172 (182)
Q Consensus       108 a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~---l--~~~~v~AAclY~acr~~~---~eia~~~~v~~~~i~r  172 (182)
                      .++.|.+++..|+++..+...  .+...+...   +  .|..|||||||+|++..+   ...-+.++++..+|..
T Consensus       157 P~~fL~~~~~~l~~~~~~~~~A~~~l~~sl~t~~~l~~~Ps~IAaAaiylA~~~~~~~~~~W~~~~~~~~~~l~~  231 (285)
T 3rgf_B          157 PYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSVDMEKILE  231 (285)
T ss_dssp             SHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSHHHHSCHHHHHHHHHHHHHHHTTCCCHHHHHTSCSCHHHHHH
T ss_pred             hHHHHHHHHHHhCCCHHHHHHHHHHHHHHHccChhhccCHHHHHHHHHHHHHHHcCCChhhHHHHHCCCHHHHHH
Confidence            467899999999998877666  665555433   2  999999999999999875   4556677777666543

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=95.83  E-value=0.0074  Score=37.01  Aligned_cols=28  Identities=25%  Similarity=0.646  Sum_probs=21.7

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ..||.||+ ..+..+ ......|..||.+.
T Consensus        20 k~CP~CG~-~~fm~~-~~~R~~C~kCG~t~   47 (50)
T 3j20_Y           20 KFCPRCGP-GVFMAD-HGDRWACGKCGYTE   47 (50)
T ss_dssp             EECSSSCS-SCEEEE-CSSEEECSSSCCEE
T ss_pred             ccCCCCCC-ceEEec-CCCeEECCCCCCEE
Confidence            46999997 555554 45789999999874

>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe}

Probab=95.77  E-value=0.016  Score=46.01  Aligned_cols=50  Identities=10%  Similarity=0.005  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHhCChHHHHHH--HHHHHHHhc---c--CHHHHHHHHHHHHHhhCCH
Q 030129          108 AFKTIATMSDRIGQMRYIRRW--KIKSLVEAE---I--KTHYWLLACTLLVDKKTSH  157 (182)
Q Consensus       108 a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~---l--~~~~v~AAclY~acr~~~~  157 (182)
                      .++.|.+++..++++..+...  .+...+...   +  +|..|||||||+|++..+.
T Consensus       134 P~~~l~~~~~~~~~~~~~~~~A~~~l~~s~~~~~~l~~~Ps~IAaAai~lA~~~~~~  190 (235)
T 1zp2_A          134 PYTSLEQAFHDGIINQKQLEFAWSIVNDSYASSLCLMAHPHQLAYAALLISCCNDEN  190 (235)
T ss_dssp             THHHHHHHHHTTSSCHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHTSCTT
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCchhccCHHHHHHHHHHHHHHhcCC
Confidence            567889999999998877666  666666433   2  9999999999999998864

>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=95.71  E-value=0.0035  Score=42.62  Aligned_cols=30  Identities=37%  Similarity=0.666  Sum_probs=27.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      .+||.|+. ..+|+.+++-.+.|..||.||-
T Consensus        37 VkCp~C~~-~~~VFShA~t~V~C~~CgtvL~   66 (86)
T 3iz6_X           37 VKCQGCFN-ITTVFSHSQTVVVCPGCQTVLC   66 (86)
T ss_dssp             EECTTTCC-EEEEETTCSSCCCCSSSCCCCS
T ss_pred             EECCCCCC-eeEEEecCCcEEEccCCCCEee
Confidence            57999997 6899999999999999999995

>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A

Probab=95.53  E-value=0.027  Score=45.63  Aligned_cols=69  Identities=9%  Similarity=0.051  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC------HHHHHhcC--CCcee
Q 030129          105 LILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS------HALLRKSA--LSPME  169 (182)
Q Consensus       105 L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~------~eia~~~~--v~~~~  169 (182)
                      -..+.+.|.+++..++|+..+.-.  .++++....  +   +...+++||||+||+.+.      .|++..++  .+..+
T Consensus        57 R~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~v~~~~lqlv~~acL~iAsK~EE~~p~~~~~~~~~~~~~~~~~e  136 (271)
T 2w96_A           57 RKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPEE  136 (271)
T ss_dssp             HHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHTTSCCCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTSSCHHH
T ss_pred             HHHHHHHHHHHHHHHCCchhHHHHHHHHHHHhCCcCCcCHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCHHH
Confidence            346788899999999998776655  888887765  4   899999999999999873      57776654  45555


Q ss_pred             eece
Q 030129          170 LQRR  173 (182)
Q Consensus       170 i~r~  173 (182)
                      |.+.
T Consensus       137 I~~m  140 (271)
T 2w96_A          137 LLQM  140 (271)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5544

>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A

Probab=95.12  E-value=0.026  Score=45.74  Aligned_cols=68  Identities=9%  Similarity=0.029  Sum_probs=49.2

Q ss_pred             HHHHHHHHHHHHhCChHHHHH----H--HHHHHHH-hc-c---CHHHHHHHHHHHHHhhCC--------------HHHHH
Q 030129          107 LAFKTIATMSDRIGQMRYIRR----W--KIKSLVE-AE-I---KTHYWLLACTLLVDKKTS--------------HALLR  161 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~~v~~----~--~i~k~a~-~~-l---~~~~v~AAclY~acr~~~--------------~eia~  161 (182)
                      ..+++|.++...++++....+    .  .+...+. +. +   +|..+||||||+|++..+              .+++.
T Consensus       156 tp~~fl~~~~~~l~~~~~~~~~~~~~a~~~l~~~~~d~~~~~~~PS~iAaAai~lA~~~l~~~~~~~~~w~~~~~~~l~~  235 (271)
T 2w96_A          156 TPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNPPSMVAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSR  235 (271)
T ss_dssp             CHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHTSTHHHHSCHHHHHHHHHHHHHHHHHHHSTTSCGGGTTHHHHHHH
T ss_pred             CHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHHHhhhhhhccCHHHHHHHHHHHHHHHhCcCCCCCCCcHHHHHHHHHH
Confidence            366788899999999876532    2  4444443 22 3   999999999999987531              46888


Q ss_pred             hcCCCceeeecee
Q 030129          162 KSALSPMELQRRK  174 (182)
Q Consensus       162 ~~~v~~~~i~r~~  174 (182)
                      ++|+++.+|-..+
T Consensus       236 ~~~v~~~~l~~c~  248 (271)
T 2w96_A          236 VIKCDPDCLRACQ  248 (271)
T ss_dssp             HHTSCHHHHHHHH
T ss_pred             HHCcCHHHHHHHH
Confidence            9999988876544

>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ...

Probab=95.08  E-value=0.02  Score=46.12  Aligned_cols=70  Identities=10%  Similarity=-0.036  Sum_probs=52.7

Q ss_pred             HHHHHHHHHHHHhCChH-HHHHH--HHHHHHH-hc--c---CHHHHHHHHHHHHHhhC-----CHHHHHhcCCCceeeec
Q 030129          107 LAFKTIATMSDRIGQMR-YIRRW--KIKSLVE-AE--I---KTHYWLLACTLLVDKKT-----SHALLRKSALSPMELQR  172 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~-~v~~~--~i~k~a~-~~--l---~~~~v~AAclY~acr~~-----~~eia~~~~v~~~~i~r  172 (182)
                      ..++.|.+++..++++. .+...  .+...+. +.  +   +|..+||||||+|++..     ..+++.++|+++.+|-.
T Consensus       138 tp~~fl~~~~~~l~~~~~~~~~~a~~l~e~sl~~~~~~~~~~Ps~iAaAai~lA~~~~~~~~w~~~l~~~~g~~~~~i~~  217 (260)
T 2cch_B          138 TVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKP  217 (260)
T ss_dssp             CHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHHHHHHHHHHHHSCCSCHHHHHHHCCCHHHHHH
T ss_pred             CHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHhHHHHhCCCHHHHHHHHHHHHHHHhCCCcchHHHHHHhCcCHHHHHH
Confidence            46788999999999876 55444  5555543 32  2   99999999999999865     37889999999888766


Q ss_pred             eeee
Q 030129          173 RKLA  176 (182)
Q Consensus       173 ~~~~  176 (182)
                      .+-.
T Consensus       218 ~~~~  221 (260)
T 2cch_B          218 CLMD  221 (260)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5533

>1g3n_C V-cyclin; cyclin-dependent kinase, INK4 inhibitor, viral cyclin, cell cycle, signaling protein; 2.90A {Human herpesvirus 8} SCOP: a.74.1.1 a.74.1.1

Probab=94.99  E-value=0.035  Score=44.63  Aligned_cols=69  Identities=16%  Similarity=0.049  Sum_probs=52.7

Q ss_pred             HHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC------HHHHHhcC--CCcee
Q 030129          105 LILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS------HALLRKSA--LSPME  169 (182)
Q Consensus       105 L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~------~eia~~~~--v~~~~  169 (182)
                      -....+.|-+++..++|+..+.-.  .++++....  +   +...+++||+|+||+.+.      .|++...+  .+..+
T Consensus        51 R~~lvdwl~ev~~~~~l~~etl~lAv~~~DRfls~~~v~~~~lqLv~~acl~iA~K~eE~~~p~~~d~~~~~~~~~~~~~  130 (257)
T 1g3n_C           51 RKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQE  130 (257)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTCSCHHH
T ss_pred             HHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHccccCCCHHHHHHHHCCCCCHHH
Confidence            345789999999999999887766  888888665  4   889999999999999652      67776654  35555


Q ss_pred             eece
Q 030129          170 LQRR  173 (182)
Q Consensus       170 i~r~  173 (182)
                      |.+.
T Consensus       131 i~~m  134 (257)
T 1g3n_C          131 LIDQ  134 (257)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>1w98_B Cyclin E, G1/S-specific cyclin E1; cell cycle, transferase; HET: TPO; 2.15A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1

Probab=94.58  E-value=0.091  Score=42.91  Aligned_cols=69  Identities=9%  Similarity=-0.004  Sum_probs=51.9

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc---c---CHHHHHHHHHHHHHhhCC------HHHHHhcC--CCcee
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE---I---KTHYWLLACTLLVDKKTS------HALLRKSA--LSPME  169 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~---l---~~~~v~AAclY~acr~~~------~eia~~~~--v~~~~  169 (182)
                      ....+.|.+++..++|+..+.-.  .++++....   +   +...+++||+|+||+.+.      .|++.+.+  .+..+
T Consensus        51 ~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~~v~~~~lqlv~~acL~iA~K~eE~~~p~l~~~~~i~~~~~~~~e  130 (283)
T 1w98_B           51 AILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDE  130 (283)
T ss_dssp             HHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTSSCHHH
T ss_pred             HHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcccCCCcHHHHHHHHcCCCCHHH
Confidence            45778899999999998877666  777776542   3   889999999999999872      67776653  45555


Q ss_pred             eecee
Q 030129          170 LQRRK  174 (182)
Q Consensus       170 i~r~~  174 (182)
                      |.+..
T Consensus       131 i~~mE  135 (283)
T 1w98_B          131 ILTME  135 (283)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55543

>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8

Probab=94.40  E-value=0.02  Score=35.77  Aligned_cols=28  Identities=25%  Similarity=0.651  Sum_probs=21.2

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLV   32 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V   32 (182)
                      +..||.||+ ..++. ...+...|..||+.
T Consensus        18 ~~fCPkCG~-~~~ma-~~~dr~~C~kCgyt   45 (55)
T 2k4x_A           18 HRFCPRCGP-GVFLA-EHADRYSCGRCGYT   45 (55)
T ss_dssp             SCCCTTTTT-TCCCE-ECSSEEECTTTCCC
T ss_pred             cccCcCCCC-ceeEe-ccCCEEECCCCCCE
Confidence            467999997 44433 44578999999998

>3m03_A ORC6, origin recognition complex subunit 6; helix turn helix, DNA binding protein, origin recognition CO DNA replication; HET: MES; 2.50A {Homo sapiens}

Probab=94.31  E-value=0.15  Score=35.35  Aligned_cols=58  Identities=10%  Similarity=0.039  Sum_probs=40.9

Q ss_pred             HHHHHHHhCChHHHHHH----HHHHHHH---hc----cCHHHHHHHHHHHHHhhCC-----HHHHHhcCCCcee
Q 030129          112 IATMSDRIGQMRYIRRW----KIKSLVE---AE----IKTHYWLLACTLLVDKKTS-----HALLRKSALSPME  169 (182)
Q Consensus       112 I~~i~~~L~L~~~v~~~----~i~k~a~---~~----l~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~  169 (182)
                      |+.+|-+||+++-+...    ..|+...   ..    |+....+||++|.+||...     .-+.+.+++++.+
T Consensus         6 v~dLcVqfgc~e~~~~a~~lL~~Yk~~l~~~~~~~~D~s~P~f~aaA~~~acr~~K~kVdK~KL~~~s~lk~~~   79 (95)
T 3m03_A            6 IRDLAVQFSCIEAVNMASKILKSYESSLPQTQQVDLDLSRPLFTSAALLSACKILKLKVDKNKMVATSGVKKAI   79 (95)
T ss_dssp             HHHHHHHHTCGGGHHHHHHHHHHHHTTSCHHHHHHCCTTSHHHHHHHHHHHHHHTTCCCCHHHHHHTTCBCHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhhccccccccHHHHHHHHHHHHHHccCCCHHHHHHHHCCCHHH
Confidence            78899999999854333    6666531   11    4667899999999999983     3566667766543

