Citrus Sinensis ID: 040426

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120
Protein Sequence
MADPLGRDFLFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES
Secondary Structure (PSIPRED)
ccccccccccccccccccEEEcccEEEccccccEEEcccccccEEEEEEEHHHHHHHHccEEEccccccccccccccccccccccccccEEEEEEEccccccccEEEEEccccccEEccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccEEEEcccccEccHHHccccEEEEEEccccccHHHcccEEEEcccccHHccccEEEccccccccccEEEEEEEEEccccccEEEEEEcccccEEEcc
Coil and Loop (DISEMBL)
madplgrdfLFCKFCGTmlrmesnhvvcssckfkkNVQDVADREISYAVTAEEIKRELGIslfeqpqgdkgetQLSKVKRACekcqnpemyystrqtrsadegqttyyicprcghrcqes
Flexible Loop (DISEMBL)
madplgrdFLFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELgislfeqpqgdkgetqLSKVKRACekcqnpemyystrqtrsadegqtTYYICprcghrcqes
Low Complexity Region (SEG)
MADPLGRDFLFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES
Disordered region (IsUnstruct)
******RDFLFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLF*****************************************TTYYICPRCGH*****
Disordered Region (DISOPRED)
****LGR*FLFCKFCGTMLRMESNHVVCSSCKFKKNVQDVAD**********************************KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC***
Disordered Region (DISEMBL)
MADPLGRDFLFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES
Disordered Region (DISPRO)
*ADPLGRDFLFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MADPLGRDFLFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES
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	120	2.2.26 [Sep-21-2011]
Q1RMP0	123	DNA-directed RNA polymera	yes	no	0.841	0.821	0.361	3e-12
Q5TM50	126	DNA-directed RNA polymera	yes	no	0.841	0.801	0.361	3e-12
Q791N7	123	DNA-directed RNA polymera	yes	no	0.841	0.821	0.351	6e-12
Q6MFY5	123	DNA-directed RNA polymera	yes	no	0.841	0.821	0.351	6e-12
Q1XHV8	126	DNA-directed RNA polymera	yes	no	0.841	0.801	0.361	9e-12
Q9P1U0	126	DNA-directed RNA polymera	yes	no	0.841	0.801	0.361	9e-12
Q56254	110	DNA-directed RNA polymera	N/A	no	0.833	0.909	0.317	1e-07
Q2M2S7	108	DNA-directed RNA polymera	no	no	0.833	0.925	0.313	4e-07
O94703	119	DNA-directed RNA polymera	yes	no	0.9	0.907	0.272	7e-07
Q9CQZ7	108	DNA-directed RNA polymera	no	no	0.833	0.925	0.305	8e-07

>sp|Q1RMP0|RPA12_BOVIN DNA-directed RNA polymerase I subunit RPA12 OS=Bos taurus GN=ZNRD1 PE=2 SV=1

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 39/108 (36%), Positives = 56/108 (51%), Gaps = 7/108 (6%)

Query: 8   DFLFCKFCGTMLRMES--NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
           D  FC  CG++L +    + V C+ C F  NV+D   + +  +V   ++   + +S+ E 
Sbjct: 13  DLDFCPDCGSVLPLPGVQDAVACTRCGFSINVRDFEGKVVKTSVVFNKLGTAMPLSMEEG 72

Query: 66  PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
           P     E Q   V R C +C +  M Y TRQ RSADEGQT +Y C  C
Sbjct: 73  P-----EFQGPVVDRRCSRCGHEGMAYHTRQMRSADEGQTVFYTCTNC 115

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.
Bos taurus (taxid: 9913)

>sp|Q5TM50|RPA12_MACMU DNA-directed RNA polymerase I subunit RPA12 OS=Macaca mulatta GN=ZNRD1 PE=3 SV=1

 Score = 70.1 bits (170), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 39/108 (36%), Positives = 56/108 (51%), Gaps = 7/108 (6%)

Query: 8   DFLFCKFCGTMLRMES--NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
           D  FC  CG++L +    + V C+ C F  NV+D   + +  +V   ++   + +S+ E 
Sbjct: 16  DLDFCSDCGSVLPLPGAQDTVTCTRCGFNINVRDFEGKVVKTSVVFHQLGTAMPMSVEEG 75

Query: 66  PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
           P     E Q   V R C +C +  M Y TRQ RSADEGQT +Y C  C
Sbjct: 76  P-----ECQGPVVDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNC 118

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.

Macaca mulatta (taxid: 9544)

>sp|Q791N7|RPA12_MOUSE DNA-directed RNA polymerase I subunit RPA12 OS=Mus musculus GN=Znrd1 PE=2 SV=1

 Score = 69.3 bits (168), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 38/108 (35%), Positives = 57/108 (52%), Gaps = 7/108 (6%)

Query: 8   DFLFCKFCGTMLRMES--NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
           D  FC  CG++L +    + V+CS C F  +V+D   + +  +V   ++   + +S+ E 
Sbjct: 13  DLDFCPDCGSVLPLPGIQDTVICSRCGFSIDVRDCEGKVVKTSVVFNKLGATIPLSVDEG 72

Query: 66  PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
           P     E Q   + R C +C +  M Y TRQ RSADEGQT +Y C  C
Sbjct: 73  P-----ELQGPVIDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCINC 115

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.

Mus musculus (taxid: 10090)

>sp|Q6MFY5|RPA12_RAT DNA-directed RNA polymerase I subunit RPA12 OS=Rattus norvegicus GN=Znrd1 PE=3 SV=1

 Score = 69.3 bits (168), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 38/108 (35%), Positives = 57/108 (52%), Gaps = 7/108 (6%)

Query: 8   DFLFCKFCGTMLRMES--NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
           D  FC  CG++L +    + V+C  C F  +V+D   + +  +V   ++   + +S+ E 
Sbjct: 13  DLDFCPDCGSVLPLPGVQDTVICPRCGFSIDVRDFGGKVVKTSVVFNKLGTVIPMSVDEG 72

Query: 66  PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
           P     E+Q   V R C +C +  M Y TRQ RSADEGQT +Y C  C
Sbjct: 73  P-----ESQGPVVDRRCSRCGHEGMAYYTRQMRSADEGQTVFYTCINC 115

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.

Rattus norvegicus (taxid: 10116)

>sp|Q1XHV8|RPA12_PANTR DNA-directed RNA polymerase I subunit RPA12 OS=Pan troglodytes GN=ZNRD1 PE=3 SV=1

 Score = 68.9 bits (167), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 39/108 (36%), Positives = 55/108 (50%), Gaps = 7/108 (6%)

Query: 8   DFLFCKFCGTMLRMES--NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
           D  FC  CG++L +    + V C  C F  NV+D   + +  +V   ++   + +S+ E 
Sbjct: 16  DLDFCSDCGSVLPLPGAQDTVTCIRCGFNINVRDFEGKVVKTSVVFHQLGTAMPMSVEEG 75

Query: 66  PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
           P     E Q   V R C +C +  M Y TRQ RSADEGQT +Y C  C
Sbjct: 76  P-----ECQGPVVDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNC 118

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.

Pan troglodytes (taxid: 9598)

>sp|Q9P1U0|RPA12_HUMAN DNA-directed RNA polymerase I subunit RPA12 OS=Homo sapiens GN=ZNRD1 PE=1 SV=1

 Score = 68.9 bits (167), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 39/108 (36%), Positives = 55/108 (50%), Gaps = 7/108 (6%)