>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1

Probab=94.06  E-value=0.063  Score=42.89  Aligned_cols=53  Identities=4%  Similarity=0.078  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHhCChHH----HHHH--HHHHHHHhc---c--CHHHHHHHHHHHHHhhCCHHH
Q 030129          107 LAFKTIATMSDRIGQMRY----IRRW--KIKSLVEAE---I--KTHYWLLACTLLVDKKTSHAL  159 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~~----v~~~--~i~k~a~~~---l--~~~~v~AAclY~acr~~~~ei  159 (182)
                      ..+++|.+++..|+++..    +...  .+...+...   +  +|..|||||||+|++..+.++
T Consensus       150 ~P~~fl~~~~~~l~~~~~~~~~~~~~A~~l~~~s~~~~~~l~~~Ps~IAaAai~lA~~~~~~~~  213 (258)
T 2i53_A          150 HPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEI  213 (258)
T ss_dssp             CHHHHHHHHHHTBCSCHHHHHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHHHHTCCG
T ss_pred             ChHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHHHcCCchhccChHHHHHHHHHHHHHHhCCCC
Confidence            356788899999988763    3333  444444322   2  999999999999999876443

>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B*

Probab=93.99  E-value=0.15  Score=40.72  Aligned_cols=50  Identities=8%  Similarity=0.043  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHHhCChHHHHHH--HHHHHHH-h-c--c--CHHHHHHHHHHHHHhhCC
Q 030129          107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVE-A-E--I--KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~-~-~--l--~~~~v~AAclY~acr~~~  156 (182)
                      ..+++|.+++..++++..+...  .+..... . .  +  .|..|||||||+|++..+
T Consensus       145 ~P~~fl~~~~~~l~~~~~~~~~A~~~~~~sl~~~~~~l~~~Ps~IAaAai~lA~~~~~  202 (257)
T 2ivx_A          145 HPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSN  202 (257)
T ss_dssp             CHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCGGGTSCHHHHHHHHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHhCCCcHHHHHHHHHHHhhhhcccHHHcCCHHHHHHHHHHHHHHHhC
Confidence            4567899999999998887766  5665554 2 2  3  999999999999999764

>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}

Probab=93.97  E-value=0.06  Score=33.64  Aligned_cols=26  Identities=23%  Similarity=0.747  Sum_probs=21.4

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeC--CCceee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCS--ECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~--~CG~Vl   33 (182)
                      ..||.|++  .+..+.  |+++|.  +||+..
T Consensus        11 L~CP~c~~--~L~~~~--~~L~C~~~~c~~~Y   38 (56)
T 2kpi_A           11 LACPACHA--PLEERD--AELICTGQDCGLAY   38 (56)
T ss_dssp             CCCSSSCS--CEEEET--TEEEECSSSCCCEE
T ss_pred             eeCCCCCC--cceecC--CEEEcCCcCCCcEE
Confidence            47999997  466664  999999  999886

>2akl_A PHNA-like protein PA0128; two domains, Zn binding protein, beta-strand protein, structural genomics, PSI; NMR {Pseudomonas aeruginosa PAO1} SCOP: b.34.11.2 g.41.3.5

Probab=93.44  E-value=0.2  Score=36.63  Aligned_cols=28  Identities=25%  Similarity=0.438  Sum_probs=20.2

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ...||.|++ .-.-.|  ...+||.+||.--
T Consensus        27 lP~CP~C~s-eytYeD--g~l~vCPeC~hEW   54 (138)
T 2akl_A           27 LPPCPQCNS-EYTYED--GALLVCPECAHEW   54 (138)
T ss_dssp             SCCCTTTCC-CCCEEC--SSSEEETTTTEEE
T ss_pred             CCCCCCCCC-cceEec--CCeEECCcccccc
Confidence            457999998 333333  4579999999865

>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A

Probab=93.44  E-value=0.059  Score=43.21  Aligned_cols=67  Identities=9%  Similarity=-0.060  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHHhCChHHHH----HH--HHHHHHH-hc-c---CHHHHHHHHHHHHHhhC----------CHHHHHhcCCC
Q 030129          108 AFKTIATMSDRIGQMRYIR----RW--KIKSLVE-AE-I---KTHYWLLACTLLVDKKT----------SHALLRKSALS  166 (182)
Q Consensus       108 a~~~I~~i~~~L~L~~~v~----~~--~i~k~a~-~~-l---~~~~v~AAclY~acr~~----------~~eia~~~~v~  166 (182)
                      .++.+.++...++++....    ..  .+...+. +. +   +|..+||||||+|.+..          ..+++.++|++
T Consensus       152 p~~fl~~~~~~~~~~~~~~~~~~~~a~~ll~~~l~d~~~~~~~PS~iAaAai~la~~~~~~~~~~w~~~~~~l~~~tg~~  231 (254)
T 2f2c_A          152 ATDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNIALLSPGLICAGGLLTTIETDNTNCRPWTCYLEDLSSILNFS  231 (254)
T ss_dssp             GGGSHHHHHHHTTCCGGGHHHHHHHHHHHHHHHTTSGGGTTSCHHHHHHHHHHHHHHTTCCSSCCTHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHcCcchhccCHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHCcC
Confidence            3467888899998876432    22  3334332 22 2   99999999999999875          25678889998


Q ss_pred             ceeeecee
Q 030129          167 PMELQRRK  174 (182)
Q Consensus       167 ~~~i~r~~  174 (182)
                      +.+|-..+
T Consensus       232 ~~~l~~c~  239 (254)
T 2f2c_A          232 TNTVRTVK  239 (254)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            87775543

>1g3n_C V-cyclin; cyclin-dependent kinase, INK4 inhibitor, viral cyclin, cell cycle, signaling protein; 2.90A {Human herpesvirus 8} SCOP: a.74.1.1 a.74.1.1

Probab=93.42  E-value=0.07  Score=42.82  Aligned_cols=68  Identities=10%  Similarity=-0.116  Sum_probs=47.5

Q ss_pred             HHHHHHHHHHHHhCChHHH----HHH--HHHHHHH-hc-c---CHHHHHHHHHHHHHhhCC-----------HHHHHhcC
Q 030129          107 LAFKTIATMSDRIGQMRYI----RRW--KIKSLVE-AE-I---KTHYWLLACTLLVDKKTS-----------HALLRKSA  164 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~~v----~~~--~i~k~a~-~~-l---~~~~v~AAclY~acr~~~-----------~eia~~~~  164 (182)
                      ..++.|.++...++++...    ...  .+...+. +. +   +|..+||||||+|.+..+           .+++.++|
T Consensus       150 tp~~fl~~~~~~~~~~~~~~~~~~~~a~~~le~~l~d~~~~~~~PS~iAaAai~lA~~~l~~~~~~~~~~w~~~l~~~t~  229 (257)
T 1g3n_C          150 LATDVTSFLLLKLVGGSQHLDFWHHEVNTLITKALVDPLTGSLPASIISAAGCALLVPANVIPQDTHSGGVVPQLASILG  229 (257)
T ss_dssp             CHHHHHHHHHHHHSCSSTTHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHCCGGGSCC-----CHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhCcchhCcCHHHHHHHHHHHHHHHhCCCcccchhhHHHHHHHHHC
Confidence            3677899999999987543    222  3444443 22 2   999999999999987542           56777889


Q ss_pred             CCceeeecee
Q 030129          165 LSPMELQRRK  174 (182)
Q Consensus       165 v~~~~i~r~~  174 (182)
                      +++.+|-..+
T Consensus       230 ~~~~~l~~c~  239 (257)
T 1g3n_C          230 CDVSVLQAAV  239 (257)
T ss_dssp             CCHHHHHHHH
T ss_pred             cCHHHHHHHH
Confidence            9887775543

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...

Probab=93.14  E-value=0.058  Score=38.93  Aligned_cols=34  Identities=29%  Similarity=0.402  Sum_probs=23.4

Q ss_pred             CCCCCCCCCCCCCceeEe--CCCCceEeCCCceeee
Q 030129            1 MTDAFCSDCKKHTEVVFD--HSAGDTVCSECGLVLE   34 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D--~~~G~~vC~~CG~Vl~   34 (182)
                      |.+..||+||+-=.+..|  ...+.+.|..||+...
T Consensus         2 ~~~~FCp~CgnlL~~~~~~~~~~~~~~C~~C~y~~~   37 (122)
T 1twf_I            2 TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEE   37 (122)
T ss_dssp             CCCCBCSSSCCBCEEEEETTTTEEEEECSSSSCEEE
T ss_pred             CCCCcccccCccCcccccCcCCCCEEECCcCCCeee
Confidence            566799999962122233  3356799999999865

>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2

Probab=92.70  E-value=0.062  Score=43.04  Aligned_cols=29  Identities=24%  Similarity=0.449  Sum_probs=22.3

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLV   32 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V   32 (182)
                      +..||.||+...+-++ ..|...|..||.-
T Consensus        14 ~~~CP~Cg~~d~~~~~-~dg~~~C~~Cg~~   42 (255)
T 1nui_A           14 HIPCDNCGSSDGNSLF-SDGHTFCYVCEKW   42 (255)
T ss_dssp             EECCSSSCCSSCEEEE-TTSCEEETTTCCE
T ss_pred             CCcCCCCCCCCCceEe-CCCCeecccCCCc
Confidence            3579999984456555 4688999999975

>2k5r_A Uncharacterized protein XF2673; solution structure, structural genomics, PSI-2, protein structure initiative; NMR {Xylella fastidiosa TEMECULA1}

Probab=92.63  E-value=0.067  Score=37.22  Aligned_cols=31  Identities=10%  Similarity=0.070  Sum_probs=23.7

Q ss_pred             CCCCCCCCCCCCceeEeCC---------------------------CCceEeCCCceeee
Q 030129            2 TDAFCSDCKKHTEVVFDHS---------------------------AGDTVCSECGLVLE   34 (182)
Q Consensus         2 ~~~~Cp~Cg~~~~iv~D~~---------------------------~G~~vC~~CG~Vl~   34 (182)
                      ....||.|+.  .+..+..                           +|.++|..||+...
T Consensus         7 dILaCP~cK~--pL~l~~~~~~~~~~ca~~~~~~~~~~~~~~~e~~~~~LvC~~c~~~YP   64 (97)
T 2k5r_A            7 HLLCSPDTRQ--PLSLLESKGLEALNKAIVSGTVQRADGSIQNQSLHEALITRDRKQVFR   64 (97)
T ss_dssp             SSCCCCTTSS--CCEECCHHHHHHHHHHHHHTCCBCTTSCBCCCCCSEEEECTTSCEEEE
T ss_pred             hheECCCCCC--cccccccchhhhhhhhhhccccccccccccccccCCeEEcCCCCCCcc
Confidence            4467999996  4555554                           78999999999863

>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens}

Probab=92.55  E-value=0.21  Score=41.33  Aligned_cols=61  Identities=8%  Similarity=-0.087  Sum_probs=48.9

Q ss_pred             HHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhC------CHHHHHhcC
Q 030129          104 GLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKT------SHALLRKSA  164 (182)
Q Consensus       104 ~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~------~~eia~~~~  164 (182)
                      .-..+.+.|-+++..++|+..+.-.  .++++....  +   ....+++||+|+||+.+      ..|+....+
T Consensus        70 ~R~~lvdwl~ev~~~~~l~~~t~~lAv~~lDRfls~~~v~~~~lqLv~~tcL~lAsK~eE~~p~~~~~l~~~~~  143 (306)
T 3g33_B           70 MRKMLAYWMLEVCEEQRCEEEVFPLAMNYLDRYLSCVPTRKAQLQLLGAVCMLLASKLRETTPLTIEKLCIYTD  143 (306)
T ss_dssp             HHHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHCCCCGGGHHHHHHHHHHHHHHHHCSSCCCTTHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHhCCcHhHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHhc
Confidence            3356889999999999999887776  888887665  4   88999999999999974      256665544

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=92.28  E-value=0.13  Score=36.63  Aligned_cols=31  Identities=13%  Similarity=0.374  Sum_probs=21.1

Q ss_pred             CCCCCCCCCCCCceeEeCCCC----ceEeCCCceeee
Q 030129            2 TDAFCSDCKKHTEVVFDHSAG----DTVCSECGLVLE   34 (182)
Q Consensus         2 ~~~~Cp~Cg~~~~iv~D~~~G----~~vC~~CG~Vl~   34 (182)
                      .+.+||+||+-  +......|    .++|..||++..
T Consensus         3 ~m~FCp~Cgn~--L~~~~~~~~~~~~~~C~~C~y~~~   37 (113)
T 3h0g_I            3 NFQYCIECNNM--LYPREDKVDRVLRLACRNCDYSEI   37 (113)
T ss_dssp             CCCCCSSSCCC--CEECCCTTTCCCCEECSSSCCEEC
T ss_pred             cceeCcCCCCE--eeEcccCCCCeeEEECCCCCCeEE
Confidence            35789999972  33332222    699999999864

>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A

Probab=92.19  E-value=0.22  Score=39.77  Aligned_cols=50  Identities=10%  Similarity=0.022  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhC
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKT  155 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~  155 (182)
                      ....+.|-+++..++|+..+.-.  .++++....  +   +...+++||+|+||+.+
T Consensus        53 ~~lvdwl~~v~~~~~l~~etl~lAv~~~DRfls~~~v~~~~lqLv~~acl~iA~K~e  109 (254)
T 2f2c_A           53 TILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIR  109 (254)
T ss_dssp             HHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSCCCTTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCchHHHHHHHHHHHHHccCCcCHHHccHHHHHHHHHHHHhc
Confidence            45789999999999998877666  888888665  4   88999999999999985

>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=91.55  E-value=0.14  Score=34.62  Aligned_cols=32  Identities=25%  Similarity=0.508  Sum_probs=25.6

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH   36 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~   36 (182)
                      ...||.||+ .. +.....|-.-|..||.++.-.
T Consensus        35 ky~CpfCGk-~~-vkR~a~GIW~C~kCg~~~AGG   66 (83)
T 3j21_i           35 KHTCPVCGR-KA-VKRISTGIWQCQKCGATFAGG   66 (83)
T ss_dssp             CBCCSSSCS-SC-EEEEETTEEEETTTCCEEECC
T ss_pred             ccCCCCCCC-ce-eEecCcCeEEcCCCCCEEeCC
Confidence            357999998 44 566789999999999998643

>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1

Probab=91.20  E-value=0.057  Score=32.43  Aligned_cols=18  Identities=22%  Similarity=0.501  Sum_probs=9.2

Q ss_pred             CCCCCCCCCCCCCceeEeCCCC
Q 030129            1 MTDAFCSDCKKHTEVVFDHSAG   22 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D~~~G   22 (182)
                      |....|+.||-    |+|++.|
T Consensus         2 m~~y~C~vCGy----vyd~~~G   19 (46)
T 6rxn_A            2 MQKYVCNVCGY----EYDPAEH   19 (46)
T ss_dssp             CCCEEETTTCC----EECGGGG
T ss_pred             CCEEECCCCCe----EEeCCcC
Confidence            44445666652    4555444

>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, ribosoma protein, RNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z* 3i56_Z* 3cpw_Y* 4adx_Z

Probab=91.20  E-value=0.11  Score=37.18  Aligned_cols=30  Identities=23%  Similarity=0.499  Sum_probs=24.3

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      ..||.||+ .. +.-...|-.-|..||.++.-
T Consensus        61 ytCPfCGk-~~-vKR~avGIW~C~~Cgk~fAG   90 (116)
T 3cc2_Z           61 HACPNCGE-DR-VDRQGTGIWQCSYCDYKFTG   90 (116)
T ss_dssp             EECSSSCC-EE-EEEEETTEEEETTTCCEEEC
T ss_pred             CcCCCCCC-ce-eEecCceeEECCCCCCEEEC
Confidence            46999997 34 55667899999999999853

>1ffk_W Ribosomal protein L37AE; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1jj2_Y 1k73_1* 1k8a_1* 1k9m_1* 1kc8_1* 1kd1_1* 1kqs_Y* 1m1k_1* 1m90_1* 1n8r_1* 1nji_1* 1q7y_1* 1q81_1* 1q82_1* 1q86_1* 1qvf_Y 1qvg_Y 1w2b_Y 3cxc_Y*

Probab=90.98  E-value=0.12  Score=34.01  Aligned_cols=31  Identities=23%  Similarity=0.422  Sum_probs=24.7

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeCC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH   36 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~   36 (182)
                      ..||.||+ .. +.....|-..|..||.++.-.
T Consensus        28 y~C~fCgk-~~-vkR~a~GIW~C~~C~~~~AGG   58 (73)
T 1ffk_W           28 YKCPVCGF-PK-LKRASTSIWVCGHCGYKIAGG   58 (73)
T ss_pred             ccCCCCCC-ce-eEEEEeEEEECCCCCcEEECC
Confidence            47999997 44 556678999999999998543

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=90.98  E-value=0.25  Score=30.60  Aligned_cols=31  Identities=19%  Similarity=0.446  Sum_probs=21.4

Q ss_pred             CCCCCCCCCCceeEeC------CCC---ceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFDH------SAG---DTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~------~~G---~~vC~~CG~Vl~e   35 (182)
                      ..||.||. ...++..      +++   .++|.+||....+
T Consensus        16 ~~Cp~Cg~-~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~~   55 (57)
T 1qyp_A           16 ITCPKCGN-DTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             CCCTTTCC-SEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred             eECCCCCC-CEEEEEEeecccCCCCCcEEEEcCCCCCEecc
Confidence            46999997 5555432      233   4899999987654

>4rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.20A {Clostridium pasteurianum} SCOP: g.41.5.1 PDB: 5rxn_A 1bfy_A 1fhh_A 1fhm_A 1irn_A 1iro_A 1r0f_A 1r0g_A 1r0h_A 1r0i_A 1r0j_A 1t9q_A 1c09_A 1b2j_A 1b13_A 1smm_A 1smu_A 1smw_A 1be7_A 1t9o_A ...

Probab=90.92  E-value=0.099  Score=32.44  Aligned_cols=18  Identities=28%  Similarity=0.689  Sum_probs=8.8

Q ss_pred             CCCCCCCCCCCCCceeEeCCCC
Q 030129            1 MTDAFCSDCKKHTEVVFDHSAG   22 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D~~~G   22 (182)
                      |....|+.||-    |+|++.|
T Consensus         1 m~~y~C~vCGy----vYd~~~G   18 (54)
T 4rxn_A            1 MKKYTCTVCGY----IYDPEDG   18 (54)
T ss_dssp             CCCEEETTTCC----EECTTTC
T ss_pred             CCceECCCCCe----EECCCcC
Confidence            44445555552    4555444

>1e8j_A Rubredoxin; iron-sulfur-protein, zinc-substitution, thermostability; NMR {Desulfovibrio gigas} SCOP: g.41.5.1 PDB: 1rdg_A 2dsx_A 1spw_A

Probab=90.59  E-value=0.092  Score=32.29  Aligned_cols=10  Identities=30%  Similarity=0.630  Sum_probs=4.7

Q ss_pred             CCCCCCCCCC
Q 030129            1 MTDAFCSDCK   10 (182)
Q Consensus         1 m~~~~Cp~Cg   10 (182)
                      |....|+.||
T Consensus         1 m~~y~C~~CG   10 (52)
T 1e8j_A            1 MDIYVCTVCG   10 (52)
T ss_dssp             CCCEECSSSC
T ss_pred             CCcEEeCCCC
Confidence            3344455554

>4a17_Y RPL37A, 60S ribosomal protein L32; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_Y 4a1c_Y 4a1e_Y

Probab=90.49  E-value=0.16  Score=35.61  Aligned_cols=29  Identities=24%  Similarity=0.423  Sum_probs=24.1

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ..||.||+ .. +.....|-.-|..||.++.
T Consensus        37 y~CpfCgk-~~-vKR~a~GIW~C~kCg~~~A   65 (103)
T 4a17_Y           37 YGCPFCGK-VA-VKRAAVGIWKCKPCKKIIA   65 (103)
T ss_dssp             EECTTTCC-EE-EEEEETTEEEETTTTEEEE
T ss_pred             CCCCCCCC-ce-eeecCcceEEcCCCCCEEe
Confidence            46999997 44 5677899999999999984

>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens}

Probab=90.33  E-value=0.26  Score=40.67  Aligned_cols=65  Identities=9%  Similarity=-0.007  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHhCChHH----HHHH--HHHHHHH-hc-c---CHHHHHHHHHHHHHhhCC----------HHHHHhcCCCc
Q 030129          109 FKTIATMSDRIGQMRY----IRRW--KIKSLVE-AE-I---KTHYWLLACTLLVDKKTS----------HALLRKSALSP  167 (182)
Q Consensus       109 ~~~I~~i~~~L~L~~~----v~~~--~i~k~a~-~~-l---~~~~v~AAclY~acr~~~----------~eia~~~~v~~  167 (182)
                      ++.|..+...++++..    +...  .+...+. +. |   +|..+||||||+|.+..+          ..++.++|+++
T Consensus       172 ~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~lsl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~w~~~w~~~L~~~tg~~~  251 (306)
T 3g33_B          172 HDFLAFILHRLSLPRDRQALVKKHAQTFLALCATDYTFAMYPPSMIATGSIGAAVQGLGACSMSGDELTELLAGITGTEV  251 (306)
T ss_dssp             GGGHHHHHHTSSCCTTTHHHHHHHHHHHHHHHHHCGGGTTSCHHHHHHHHHHHHHHTCC---CCHHHHHHHHHHHHTCCH
T ss_pred             HHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhhhhhccCCHHHHHHHHHHHHHHHhcCCCCchhhHHHHHHHHHCCCH
Confidence            4577888888877643    2222  3344332 22 3   999999999999998663          45678889888


Q ss_pred             eeeece
Q 030129          168 MELQRR  173 (182)
Q Consensus       168 ~~i~r~  173 (182)
                      .+|-..
T Consensus       252 ~~l~~c  257 (306)
T 3g33_B          252 DCLRAC  257 (306)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766543

>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor, cell cycle; 1.98A {Homo sapiens}

Probab=90.21  E-value=0.9  Score=39.28  Aligned_cols=51  Identities=10%  Similarity=0.113  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHHhCChH-HHHHH--HHHHHHHhc---c----CHHHHHHHHHHHHHhhCC
Q 030129          106 ILAFKTIATMSDRIGQMR-YIRRW--KIKSLVEAE---I----KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~-~v~~~--~i~k~a~~~---l----~~~~v~AAclY~acr~~~  156 (182)
                      .-|...|..+|.+|+++. .+.+.  .+|+.+..+   |    ..+.++-+|+|+.|+...
T Consensus       280 ~LAa~Rl~~LC~~L~~~~~~l~~~IWt~fe~~l~~~teLm~dRHLDQiiLCsiY~i~Kv~~  340 (411)
T 4ell_A          280 RLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKN  340 (411)
T ss_dssp             HHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHhhhHhhccccHHHHHHHHHHHHHhhcc
Confidence            459999999999999875 56655  778776544   3    899999999999999874

>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=90.08  E-value=0.15  Score=33.45  Aligned_cols=30  Identities=33%  Similarity=0.429  Sum_probs=24.4

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      ..||.||+ .. +.....|-.-|..||.++.-
T Consensus        27 y~C~fCgk-~~-vkR~a~GIW~C~~C~~~~AG   56 (72)
T 3jyw_9           27 YDCSFCGK-KT-VKRGAAGIWTCSCCKKTVAG   56 (72)
T ss_dssp             BCCSSCCS-SC-BSBCSSSCBCCSSSCCCCCC
T ss_pred             ccCCCCCC-ce-eEecCCCeEECCCCCCEEeC
Confidence            47999997 44 56678999999999999753

>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1

Probab=89.80  E-value=0.23  Score=32.46  Aligned_cols=27  Identities=22%  Similarity=0.575  Sum_probs=21.9

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ..|| |+.  -.+.+...-..-|. ||.++.
T Consensus         5 v~C~-C~~--~~~~~~~~kT~~C~-CG~~~~   31 (71)
T 1gh9_A            5 FRCD-CGR--ALYSREGAKTRKCV-CGRTVN   31 (71)
T ss_dssp             EEET-TSC--CEEEETTCSEEEET-TTEEEE
T ss_pred             EECC-CCC--EEEEcCCCcEEECC-CCCeee
Confidence            3599 997  35677777889999 999986

>1w98_B Cyclin E, G1/S-specific cyclin E1; cell cycle, transferase; HET: TPO; 2.15A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1

Probab=89.60  E-value=0.22  Score=40.57  Aligned_cols=65  Identities=5%  Similarity=-0.106  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHhCChHHH------------HHH-HHHHHHH-hc-c---CHHHHHHHHHHHHHhhCCHHHHHhcCCCcee
Q 030129          108 AFKTIATMSDRIGQMRYI------------RRW-KIKSLVE-AE-I---KTHYWLLACTLLVDKKTSHALLRKSALSPME  169 (182)
Q Consensus       108 a~~~I~~i~~~L~L~~~v------------~~~-~i~k~a~-~~-l---~~~~v~AAclY~acr~~~~eia~~~~v~~~~  169 (182)
                      .++.|.+++..+++++..            ... .+...+. +. +   +|..+||||||+|+.  ..+++.++|+++.+
T Consensus       151 p~~fL~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~llelsl~d~~~l~~~PS~iAaAai~la~~--~~~l~~~tg~~~~~  228 (283)
T 1w98_B          151 IVSWLNVYMQVAYLNDLHEVLLPQYPQQIFIQIAELLDLCVLDVDCLEFPYGILAASALYHFSS--SELMQKVSGYQWCD  228 (283)
T ss_dssp             HHHHHHHHHHHHTCCSSCCSSSCCSCHHHHHHHHHHHHHHHHSGGGGGSCHHHHHHHHHHHTSC--HHHHHHHSCCCHHH
T ss_pred             HHHHHHHHHHHhccCchhhHHHHhhhHHHHHHHHHHHHHHHhhhhhhcCCHHHHHHHHHHHHHC--hHHHHHHhCCCHHH
Confidence            567888888888775321            111 3444443 33 2   999999999999974  46778888888877


Q ss_pred             eecee
Q 030129          170 LQRRK  174 (182)
Q Consensus       170 i~r~~  174 (182)
                      |...+
T Consensus       229 i~~c~  233 (283)
T 1w98_B          229 IENCV  233 (283)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65443

>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...

Probab=89.58  E-value=0.13  Score=33.63  Aligned_cols=26  Identities=23%  Similarity=0.875  Sum_probs=15.2

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCce-ee
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGL-VL   33 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~-Vl   33 (182)
                      .|++||.  .+..+ ....+.|..||. ||
T Consensus        30 ~C~~CG~--~~e~~-~~d~irCp~CG~RIL   56 (70)
T 1twf_L           30 ICAECSS--KLSLS-RTDAVRCKDCGHRIL   56 (70)
T ss_dssp             ECSSSCC--EECCC-TTSTTCCSSSCCCCC
T ss_pred             ECCCCCC--cceeC-CCCCccCCCCCceEe
Confidence            5888885  22222 334466888887 54

>3h4c_A Transcription factor TFIIB-like; cyclin, transcription factor TFIIB repeat; 2.30A {Trypanosoma brucei brucei}

Probab=89.14  E-value=1  Score=35.58  Aligned_cols=50  Identities=4%  Similarity=0.091  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-------c-CHHHHHHHHHHHHHhhCC
Q 030129          107 LAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-------I-KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       107 ~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-------l-~~~~v~AAclY~acr~~~  156 (182)
                      ...+.|.++..+-.+|+.|.+.  ++.+.....       . ++..|+|||+.+|..+.+
T Consensus        14 ~M~nclr~L~kKs~~~eaVL~~AieLar~fvg~rR~rgqRvE~q~dVAAAc~miAae~~~   73 (260)
T 3h4c_A           14 TMLNCMRGLHKKAVLPEPVLDRGIELARAFVGGRRARGQRVERQPDVAAACLMIAAEEAQ   73 (260)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHHHhhhhhhhcccccccHHHHHHHHHHHHHHcC
Confidence            4668889999999999999888  888776543       2 999999999999998873

>2r7g_A PP110, retinoblastoma-associated protein, P105-RB, RB; retinoblastoma protein, E2F displacement, transcription repressor; 1.67A {Homo sapiens} SCOP: a.74.1.3 a.74.1.3 PDB: 1n4m_A 3pom_A 1gh6_B 1gux_A 1o9k_A 1ad6_A 1gux_B 1o9k_B

Probab=88.64  E-value=1.4  Score=37.16  Aligned_cols=53  Identities=9%  Similarity=0.088  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHHHHHhCChH-HHHHH--HHHHHHHhc---c----CHHHHHHHHHHHHHhhCC
Q 030129          104 GLILAFKTIATMSDRIGQMR-YIRRW--KIKSLVEAE---I----KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       104 ~L~~a~~~I~~i~~~L~L~~-~v~~~--~i~k~a~~~---l----~~~~v~AAclY~acr~~~  156 (182)
                      .+.-|...|..+|+.|+++. .+.+.  .+|+.+..+   |    ..+.++-+|+|+.||.+.
T Consensus       214 vy~La~~Rl~~LC~~L~~~~~~~~~~iWt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~  276 (347)
T 2r7g_A          214 VYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKN  276 (347)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHhChHhhcCCcHHHHHHHHHHHHHHhcC
Confidence            34558899999999999875 46665  777776443   3    899999999999999884

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=88.56  E-value=0.22  Score=36.53  Aligned_cols=29  Identities=28%  Similarity=0.484  Sum_probs=19.2

Q ss_pred             CCCCCCCCCCCceeE--eCC--CCceEeCCCceee
Q 030129            3 DAFCSDCKKHTEVVF--DHS--AGDTVCSECGLVL   33 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~--D~~--~G~~vC~~CG~Vl   33 (182)
                      +.+||+|++  -+..  |.+  ...++|..||++.
T Consensus        24 ~~FCPeCgN--mL~pked~~~~~l~~~CrtCgY~~   56 (133)
T 3qt1_I           24 FRFCRDCNN--MLYPREDKENNRLLFECRTCSYVE   56 (133)
T ss_dssp             CCBCTTTCC--BCBCCBCTTTCCBCCBCSSSCCBC
T ss_pred             CeeCCCCCC--EeeECccCCCceeEEECCCCCCcE
Confidence            468999996  2222  211  2259999999975

>3ga8_A HTH-type transcriptional regulator MQSA (YGIT/B30; helix-turn-helix, Zn-binding protein, DNA-binding, transcrip transcription regulation; HET: PE4; 1.70A {Escherichia coli k-12} PDB: 3hi2_A

Probab=88.27  E-value=0.35  Score=31.78  Aligned_cols=29  Identities=24%  Similarity=0.637  Sum_probs=18.6

Q ss_pred             CCCCCCCCCCCcee-------EeCCCCc---------eEeCCCceee
Q 030129            3 DAFCSDCKKHTEVV-------FDHSAGD---------TVCSECGLVL   33 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv-------~D~~~G~---------~vC~~CG~Vl   33 (182)
                      +|+||.||+ ..++       +++ .|.         .+|..||.++
T Consensus         2 ~m~Cp~Cg~-~~l~~~~~~~~~~~-~G~~~~I~~Vp~~~C~~CGE~~   46 (78)
T 3ga8_A            2 HMKCPVCHQ-GEMVSGIKDIPYTF-RGRKTVLKGIHGLYCVHCEESI   46 (78)
T ss_dssp             -CBCTTTSS-SBEEEEEEEEEEEE-TTEEEEEEEEEEEEETTTCCEE
T ss_pred             ceECCCCCC-CeeEeEEEEEEEEE-CCEEEEEcCceeEECCCCCCEE
Confidence            588999996 3332       222 232         6799999886

>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C

Probab=88.22  E-value=0.22  Score=42.17  Aligned_cols=49  Identities=6%  Similarity=0.023  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHhCChHHHHHH--HHHHHHH-h-c--c--CHHHHHHHHHHHHHhhCC
Q 030129          108 AFKTIATMSDRIGQMRYIRRW--KIKSLVE-A-E--I--KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       108 a~~~I~~i~~~L~L~~~v~~~--~i~k~a~-~-~--l--~~~~v~AAclY~acr~~~  156 (182)
                      .+++|.+++..|+++..+...  .|...+. . .  +  .|..|||||||+|++..+
T Consensus       153 P~~fL~~~~~~l~~~~~l~~~A~~ll~~sl~~t~l~l~y~Ps~IAaAAI~lA~~~l~  209 (358)
T 2pk2_A          153 PHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSN  209 (358)
T ss_dssp             TTHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCGGGTSCHHHHTTTTTTTHHHHTT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhccCHHHHHHHHHHHHHHHhC
Confidence            457889999999998877666  5665654 2 2  2  999999999999999765

>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A

Probab=88.03  E-value=0.84  Score=37.87  Aligned_cols=47  Identities=6%  Similarity=0.085  Sum_probs=29.4

Q ss_pred             HHHHHHHHHh-------CChHHHHHH--HHHHHHHhc---c--CHHHHHHHHHHHHHhhCC
Q 030129          110 KTIATMSDRI-------GQMRYIRRW--KIKSLVEAE---I--KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       110 ~~I~~i~~~L-------~L~~~v~~~--~i~k~a~~~---l--~~~~v~AAclY~acr~~~  156 (182)
                      +.|.+++..|       +.++.+...  .+...+...   +  .|..|||||||+|++..+
T Consensus       165 ~~L~~~l~~l~~~~~~~~~~~~l~~~A~~~l~~sl~t~~~l~~~Ps~IAaAai~lA~~~~~  225 (323)
T 1jkw_A          165 RPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAG  225 (323)
T ss_dssp             HHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHTTSTHHHHSCHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHhccHHHcCCHHHHHHHHHHHHHHHcC
Confidence            4455555443       344444444  555544332   2  999999999999999765

>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1

Probab=87.94  E-value=0.26  Score=27.87  Aligned_cols=28  Identities=21%  Similarity=0.649  Sum_probs=17.7

Q ss_pred             CCCCCCCCC-ceeEeCCCCceEeCCCcee
Q 030129            5 FCSDCKKHT-EVVFDHSAGDTVCSECGLV   32 (182)
Q Consensus         5 ~Cp~Cg~~~-~iv~D~~~G~~vC~~CG~V   32 (182)
                      .||.|++.. .++.+...=.+-|..||..
T Consensus         2 lC~~C~~peT~l~~~~~~~~l~C~aCG~~   30 (36)
T 1k81_A            2 ICRECGKPDTKIIKEGRVHLLKCMACGAI   30 (36)
T ss_dssp             CCSSSCSCEEEEEEETTEEEEEEETTTEE
T ss_pred             CCcCCCCCCcEEEEeCCcEEEEhhcCCCc
Confidence            599999832 2333323333669999986

>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens}

Probab=85.87  E-value=2.8  Score=38.31  Aligned_cols=52  Identities=10%  Similarity=0.111  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHHHhCChH-HHHHH--HHHHHHHhc---c----CHHHHHHHHHHHHHhhCC
Q 030129          105 LILAFKTIATMSDRIGQMR-YIRRW--KIKSLVEAE---I----KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       105 L~~a~~~I~~i~~~L~L~~-~v~~~--~i~k~a~~~---l----~~~~v~AAclY~acr~~~  156 (182)
                      +.-|...|..+|+.|+++. .+.+.  .+|+.+..+   |    ..+.++-+|+|+.||...
T Consensus       524 y~LAa~Rl~~LC~~L~~~~~~i~~~IWt~fe~~l~~~t~L~~dRHLDQiilCsiY~icKv~~  585 (656)
T 4elj_A          524 YRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKN  585 (656)
T ss_dssp             HHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHHHHHCGGGSTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhcc
Confidence            3559999999999998874 56655  777776443   3    999999999999999884

>1dxg_A Desulforedoxin; non-heme iron protein, rubredoxin type metal center, electron transport; 1.80A {Desulfovibrio gigas} SCOP: g.41.5.2 PDB: 1dcd_A 1dhg_A 1cfw_A 2lk5_A 2lk6_A

Probab=85.73  E-value=0.53  Score=26.42  Aligned_cols=27  Identities=30%  Similarity=0.683  Sum_probs=15.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      .+|+.||. --.+.....|.++|  ||.=+
T Consensus         7 Y~C~~CGn-ivev~~~g~~~l~C--CG~~M   33 (36)
T 1dxg_A            7 YKCELCGQ-VVKVLEEGGGTLVC--CGEDM   33 (36)
T ss_dssp             EECTTTCC-EEEEEECCSSCEEE--TTEEC
T ss_pred             EEcCCCCc-EEEEEeCCCcCEEe--CCccc
Confidence            46888875 22233346677777  66543

>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4

Probab=85.70  E-value=0.36  Score=32.66  Aligned_cols=31  Identities=23%  Similarity=0.562  Sum_probs=22.3

Q ss_pred             CCCCCCCCC--ceeEeC--CCCceEeCCCceeeeC
Q 030129            5 FCSDCKKHT--EVVFDH--SAGDTVCSECGLVLES   35 (182)
Q Consensus         5 ~Cp~Cg~~~--~iv~D~--~~G~~vC~~CG~Vl~e   35 (182)
                      .||.|+...  .+..|.  ..|.+.|..||.-.+-
T Consensus        25 ~CPfCnh~~sV~vkidk~~~~g~l~C~~Cg~~~~~   59 (85)
T 1wii_A           25 TCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQT   59 (85)
T ss_dssp             CCTTTCCSSCEEEEEETTTTEEEEEESSSCCEEEE
T ss_pred             cCCCCCCCCeEEEEEEccCCEEEEEcccCCCeEEe
Confidence            599999642  334444  4678999999988763

>2qdj_A Retinoblastoma-associated protein; cyclin fold, cyclin wedge, antitumor protein; 2.00A {Homo sapiens}

Probab=85.29  E-value=1.7  Score=36.06  Aligned_cols=57  Identities=12%  Similarity=0.123  Sum_probs=41.9

Q ss_pred             HHHHHHHHhCChHHHHHH--HHHHHHHhc-------c-CHHHHHHHHHHHHHhhC------CHHHHHhcCCCc
Q 030129          111 TIATMSDRIGQMRYIRRW--KIKSLVEAE-------I-KTHYWLLACTLLVDKKT------SHALLRKSALSP  167 (182)
Q Consensus       111 ~I~~i~~~L~L~~~v~~~--~i~k~a~~~-------l-~~~~v~AAclY~acr~~------~~eia~~~~v~~  167 (182)
                      ....+|..|+|++.+.++  .+|+.+...       . ..+..-.||||+||...      .-.|.+.++++.
T Consensus         5 rF~~lC~~Lnld~~~~~~Aw~~~~~~~~~~~~~~~~~~~~~~~w~acLY~a~~~~~~n~vsLt~LLr~~~lsi   77 (304)
T 2qdj_A            5 DFTALCQKLKIPDHVRERAWLTWEKVSSVDGVLGGYIQKKKELWGICIFIAAVDLDEMSFTFTELQKNIEISV   77 (304)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHC----------CHHHHHHHHHHHHHHHHTCCCSCHHHHHHHHTCCH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCCccchHHHHHHhHHHHhhccCCCcCcHHHHHHHcCCCH
Confidence            456789999999999888  999998662       2 67777777799999743      145555555554

>2v3b_B Rubredoxin 2, rubredoxin; alkane degradation, iron-sulfur protein, oxidoreductase, ELE transfer, electron transport, FAD, NAD, iron; HET: FAD; 2.45A {Pseudomonas aeruginosa}

Probab=85.00  E-value=0.31  Score=30.21  Aligned_cols=12  Identities=25%  Similarity=0.825  Sum_probs=6.6

Q ss_pred             eEeCCCceeeeC
Q 030129           24 TVCSECGLVLES   35 (182)
Q Consensus        24 ~vC~~CG~Vl~e   35 (182)
                      ++|+.||.|.++
T Consensus         4 y~C~~CGyvYd~   15 (55)
T 2v3b_B            4 WQCVVCGFIYDE   15 (55)
T ss_dssp             EEETTTCCEEET
T ss_pred             EEeCCCCeEECC
Confidence            455555555554

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=83.54  E-value=0.57  Score=33.28  Aligned_cols=31  Identities=19%  Similarity=0.422  Sum_probs=19.7

Q ss_pred             CCCCCCCCCCCceeE-------eC-------CC-CceEeCCCceeee
Q 030129            3 DAFCSDCKKHTEVVF-------DH-------SA-GDTVCSECGLVLE   34 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~-------D~-------~~-G~~vC~~CG~Vl~   34 (182)
                      .|+||.||+ ...+.       ++       .. --.+|..||.++-
T Consensus         2 ~M~Cp~Cg~-~~~~~~~~~~~~~~kg~~~~v~~v~~~~C~~CGE~~~   47 (133)
T 3o9x_A            2 HMKCPVCHQ-GEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIM   47 (133)
T ss_dssp             CCBCTTTSS-SBEEEEEEEEEEEETTEEEEEEEEEEEEESSSSCEEC
T ss_pred             CcCCCcCCC-CceeeceEEEEEEECCEEEEECCCceeECCCCCCEee
Confidence            578999996 32221       11       11 2478999999874

>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=83.49  E-value=0.33  Score=29.71  Aligned_cols=23  Identities=26%  Similarity=0.700  Sum_probs=18.7

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV   32 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V   32 (182)
                      ..||.|+..      ...|-.-|..||..
T Consensus        15 ~iCpkC~a~------~~~gaw~CrKCG~~   37 (51)
T 3j21_g           15 YVCLRCGAT------NPWGAKKCRKCGYK   37 (51)
T ss_dssp             EECTTTCCE------ECTTCSSCSSSSSC
T ss_pred             ccCCCCCCc------CCCCceecCCCCCc
Confidence            469999972      35788999999987

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4

Probab=83.37  E-value=0.89  Score=30.35  Aligned_cols=27  Identities=15%  Similarity=0.731  Sum_probs=20.2

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      +||.|+.  .++.++......|..||..+
T Consensus        27 wCP~C~~--~~~~~~~~~~v~C~~C~~~F   53 (86)
T 2ct7_A           27 WCAQCSF--GFIYEREQLEATCPQCHQTF   53 (86)
T ss_dssp             CCSSSCC--CEECCCSCSCEECTTTCCEE
T ss_pred             ECcCCCc--hheecCCCCceEeCCCCCcc
Confidence            5999985  45556666668899999876

>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A

Probab=83.03  E-value=0.45  Score=30.96  Aligned_cols=13  Identities=31%  Similarity=0.861  Sum_probs=7.8

Q ss_pred             ceEeCCCceeeeC
Q 030129           23 DTVCSECGLVLES   35 (182)
Q Consensus        23 ~~vC~~CG~Vl~e   35 (182)
                      .++|+.||.|.++
T Consensus         7 ~y~C~vCGyiYd~   19 (70)
T 1dx8_A            7 KYECEACGYIYEP   19 (70)
T ss_dssp             CEEETTTCCEECT
T ss_pred             eEEeCCCCEEEcC
Confidence            4566666666653

>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle structural genomics center for infectious electron transport, iron; NMR {Mycobacterium tuberculosis}

Probab=82.06  E-value=0.47  Score=31.81  Aligned_cols=16  Identities=19%  Similarity=0.424  Sum_probs=12.7

Q ss_pred             CceEeCCCceeeeCCC
Q 030129           22 GDTVCSECGLVLESHS   37 (182)
Q Consensus        22 G~~vC~~CG~Vl~e~~   37 (182)
                      ..++|..||.|.++..
T Consensus        26 ~~y~C~vCGyvYD~~~   41 (81)
T 2kn9_A           26 KLFRCIQCGFEYDEAL   41 (81)
T ss_dssp             CEEEETTTCCEEETTT
T ss_pred             ceEEeCCCCEEEcCCc
Confidence            4699999999988643

>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A

Probab=81.14  E-value=0.52  Score=29.80  Aligned_cols=25  Identities=20%  Similarity=0.542  Sum_probs=18.6

Q ss_pred             CCCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         2 ~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      .+.+||.|+. ..+       ..+|..||....
T Consensus         5 ~mr~C~~Cgv-YTL-------k~~CP~CG~~T~   29 (60)
T 2apo_B            5 RMKKCPKCGL-YTL-------KEICPKCGEKTV   29 (60)
T ss_dssp             CCEECTTTCC-EES-------SSBCSSSCSBCB
T ss_pred             hceeCCCCCC-Eec-------cccCcCCCCcCC
Confidence            3568999996 333       568999998853

>1gnf_A Transcription factor GATA-1; zinc finger, transcription regulation; NMR {Mus musculus} SCOP: g.39.1.1 PDB: 1y0j_A 2l6y_A 2l6z_A

Probab=80.93  E-value=0.48  Score=28.29  Aligned_cols=31  Identities=23%  Similarity=0.579  Sum_probs=18.4

Q ss_pred             CCCCCCCCCCCcee-EeCCCCceEeCCCceee
Q 030129            3 DAFCSDCKKHTEVV-FDHSAGDTVCSECGLVL   33 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv-~D~~~G~~vC~~CG~Vl   33 (182)
                      ...|.+|+...... -....|.++|..||+-.
T Consensus         4 ~~~C~~C~tt~Tp~WR~gp~G~~LCNaCGl~~   35 (46)
T 1gnf_A            4 ARECVNCGATATPLWRRDRTGHYLCNACGLYH   35 (46)
T ss_dssp             SCCCTTTCCCCCSSCBCCTTCCCBCSHHHHHH
T ss_pred             CCCCCCcCCCCCCcCccCCCCCccchHHHHHH
Confidence            35688887632211 12246778888888753

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=80.72  E-value=1.3  Score=26.71  Aligned_cols=29  Identities=31%  Similarity=0.631  Sum_probs=18.6

Q ss_pred             CCCCCCCCCCCceeE-e-----CCCC---ceEeCCCcee
Q 030129            3 DAFCSDCKKHTEVVF-D-----HSAG---DTVCSECGLV   32 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~-D-----~~~G---~~vC~~CG~V   32 (182)
                      ...||.||. .+.++ .     .++|   .++|.+||..
T Consensus         9 ~~~Cp~Cg~-~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~   46 (50)
T 1tfi_A            9 LFTCGKCKK-KNCTYTQVQTRSADEPMTTFVVCNECGNR   46 (50)
T ss_dssp             CSCCSSSCS-SCEEEEEECSSSSSSCCEEEEEESSSCCE
T ss_pred             ccCCCCCCC-CEEEEEEecCcCCCCCceEEEEcCCCCCe
Confidence            357999997 44433 1     1223   3799999964

---

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	182
d1dl6a_	58	g.41.3.1 (A:) Transcription initiation factor TFII	3e-16
d1pfta_	50	g.41.3.1 (A:) Transcription initiation factor TFII	6e-15

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.2 bits (164), Expect = 3e-16
 Identities = 21/45 (46%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 6  CSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANE 50
          C +      +V D+ AGD +C ECGLV+    ID  SEWRTF+N+
Sbjct: 14 CPNHPD-AILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 57

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 50

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 63.6 bits (155), Expect = 6e-15
 Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 6  CSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTF 47
          C  C+   E+++D   G+ VC++CG V+E + ID   EWR F
Sbjct: 8  CPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAF 48

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	182
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	99.84
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	99.83
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	99.69
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	99.68
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	99.53
d1vola2	109	Transcription factor IIB (TFIIB), core domain {Hum	99.53
d2ivxa1	143	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	97.06
d2i53a1	144	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	96.95
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	96.88
d1jkwa1	151	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	96.21
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	96.17
d2hf1a1	59	Hypothetical protein CV3345 {Chromobacterium viola	95.91
d2pk7a1	59	Uncharacterized protein PFL1779 {Pseudomonas fluor	95.86
d1vd4a_	62	Transcription initiation factor TFIIE-alpha {Human	95.46
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	95.19
d2ivxa2	113	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	94.88
d2i53a2	110	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	94.39
d2cchb1	128	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	92.86
d2r7ga2	142	Retinoblastoma tumor suppressor domains {Human (Ho	92.83
d1bu2a1	127	Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}	91.78
d1nuia2	54	Zinc-binding domain of primase-helicase {Bacteriop	91.69
d1neea2	37	Zinc-binding domain of translation initiation fact	91.6
d1f5qb1	141	Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]	91.54
d1vqoz1	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	91.31
d1jj2y_	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	91.25
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	91.09
d1w98b2	140	G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax	90.99
d1k81a_	36	Zinc-binding domain of translation initiation fact	90.28
d1g3nc1	132	Viral cyclin {Kaposi's sarcoma-associated herpesvi	90.0
d2ak3a2	37	Microbial and mitochondrial ADK, insert "zinc fing	89.57
d1y0ja1	39	Erythroid transcription factor GATA-1 {Mouse (Mus	88.48
d1zina2	35	Microbial and mitochondrial ADK, insert "zinc fing	88.06
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	87.95
d1pfva3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch	87.89
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	87.54
d1rqga3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro	87.23
d1iroa_	53	Rubredoxin {Clostridium pasteurianum [TaxId: 1501]	87.19
d1e4va2	35	Microbial and mitochondrial ADK, insert "zinc fing	87.14
d1s3ga2	35	Microbial and mitochondrial ADK, insert "zinc fing	87.12
d1akya2	38	Microbial and mitochondrial ADK, insert "zinc fing	86.97
d1u5ka2	157	Recombinational repair protein RecO, C-terminal do	86.38
d2dsxa1	52	Rubredoxin {Desulfovibrio gigas [TaxId: 879]}	86.34
d1l1oc_	178	Replication protein A 70 KDa subunit (RPA70) {Huma	85.75
d6rxna_	45	Rubredoxin {Desulfovibrio desulfuricans, strain 27	84.81
d2vuti1	42	Erythroid transcription factor GATA-1 {Emericella	82.95
d3gata_	66	Erythroid transcription factor GATA-1 {Chicken (Ga	82.26
d1jkwa2	126	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	81.88
d1dx8a_	70	Rubredoxin {Guillardia theta [TaxId: 55529]}	81.58
d1wiia_	85	Hypothetical UPF0222 protein MGC4549 {Mouse (Mus m	80.97
d2apob1	55	Ribosome biogenesis protein Nop10 {Archaeon Methan	80.06

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=5e-22  Score=126.57  Aligned_cols=49  Identities=43%  Similarity=0.819  Sum_probs=45.8

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCcccccccccccCC
Q 030129            1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANE   50 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~   50 (182)
                      |..++||+||+ +++++|+.+|++||.+||+|++|++||+|||||+|+++
T Consensus         9 ~~~~~Cp~Cgs-~~ii~D~~~Ge~vC~~CG~Vlee~~ID~g~EWR~f~~d   57 (58)
T d1dl6a_           9 LPRVTCPNHPD-AILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND   57 (58)
T ss_dssp             CSCCSBTTBSS-SCCEECSSSCCEECTTTCCEECCSCCCCCCSCCCSCCC
T ss_pred             ccccCCCCCCC-CCEEEECCCCcEecccCCCEeccccccCCCcccccCCC
Confidence            45679999998 78999999999999999999999999999999999976

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.83  E-value=2.4e-21  Score=120.00  Aligned_cols=45  Identities=38%  Similarity=0.974  Sum_probs=42.5

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeeeCCCccccccccccc
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFA   48 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~   48 (182)
                      ...||+|++ +++++|+.+|++||++||+|++|++||+|||||+|+
T Consensus         5 ~~~Cp~Cgs-~~iv~D~~~Ge~vC~~CG~Viee~~iD~gpEWR~f~   49 (50)
T d1pfta_           5 QKVCPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAFD   49 (50)
T ss_dssp             CCSCTTTSC-CCEEEETTTTEEEESSSCCBCCCCCCCCCSSSSCCC
T ss_pred             cccCcCCCC-CcEEEECCCCeEecccCCcEeccccccCCCcccccC
Confidence            357999998 689999999999999999999999999999999996

>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=8.6e-18  Score=116.95  Aligned_cols=76  Identities=22%  Similarity=0.196  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeeec
Q 030129          105 LILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQR  172 (182)
Q Consensus       105 L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~r  172 (182)
                      |.+||+.|+++|++|+||+.+.++  .||+++.+. +    ++.+++|||||+|||+++     +|||+++++++++|++
T Consensus         2 L~~a~~~I~~~~~~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~~~~i~AA~iY~acr~~~~p~t~~eIa~~~~i~~~~i~k   81 (95)
T d1vola1           2 MMNAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGR   81 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTCCCTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHTTTCSCHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHH
Confidence            678999999999999999999999  999999988 4    899999999999999985     9999999999999999


Q ss_pred             eeeehhcc
Q 030129          173 RKLAEQKN  180 (182)
Q Consensus       173 ~~~~~~~~  180 (182)
                      .|....++
T Consensus        82 ~~k~i~~~   89 (95)
T d1vola1          82 CFKLILKA   89 (95)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876654

>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=99.68  E-value=1.2e-17  Score=116.80  Aligned_cols=76  Identities=9%  Similarity=0.128  Sum_probs=70.4

Q ss_pred             HHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeee
Q 030129          104 GLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQ  171 (182)
Q Consensus       104 ~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~  171 (182)
                      +|..|+..|+++|+.|+||+.|.++  .||+++.+. +    ++.+++|||||+|||+++     +|||+++++++++|+
T Consensus         1 nL~~a~~~I~~~~~~L~L~~~i~~~A~~i~k~~~~~~~~~g~~~~~iaaA~iY~Acr~~~~~~t~~eIa~~~~is~~ti~   80 (98)
T d1aisb1           1 NLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIG   80 (98)
T ss_dssp             CHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTTTTTTCCHHHHHHHHHHHHHHHHTCCCCHHHHHHHTTSCHHHHH
T ss_pred             CHHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHH
Confidence            5789999999999999999999999  999999987 4    899999999999999985     999999999999999


Q ss_pred             ceeeehhc
Q 030129          172 RRKLAEQK  179 (182)
Q Consensus       172 r~~~~~~~  179 (182)
                      +.|....+
T Consensus        81 k~yk~i~~   88 (98)
T d1aisb1          81 RSYRFIAR   88 (98)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876544

>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=99.53  E-value=2.7e-15  Score=104.11  Aligned_cols=69  Identities=10%  Similarity=0.132  Sum_probs=63.4

Q ss_pred             HHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeeeceeeeh
Q 030129          110 KTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQRRKLAE  177 (182)
Q Consensus       110 ~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~r~~~~~  177 (182)
                      ++|++||++|+||+.+.+.  .||+++.+. +    +|.+++|||||+|||+++     +|||++++++++||+++|-..
T Consensus         5 d~I~R~~~~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~vaAA~iY~a~r~~~~~~t~~eIa~~~~vs~~tI~~~yk~l   84 (95)
T d1aisb2           5 DYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNRYKEL   84 (95)
T ss_dssp             GGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCcHHhHHHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            6899999999999999998  999999887 4    999999999999999985     999999999999999998654


Q ss_pred             h
Q 030129          178 Q  178 (182)
Q Consensus       178 ~  178 (182)
                      .
T Consensus        85 ~   85 (95)
T d1aisb2          85 V   85 (95)
T ss_dssp             H
T ss_pred             H
Confidence            4

>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=2.6e-15  Score=106.76  Aligned_cols=70  Identities=3%  Similarity=-0.014  Sum_probs=64.0

Q ss_pred             HHHHHHHHHHHhCChHHHHHH--HHHHHHHhc-c----CHHHHHHHHHHHHHhhCC-----HHHHHhcCCCceeeeceee
Q 030129          108 AFKTIATMSDRIGQMRYIRRW--KIKSLVEAE-I----KTHYWLLACTLLVDKKTS-----HALLRKSALSPMELQRRKL  175 (182)
Q Consensus       108 a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~-l----~~~~v~AAclY~acr~~~-----~eia~~~~v~~~~i~r~~~  175 (182)
                      +.++|+++|++|+||..+.+.  +||+++.+. +    ++.+++|||||+|||+++     +|||+++||+++||++.|-
T Consensus         4 ~~d~i~Rf~s~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~iaAa~iY~a~r~~~~~~t~~eIa~~~~vs~~tI~k~yk   83 (109)
T d1vola2           4 TGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYR   83 (109)
T ss_dssp             GGGTHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHHHTSSSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            457899999999999999998  999999887 4    999999999999999985     9999999999999999984


Q ss_pred             eh
Q 030129          176 AE  177 (182)
Q Consensus       176 ~~  177 (182)
                      -.
T Consensus        84 ~l   85 (109)
T d1vola2          84 LI   85 (109)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin-T2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.06  E-value=0.00085  Score=47.59  Aligned_cols=55  Identities=11%  Similarity=0.000  Sum_probs=46.1

Q ss_pred             hHHH-HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC
Q 030129          102 DRGL-ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       102 er~L-~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~  156 (182)
                      |..+ ..+.+.|.+++..|+||..+.-.  .+|.+....  +   ++..+++||||+||+.+.
T Consensus        27 E~~~R~~~~~~i~~~~~~l~l~~~t~~~A~~l~~Rf~~~~s~~~~~~~~va~acl~LA~K~eE   89 (143)
T d2ivxa1          27 ELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE   89 (143)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHhcc
Confidence            4444 45789999999999999988777  888887554  4   999999999999999883

>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin K
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.95  E-value=0.001  Score=47.37  Aligned_cols=51  Identities=12%  Similarity=-0.079  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~  156 (182)
                      ..+.+.|.+++..|+||..+.-.  .+|.+....  +   ++..+++||||+||+.+.
T Consensus        38 ~~~~~~i~~~~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~~lva~acl~LA~K~eE   95 (144)
T d2i53a1          38 REGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEE   95 (144)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhhCcccchhHHHHHHHHHHHHHHhhc
Confidence            46889999999999999988777  888887655  4   899999999999999873

>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27e
domain: Ribosomal protein S27e
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.88  E-value=0.0002  Score=43.87  Aligned_cols=30  Identities=33%  Similarity=0.801  Sum_probs=27.8

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      .+||.|+. ..+++.+++-...|..||.+|-
T Consensus         8 VkC~~C~n-~~ivFsha~t~V~C~~Cg~~L~   37 (58)
T d1qxfa_           8 VKCPDCEH-EQVIFDHPSTIVKCIICGRTVA   37 (58)
T ss_dssp             EECTTTCC-EEEEESSCSSCEECSSSCCEEE
T ss_pred             eECCCCCC-eEEEEecCceEEEccccCCEEe
Confidence            57999997 7899999999999999999995

>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin H (mcs2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.21  E-value=0.0086  Score=42.69  Aligned_cols=54  Identities=13%  Similarity=0.081  Sum_probs=43.5

Q ss_pred             hHHHH-HHHHHHHHHHHHhC--ChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhC
Q 030129          102 DRGLI-LAFKTIATMSDRIG--QMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKT  155 (182)
Q Consensus       102 er~L~-~a~~~I~~i~~~L~--L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~  155 (182)
                      +..+. ..-+.|.++|..|+  ||..+.-.  .+|++....  +   ++..+++||||+||+.+
T Consensus        43 e~~l~~~~~~~l~~~~~~~k~~l~~~~~~tA~~~~~RF~~~~s~~~~~~~li~~acl~LA~K~e  106 (151)
T d1jkwa1          43 EMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVD  106 (151)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHhhcCccccccHHHHHHHHHHHHHHHc
Confidence            44443 46688999999765  88988777  888887655  3   99999999999999987

>d2jnya1 b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg1592 {Corynebacterium glutamicum [TaxId: 1718]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein Cgl1405/cg1592
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=96.17  E-value=0.0027  Score=38.84  Aligned_cols=28  Identities=18%  Similarity=0.118  Sum_probs=25.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ..||.|++  .+..|...+.++|..||++.
T Consensus        11 L~CP~ck~--~L~~~~~~~~Lvc~~~~~~Y   38 (59)
T d2jnya1          11 LACPKDKG--PLRYLESEQLLVNERLNLAY   38 (59)
T ss_dssp             CBCTTTCC--BCEEETTTTEEEETTTTEEE
T ss_pred             hcCCCCCC--EeEEeCCCCEEEcCccCccc
Confidence            46999996  68889999999999999986

>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Hypothetical protein CV3345
species: Chromobacterium violaceum [TaxId: 536]

Probab=95.91  E-value=0.0032  Score=38.48  Aligned_cols=28  Identities=32%  Similarity=0.673  Sum_probs=25.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ..||.|++  .+.+|.+.++++|..||+..
T Consensus         8 L~CP~ck~--~L~~~~~~~~Lvc~~~~l~Y   35 (59)
T d2hf1a1           8 LVCPLCKG--PLVFDKSKDELICKGDRLAF   35 (59)
T ss_dssp             CBCTTTCC--BCEEETTTTEEEETTTTEEE
T ss_pred             hcCCCCCC--eeeEeCCCCEEecCCcCccc
Confidence            46999996  68889999999999999886

>d2pk7a1 b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pseudomonas fluorescens [TaxId: 294]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein PFL1779
species: Pseudomonas fluorescens [TaxId: 294]

Probab=95.86  E-value=0.003  Score=38.64  Aligned_cols=29  Identities=17%  Similarity=0.344  Sum_probs=25.4

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ...||.|++  .+.+|.+.++++|..||+..
T Consensus         6 iL~CP~ck~--~L~~~~~~~~Lvc~~~~laY   34 (59)
T d2pk7a1           6 ILACPICKG--PLKLSADKTELISKGAGLAY   34 (59)
T ss_dssp             TCCCTTTCC--CCEECTTSSEEEETTTTEEE
T ss_pred             heECCCCCC--cceEeCCCCEEecCCcCccc
Confidence            357999996  68899999999999999886

>d1vd4a_ g.41.3.1 (A:) Transcription initiation factor TFIIE-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIE-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.46  E-value=0.0014  Score=40.51  Aligned_cols=32  Identities=25%  Similarity=0.497  Sum_probs=25.5

Q ss_pred             CCCCCCCCCC-----ceeEeCCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHT-----EVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~-----~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      .+||.|++.-     .-.+|+.+|...|..|+..|.|
T Consensus        15 y~Cp~C~~~ys~Lda~~L~d~~~~~F~C~~C~~el~e   51 (62)
T d1vd4a_          15 FKCPVCSSTFTDLEANQLFDPMTGTFRCTFCHTEVEE   51 (62)
T ss_dssp             EECSSSCCEEEHHHHHHHEETTTTEEBCSSSCCBCEE
T ss_pred             eECCCCCCCcchhhHHHhcCcCCCeEEecCCCCEEec
Confidence            4699999731     1257999999999999999865

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: PhnA zinc-binding domain
domain: Hypothetical protein PA0128, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.19  E-value=0.0075  Score=33.34  Aligned_cols=26  Identities=23%  Similarity=0.478  Sum_probs=19.1

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV   32 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V   32 (182)
                      -.||.|++ .-.-.  +.+.+||.+||.-
T Consensus         4 P~CP~C~s-eytYe--dg~l~vCPeC~hE   29 (38)
T d2akla2           4 PPCPQCNS-EYTYE--DGALLVCPECAHE   29 (38)
T ss_dssp             CCCTTTCC-CCCEE--CSSSEEETTTTEE
T ss_pred             CcCCCCCC-cceEc--CCCEEECCcccCc
Confidence            46999997 32222  4678999999974

>d2ivxa2 a.74.1.1 (A:150-262) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin-T2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.88  E-value=0.025  Score=38.73  Aligned_cols=51  Identities=8%  Similarity=0.068  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHhCChHHHHHH--HHHHHHHh--c--c--CHHHHHHHHHHHHHhhCCHHH
Q 030129          109 FKTIATMSDRIGQMRYIRRW--KIKSLVEA--E--I--KTHYWLLACTLLVDKKTSHAL  159 (182)
Q Consensus       109 ~~~I~~i~~~L~L~~~v~~~--~i~k~a~~--~--l--~~~~v~AAclY~acr~~~~ei  159 (182)
                      .++|-.++..|+.+..+...  .+.....-  -  +  .|..||+||||+|+|..+.++
T Consensus         4 hk~ll~~~k~l~~~~~l~q~AW~~lnDs~r~T~lcL~~~P~~IA~a~I~LA~~~~~~~~   62 (113)
T d2ivxa2           4 HTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEI   62 (113)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCGGGTSCHHHHHHHHHHHHHHHHTCCC
T ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHHHhccCCeeeecCcHHHHHHHHHHHHHHhCCCC
Confidence            46778888899988888777  55555432  2  3  999999999999999875444

>d2i53a2 a.74.1.1 (A:158-267) Cyclin K {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin K
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.39  E-value=0.035  Score=37.44  Aligned_cols=51  Identities=6%  Similarity=0.100  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHhCChHHHHHH---HHHHHHHhc------c--CHHHHHHHHHHHHHhhCCHHH
Q 030129          109 FKTIATMSDRIGQMRYIRRW---KIKSLVEAE------I--KTHYWLLACTLLVDKKTSHAL  159 (182)
Q Consensus       109 ~~~I~~i~~~L~L~~~v~~~---~i~k~a~~~------l--~~~~v~AAclY~acr~~~~ei  159 (182)
                      .++|-.+...|+........   .=+..+.|.      |  .|..||+||||+|++..+.+|
T Consensus         4 ~~~L~~~~~~l~~~~~~~~~l~q~AW~~lNDs~rT~lcL~~~P~~IA~a~I~lA~~~~~~~i   65 (110)
T d2i53a2           4 YQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEI   65 (110)
T ss_dssp             HHHHHHHHHTBCSCHHHHHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHHHHTCCG
T ss_pred             cHHHHHHHHHhcCccccchHHHHHHHHHHHHHhcCCchhccCcHHHHHHHHHHHHHHhCCCC
Confidence            46777788888776543222   222333332      2  999999999999999886555

>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin A
species: Cow (Bos taurus) [TaxId: 9913]

Probab=92.86  E-value=0.17  Score=34.56  Aligned_cols=50  Identities=10%  Similarity=-0.000  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhC
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKT  155 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~  155 (182)
                      ....+.|-+++..++++..+.-.  .++.+....  +   ....+++||+|+|++.+
T Consensus        32 ~~li~W~~~v~~~~~l~~~t~~lAv~llDr~l~~~~i~~~~~qLi~~~cl~iAsK~e   88 (128)
T d2cchb1          32 AILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFE   88 (128)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcccCCchHHHHHHHHHHHHHHHHHH
Confidence            55889999999999999887766  777777555  3   77899999999999986

>d2r7ga2 a.74.1.3 (A:644-785) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Retinoblastoma tumor suppressor domains
domain: Retinoblastoma tumor suppressor domains
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.83  E-value=0.23  Score=35.05  Aligned_cols=51  Identities=10%  Similarity=0.113  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHhCChH-HHHHH--HHHHHHHhc---c----CHHHHHHHHHHHHHhhCC
Q 030129          106 ILAFKTIATMSDRIGQMR-YIRRW--KIKSLVEAE---I----KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~-~v~~~--~i~k~a~~~---l----~~~~v~AAclY~acr~~~  156 (182)
                      .-|...|..+|++|++++ .+.+.  .+|+.+..+   |    ..+.++-+|+|..|+...
T Consensus        13 ~La~~Rl~~LC~~L~~~~~~l~~~Iw~~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~   73 (142)
T d2r7ga2          13 RLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKN   73 (142)
T ss_dssp             HHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHHHHhHHHHhccchhHHHHHHHHHHHHhcc
Confidence            448889999999998864 56665  888776544   3    899999999999999774

>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Herpesvirus saimiri [TaxId: 10381]

Probab=91.78  E-value=0.41  Score=32.62  Aligned_cols=51  Identities=10%  Similarity=0.032  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~  156 (182)
                      ....+.+-+++..++|+..+.-.  .++.+....  +   ....+++||+++|++.+.
T Consensus        32 ~~lidWl~~v~~~~~l~~eTl~lAv~llDryl~~~~i~~~~lqLi~~tcL~IAsK~ee   89 (127)
T d1bu2a1          32 TILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRT   89 (127)
T ss_dssp             HHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSCCCTTTHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHCCChHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHh
Confidence            45789999999999998876665  888877665  3   889999999999999873

>d1nuia2 g.41.3.2 (A:10-63) Zinc-binding domain of primase-helicase {Bacteriophage T7 [TaxId: 10760]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: DNA primase zinc finger
domain: Zinc-binding domain of primase-helicase
species: Bacteriophage T7 [TaxId: 10760]

Probab=91.69  E-value=0.052  Score=32.25  Aligned_cols=31  Identities=23%  Similarity=0.370  Sum_probs=23.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      +.-||.||+... .--++.|-..|-.|+.-..
T Consensus         5 H~pCp~CgSSDa-~a~y~DGh~~CFsC~~~~~   35 (54)
T d1nuia2           5 HIPCDNCGSSDG-NSLFSDGHTFCYVCEKWTA   35 (54)
T ss_dssp             EECCSSSCCSSC-EEEETTSCEEETTTCCEEC
T ss_pred             ccCCCCCCCCCC-CeEccCCCeEeeeCCCCcC
Confidence            457999998443 4445789999999998764

>d1neea2 g.59.1.1 (A:99-135) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Small proteins
fold: Zinc-binding domain of translation initiation factor 2 beta
superfamily: Zinc-binding domain of translation initiation factor 2 beta
family: Zinc-binding domain of translation initiation factor 2 beta
domain: Zinc-binding domain of translation initiation factor 2 beta
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=91.60  E-value=0.051  Score=29.73  Aligned_cols=27  Identities=22%  Similarity=0.705  Sum_probs=20.9

Q ss_pred             CCCCCCCC-CceeEeCCCCceEeCCCce
Q 030129            5 FCSDCKKH-TEVVFDHSAGDTVCSECGL   31 (182)
Q Consensus         5 ~Cp~Cg~~-~~iv~D~~~G~~vC~~CG~   31 (182)
                      .|+.|++. +.++.|...=.+.|..||.
T Consensus         3 ~C~~C~spDT~l~ke~R~~~l~C~aCGa   30 (37)
T d1neea2           3 ICHECNRPDTRIIREGRISLLKCEACGA   30 (37)
T ss_dssp             HHTCCSSCSSCCEEETTTTEEECSTTSC
T ss_pred             ECCCCCCCCCEEEEcCCEEEEEeccCCC
Confidence            59999984 4566666666789999995

>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Murine herpesvirus 68 [TaxId: 33708]

Probab=91.54  E-value=0.29  Score=34.02  Aligned_cols=59  Identities=7%  Similarity=-0.075  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhCC------HHHHHhcC
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKTS------HALLRKSA  164 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~~------~eia~~~~  164 (182)
                      ....+.+-+++..++|+..+.-.  .++.+....  +   ....+++||+++|++.+.      .++...++
T Consensus        45 ~~lvdWm~~v~~~~~l~~etl~lAv~llDrfls~~~i~~~~lqL~a~tcL~IAsK~ee~~~~~~~~l~~~~~  116 (141)
T d1f5qb1          45 KVLTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLCG  116 (141)
T ss_dssp             HHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHhc
Confidence            45789999999999998877666  888877655  3   889999999999999872      55555443

>d1vqoz1 g.41.8.1 (Z:10-82) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=91.31  E-value=0.061  Score=33.86  Aligned_cols=29  Identities=24%  Similarity=0.484  Sum_probs=24.5

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      ..||.|+. . -+.....|-..|..||..+.
T Consensus        28 y~Cp~Cgk-~-~vkR~a~GIW~C~kC~~~~A   56 (73)
T d1vqoz1          28 HACPNCGE-D-RVDRQGTGIWQCSYCDYKFT   56 (73)
T ss_dssp             BCCSSSSC-S-CEEEEETTEEEETTTCCEEE
T ss_pred             ccCCCCCC-c-eeEEEEEEEEECCCCCCEEe
Confidence            47999997 3 35677999999999999985

>d1jj2y_ g.41.8.1 (Y:) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=91.25  E-value=0.072  Score=33.50  Aligned_cols=30  Identities=20%  Similarity=0.463  Sum_probs=24.9

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      ..||.||. . -+.....|-.-|..||.++.-
T Consensus        28 y~Cp~Cgk-~-~vkR~a~GIW~C~kC~~~~AG   57 (73)
T d1jj2y_          28 HKCPVCGF-K-KLKRAGTGIWMCGHCGYKIAG   57 (73)
T ss_dssp             BCCSSSCC-S-CEEEEETTEEEETTTCCEEEC
T ss_pred             ccCCCCCC-C-ceEEEEEEEEECCCCCCEEeC
Confidence            47999997 3 356779999999999999853

>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27a
domain: Ribosomal protein S27ae
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=91.09  E-value=0.08  Score=31.34  Aligned_cols=27  Identities=26%  Similarity=0.759  Sum_probs=21.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCcee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV   32 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~V   32 (182)
                      ..||.||. ..++-++. ....|..||+-
T Consensus        19 k~CP~CG~-GvFmA~H~-dR~~CGKCgyT   45 (55)
T d2k4xa1          19 RFCPRCGP-GVFLAEHA-DRYSCGRCGYT   45 (55)
T ss_dssp             CCCTTTTT-TCCCEECS-SEEECTTTCCC
T ss_pred             CcCcCCCC-cEEeeecC-CCccccCCccc
Confidence            46999995 66676665 58999999986

>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: G1/S-specific cyclin-E1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.99  E-value=0.65  Score=31.92  Aligned_cols=61  Identities=7%  Similarity=-0.027  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHHHHHHhCChHHHHHH--HHHHHHHh-c--c---CHHHHHHHHHHHHHhhCC------HHHHHhcC
Q 030129          104 GLILAFKTIATMSDRIGQMRYIRRW--KIKSLVEA-E--I---KTHYWLLACTLLVDKKTS------HALLRKSA  164 (182)
Q Consensus       104 ~L~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~-~--l---~~~~v~AAclY~acr~~~------~eia~~~~  164 (182)
                      .-....+.|-+++..++|+..+.-.  .++.+... .  .   ....+++|||++|++.+.      .++....+
T Consensus        42 ~R~~lidW~~~v~~~~~l~~et~~lAv~llDryl~~~~~v~~~~lqL~a~acL~IAsK~ee~~~~~~~~l~~~~~  116 (140)
T d1w98b2          42 MRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTD  116 (140)
T ss_dssp             HHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhccccccHHHHhHHHHHHHHHHHHHcccCCCCHHHHHHHHc
Confidence            3355889999999999999887776  88877644 3  2   678999999999999862      56655443

>d1k81a_ g.59.1.1 (A:) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Small proteins
fold: Zinc-binding domain of translation initiation factor 2 beta
superfamily: Zinc-binding domain of translation initiation factor 2 beta
family: Zinc-binding domain of translation initiation factor 2 beta
domain: Zinc-binding domain of translation initiation factor 2 beta
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=90.28  E-value=0.041  Score=29.95  Aligned_cols=28  Identities=25%  Similarity=0.679  Sum_probs=19.2

Q ss_pred             CCCCCCCC-CceeEeCCCCceEeCCCcee
Q 030129            5 FCSDCKKH-TEVVFDHSAGDTVCSECGLV   32 (182)
Q Consensus         5 ~Cp~Cg~~-~~iv~D~~~G~~vC~~CG~V   32 (182)
                      .|+.|++. +.++.|...=.+.|..||.-
T Consensus         2 ~C~~C~spDT~l~ke~R~~~l~C~aCGa~   30 (36)
T d1k81a_           2 ICRECGKPDTKIIKEGRVHLLKCMACGAI   30 (36)
T ss_dssp             CCSSSCSCEEEEEEETTEEEEEEETTTEE
T ss_pred             CCCCCCCCCCEEEEcCCEEEEEeccCCCC
Confidence            69999984 23444444445789999964

>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]

Probab=90.00  E-value=0.35  Score=33.12  Aligned_cols=50  Identities=10%  Similarity=-0.025  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHHHhCChHHHHHH--HHHHHHHhc--c---CHHHHHHHHHHHHHhhC
Q 030129          106 ILAFKTIATMSDRIGQMRYIRRW--KIKSLVEAE--I---KTHYWLLACTLLVDKKT  155 (182)
Q Consensus       106 ~~a~~~I~~i~~~L~L~~~v~~~--~i~k~a~~~--l---~~~~v~AAclY~acr~~  155 (182)
                      ....+.+-+++..++|+..+.-.  .++.+....  +   ....+++||+++|++.+
T Consensus        37 ~~lidWl~~v~~~~~l~~et~~lAv~llDrfls~~~v~~~~lqLia~tcl~iAsK~e   93 (132)
T d1g3nc1          37 KLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLR   93 (132)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCcccCcHHHHHHHHHHHHHHHHHhc
Confidence            45779999999999999877666  888877655  4   77899999999999975

>d2ak3a2 g.41.2.1 (A:125-161) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=89.57  E-value=0.013  Score=32.22  Aligned_cols=30  Identities=10%  Similarity=0.030  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ..||.||..-++.+++..=+.+|-.||.-|
T Consensus         3 ~vc~~cG~~Yh~~~~pPk~~g~CD~cg~~L   32 (37)
T d2ak3a2           3 WIHPGSGRVYNIEFNPPKTMGIDDLTGEPL   32 (37)
T ss_dssp             EEETTTTEEEETTTBCCSSTTBCTTTCCBC
T ss_pred             eeeCCcCChhhhccCCccccCCccCCCCcC
Confidence            457888865566667777777888887543

>d1y0ja1 g.39.1.1 (A:200-238) Erythroid transcription factor GATA-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Erythroid transcription factor GATA-1
domain: Erythroid transcription factor GATA-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.48  E-value=0.14  Score=28.14  Aligned_cols=31  Identities=23%  Similarity=0.566  Sum_probs=19.9

Q ss_pred             CCCCCCCCCCC-ceeEeCCCCceEeCCCceee
Q 030129            3 DAFCSDCKKHT-EVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         3 ~~~Cp~Cg~~~-~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ...|.+|+... +.--....|.+.|..||+-.
T Consensus         2 ~r~C~~Cgtt~Tp~WR~gp~G~~LCNACGl~~   33 (39)
T d1y0ja1           2 ARECVNCGATATPLWRRDRTGHYLCNACGLYH   33 (39)
T ss_dssp             CCCCSSSCCCCCSCCEECTTSCEECSSHHHHH
T ss_pred             cCCCCCCCCCCCcccccCCCCCEeeHHhHHHH
Confidence            35688998632 22223356788999998753

>d1zina2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=88.06  E-value=0.035  Score=30.05  Aligned_cols=27  Identities=30%  Similarity=0.791  Sum_probs=14.6

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCce
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGL   31 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~   31 (182)
                      .||.||..-++.+.+..=+.+|..||-
T Consensus         4 ~C~~CG~~Yh~~~~pPk~~g~CD~cG~   30 (35)
T d1zina2           4 ICRNCGATYHLIFHPPAKPGVCDKCGG   30 (35)
T ss_dssp             EETTTCCEEETTTBCCSSTTBCTTTCC
T ss_pred             CCcCcCchhccccCCCCCCCcCCCCCC
Confidence            466666533444555555556666654

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.95  E-value=0.19  Score=31.13  Aligned_cols=28  Identities=14%  Similarity=0.691  Sum_probs=23.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceee
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      ..||.|+.  .++.|+..-.+.|..||..+
T Consensus        19 k~CP~C~~--~~~~~~~~~~~~C~~C~~~f   46 (73)
T d2ct7a1          19 LWCAQCSF--GFIYEREQLEATCPQCHQTF   46 (73)
T ss_dssp             ECCSSSCC--CEECCCSCSCEECTTTCCEE
T ss_pred             CCCCCCCC--EeEECCCCCEEEcCCCCCeE
Confidence            47999996  47777777779999999986

>d1pfva3 g.41.1.1 (A:141-175) Methionyl-tRNA synthetase (MetRS), Zn-domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Escherichia coli [TaxId: 562]

Probab=87.89  E-value=0.076  Score=28.65  Aligned_cols=23  Identities=35%  Similarity=0.895  Sum_probs=16.9

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      .||.|+. .+     ..|+ -|..||..++
T Consensus         4 ~CP~C~~-~~-----a~GD-qCe~CG~~~~   26 (35)
T d1pfva3           4 TCPKCKS-PD-----QYGD-NCEVCGATYS   26 (35)
T ss_dssp             ECTTTCC-SS-----EETT-BCTTTCCBCC
T ss_pred             ECCCCCC-cc-----cccc-cHHHcCCcCC
Confidence            6999997 22     3454 4999999985

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.54  E-value=0.61  Score=28.94  Aligned_cols=32  Identities=31%  Similarity=0.581  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCCceeE-eC--------CCCceEeCCCceeeeC
Q 030129            3 DAFCSDCKKHTEVVF-DH--------SAGDTVCSECGLVLES   35 (182)
Q Consensus         3 ~~~Cp~Cg~~~~iv~-D~--------~~G~~vC~~CG~Vl~e   35 (182)
                      ...||.||.. ..++ -.        .+=.++|.+||..-.+
T Consensus        23 ~~~CpkCg~~-~a~~~q~QtRsaDE~mT~Fy~C~~C~h~Wr~   63 (72)
T d1twfi2          23 DRECPKCHSR-ENVFFQSQQRRKDTSMVLFFVCLSCSHIFTS   63 (72)
T ss_dssp             CCCCTTTCCC-CEEEEECSSCCTTCCCCEEEEETTTCCEEEC
T ss_pred             CCCCCCCCCC-eEEEEEeecCccCCCceEEEEcCCCCCCccc
Confidence            3679999974 4443 21        2224899999987443

>d1rqga3 g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyrococcus abyssi [TaxId: 29292]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Pyrococcus abyssi [TaxId: 29292]

Probab=87.23  E-value=0.13  Score=27.69  Aligned_cols=25  Identities=32%  Similarity=0.740  Sum_probs=18.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCceeeeC
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      -.||.|+. .     ...|+ -|..||..++.
T Consensus         3 G~CP~C~~-~-----~a~GD-qCe~CG~~~~p   27 (35)
T d1rqga3           3 GTCPYCGA-E-----DQKGD-QCEVCGRPLTP   27 (35)
T ss_dssp             SBCSSSCC-S-----CCCTT-TCSSSCCCCCT
T ss_pred             EECCCCCC-C-----cccCc-chhhcCCccCH
Confidence            46999996 2     24555 49999998853

>d1iroa_ g.41.5.1 (A:) Rubredoxin {Clostridium pasteurianum [TaxId: 1501]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Clostridium pasteurianum [TaxId: 1501]

Probab=87.19  E-value=0.12  Score=30.49  Aligned_cols=13  Identities=23%  Similarity=0.823  Sum_probs=7.1

Q ss_pred             eEeCCCceeeeCC
Q 030129           24 TVCSECGLVLESH   36 (182)
Q Consensus        24 ~vC~~CG~Vl~e~   36 (182)
                      +.|..||.|.++.
T Consensus         4 y~C~~CgyiYd~~   16 (53)
T d1iroa_           4 YTCTVCGYIYNPE   16 (53)
T ss_dssp             EEETTTCCEECTT
T ss_pred             eEcCCCCcEECcc
Confidence            4555566555543

>d1e4va2 g.41.2.1 (A:122-156) Microbial and mitochondrial ADK, insert "zinc finger" domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Escherichia coli [TaxId: 562]

Probab=87.14  E-value=0.029  Score=30.40  Aligned_cols=27  Identities=11%  Similarity=0.033  Sum_probs=14.1

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCce
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGL   31 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~   31 (182)
                      .||.||..-++.+++..=+.+|..||-
T Consensus         4 ~c~~cG~~Yh~~~~PPk~~g~CD~cg~   30 (35)
T d1e4va2           4 VHAPSGRVYHVKFNPPKVEGKDDVTGE   30 (35)
T ss_dssp             EETTTTEEEETTTBCCSSTTBCTTTCC
T ss_pred             CCcCcCChhhhccCccccCCcccCCCC
Confidence            355555533444455555555555554

>d1s3ga2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus globisporus [TaxId: 1459]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus globisporus [TaxId: 1459]

Probab=87.12  E-value=0.038  Score=29.88  Aligned_cols=27  Identities=19%  Similarity=0.485  Sum_probs=13.8

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCce
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGL   31 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~   31 (182)
                      .||.||..-++.+.+..=+.+|..||-
T Consensus         4 ~C~~CG~~Yh~~~~pPk~~g~CD~cg~   30 (35)
T d1s3ga2           4 ICKVCGTSYHLLFNPPQVEGKCDKDGG   30 (35)
T ss_dssp             EETTTCCEEETTTBCCSBTTBCTTTCC
T ss_pred             CCcCcCchhccccCCCCCCCccCCCCC
Confidence            355555433444455555555555554

>d1akya2 g.41.2.1 (A:131-168) Microbial and mitochondrial ADK, insert "zinc finger" domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.97  E-value=0.052  Score=29.88  Aligned_cols=27  Identities=11%  Similarity=0.121  Sum_probs=16.0

Q ss_pred             CCCCCCCCCceeEeCCCCceEeCCCce
Q 030129            5 FCSDCKKHTEVVFDHSAGDTVCSECGL   31 (182)
Q Consensus         5 ~Cp~Cg~~~~iv~D~~~G~~vC~~CG~   31 (182)
                      .||.||..-++.+.+..=+.+|-.||-
T Consensus         4 ~C~~cG~~Yh~~~~ppk~~g~CD~cg~   30 (38)
T d1akya2           4 IHPASGRSYHKIFNPPKEDMKDDVTGE   30 (38)
T ss_dssp             ECTTTCCEEETTTBCCSSTTBCTTTCC
T ss_pred             CCcCccchhhhhccCcCcCCccCCCCC
Confidence            466666544455555555566666664

>d1u5ka2 g.45.1.2 (A:81-237) Recombinational repair protein RecO, C-terminal domain {Deinococcus radiodurans [TaxId: 1299]}

class: Small proteins
fold: ArfGap/RecO-like zinc finger
superfamily: ArfGap/RecO-like zinc finger
family: RecO C-terminal domain-like
domain: Recombinational repair protein RecO, C-terminal domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=86.38  E-value=0.2  Score=35.32  Aligned_cols=28  Identities=29%  Similarity=0.571  Sum_probs=23.8

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCce
Q 030129            4 AFCSDCKKHTEVVFDHSAGDTVCSECGL   31 (182)
Q Consensus         4 ~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~   31 (182)
                      ..|..||......+|...|-.+|..|+.
T Consensus        71 ~~C~~cg~~~~~~f~~~~Gg~~C~~c~~   98 (157)
T d1u5ka2          71 ARCARCGAPDPEHPDPLGGQLLCSKCAA   98 (157)
T ss_dssp             SBCTTTCCBSCCEECTTTSSEECTTTCS
T ss_pred             hhHhcCCCCCCCcccccCCeeECCCCCC
Confidence            4699999876778899999999999974

>d2dsxa1 g.41.5.1 (A:1-52) Rubredoxin {Desulfovibrio gigas [TaxId: 879]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio gigas [TaxId: 879]

Probab=86.34  E-value=0.14  Score=30.03  Aligned_cols=14  Identities=29%  Similarity=0.743  Sum_probs=7.9

Q ss_pred             eEeCCCceeeeCCC
Q 030129           24 TVCSECGLVLESHS   37 (182)
Q Consensus        24 ~vC~~CG~Vl~e~~   37 (182)
                      ++|..||.|.++..
T Consensus         4 y~C~~CgyiYdp~~   17 (52)
T d2dsxa1           4 YVCTVCGYEYDPAK   17 (52)
T ss_dssp             EEETTTCCEECTTT
T ss_pred             EEeCCCCeEECccc
Confidence            45666666655444

>d1l1oc_ b.40.4.3 (C:) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 70 KDa subunit (RPA70)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.75  E-value=0.23  Score=36.20  Aligned_cols=27  Identities=30%  Similarity=0.716  Sum_probs=21.7

Q ss_pred             CCCC--CCCCCceeEeCCCCceEeCCCceeee
Q 030129            5 FCSD--CKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         5 ~Cp~--Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      .||.  |++  . ++|...|.+.|..||.+.+
T Consensus        42 aCp~~~C~K--K-v~~~~~g~~~C~kC~~~~~   70 (178)
T d1l1oc_          42 ACPTQDCNK--K-VIDQQNGLYRCEKCDTEFP   70 (178)
T ss_dssp             BCCSTTCCC--B-CEEETTTEEEETTTTEEES
T ss_pred             CCCCcccCC--c-cccCCCCcEECCCCCCcCC
Confidence            4997  876  3 4678889999999999864

>d6rxna_ g.41.5.1 (A:) Rubredoxin {Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]

Probab=84.81  E-value=0.11  Score=29.56  Aligned_cols=13  Identities=31%  Similarity=0.782  Sum_probs=7.3

Q ss_pred             eEeCCCceeeeCC
Q 030129           24 TVCSECGLVLESH   36 (182)
Q Consensus        24 ~vC~~CG~Vl~e~   36 (182)
                      ++|+.||.|.++.
T Consensus         4 y~C~~CgyiYd~~   16 (45)
T d6rxna_           4 YVCNVCGYEYDPA   16 (45)
T ss_dssp             EEETTTCCEECGG
T ss_pred             eEeCCCCeEECcc
Confidence            5566666665443

>d2vuti1 g.39.1.1 (I:671-712) Erythroid transcription factor GATA-1 {Emericella nidulans [TaxId: 162425]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Erythroid transcription factor GATA-1
domain: Erythroid transcription factor GATA-1
species: Emericella nidulans [TaxId: 162425]

Probab=82.95  E-value=0.17  Score=28.32  Aligned_cols=29  Identities=31%  Similarity=0.802  Sum_probs=18.4

Q ss_pred             CCCCCCCCC-ceeEeCCCCceEeCCCceee
Q 030129            5 FCSDCKKHT-EVVFDHSAGDTVCSECGLVL   33 (182)
Q Consensus         5 ~Cp~Cg~~~-~iv~D~~~G~~vC~~CG~Vl   33 (182)
                      .|-+|+... ..--.-..|..+|..||+-.
T Consensus         2 ~C~nC~tt~Tp~WRr~~~G~~lCNACGl~~   31 (42)
T d2vuti1           2 TCTNCFTQTTPLWRRNPEGQPLCNACGLFL   31 (42)
T ss_dssp             CCSSSCCCCCSCCEECTTSCEECHHHHHHH
T ss_pred             cCCCCCCCCCccceeCCCCCCchhhhhHHH
Confidence            588888632 22223356788888888753

>d3gata_ g.39.1.1 (A:) Erythroid transcription factor GATA-1 {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Erythroid transcription factor GATA-1
domain: Erythroid transcription factor GATA-1
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=82.26  E-value=0.25  Score=30.31  Aligned_cols=33  Identities=33%  Similarity=0.752  Sum_probs=22.4

Q ss_pred             CCCCCCCCCCC-ceeEeCCCCceEeCCCceeeeC
Q 030129            3 DAFCSDCKKHT-EVVFDHSAGDTVCSECGLVLES   35 (182)
Q Consensus         3 ~~~Cp~Cg~~~-~iv~D~~~G~~vC~~CG~Vl~e   35 (182)
                      ...|-+|+... .+--....|.++|..||+-..-
T Consensus         4 g~~C~nCgt~~Tp~WRr~~~G~~lCNACGl~~~~   37 (66)
T d3gata_           4 GTVCSNCQTSTTTLWRRSPMGDPVCNACGLYYKL   37 (66)
T ss_dssp             TCCCTTTCCCCCSSEEECTTSCEEEHHHHHHHHH
T ss_pred             CCCCCCCCCCCCcccccCCCCCcccchhHHHHHH
Confidence            35699998632 2223346788999999988643

>d1jkwa2 a.74.1.1 (A:162-287) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin H (mcs2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.88  E-value=0.72  Score=31.43  Aligned_cols=18  Identities=11%  Similarity=0.080  Sum_probs=16.9

Q ss_pred             CHHHHHHHHHHHHHhhCC
Q 030129          139 KTHYWLLACTLLVDKKTS  156 (182)
Q Consensus       139 ~~~~v~AAclY~acr~~~  156 (182)
                      .|..||.||||+|++..+
T Consensus        47 ~P~qIalaal~~a~~~~~   64 (126)
T d1jkwa2          47 TPSQIALTAILSSASRAG   64 (126)
T ss_dssp             CHHHHHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHHHHcC
Confidence            999999999999999875

>d1dx8a_ g.41.5.1 (A:) Rubredoxin {Guillardia theta [TaxId: 55529]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Guillardia theta [TaxId: 55529]

Probab=81.58  E-value=0.68  Score=28.58  Aligned_cols=20  Identities=25%  Similarity=0.695  Sum_probs=16.5

Q ss_pred             eCCCCceEeCCCceeeeCCC
Q 030129           18 DHSAGDTVCSECGLVLESHS   37 (182)
Q Consensus        18 D~~~G~~vC~~CG~Vl~e~~   37 (182)
                      +.++|.++|..||.|.++..
T Consensus         2 ~~~~~ky~C~~CgyiYDp~~   21 (70)
T d1dx8a_           2 EIDEGKYECEACGYIYEPEK   21 (70)
T ss_dssp             BCCSSCEEETTTCCEECTTT
T ss_pred             cccCCeEEcCCCCeEECccc
Confidence            34689999999999987665

>d1wiia_ g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Putative zinc binding domain
domain: Hypothetical UPF0222 protein MGC4549
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.97  E-value=0.27  Score=31.63  Aligned_cols=31  Identities=23%  Similarity=0.555  Sum_probs=21.9

Q ss_pred             CCCCCCCC--CceeEeC--CCCceEeCCCceeeeC
Q 030129            5 FCSDCKKH--TEVVFDH--SAGDTVCSECGLVLES   35 (182)
Q Consensus         5 ~Cp~Cg~~--~~iv~D~--~~G~~vC~~CG~Vl~e   35 (182)
                      .||.|+-.  ..+..|.  ..|.+.|.-||.-.+-
T Consensus        25 ~CPfCnh~~sV~vk~dkk~~~g~l~C~vCg~~~~~   59 (85)
T d1wiia_          25 TCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQT   59 (85)
T ss_dssp             CCTTTCCSSCEEEEEETTTTEEEEEESSSCCEEEE
T ss_pred             cCCCCCCCCeEEEEEEecCCEEEEEEecCCCeEEe
Confidence            59999932  2344455  5567999999988763

>d2apob1 g.41.16.1 (B:403-457) Ribosome biogenesis protein Nop10 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Nop10-like SnoRNP
family: Nucleolar RNA-binding protein Nop10-like
domain: Ribosome biogenesis protein Nop10
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=80.06  E-value=0.26  Score=29.14  Aligned_cols=26  Identities=23%  Similarity=0.572  Sum_probs=19.9

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEeCCCceeee
Q 030129            1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE   34 (182)
Q Consensus         1 m~~~~Cp~Cg~~~~iv~D~~~G~~vC~~CG~Vl~   34 (182)
                      |.+.+|+.|+.. .+       ..+|..||-...
T Consensus         2 ~klrkC~~C~~Y-TL-------~~~CP~CG~~t~   27 (55)
T d2apob1           2 MRMKKCPKCGLY-TL-------KEICPKCGEKTV   27 (55)
T ss_dssp             CCCEECTTTCCE-ES-------SSBCSSSCSBCB
T ss_pred             cceeeCCcccce-ec-------cccCcCCCCccC
Confidence            677899999973 22       468999998753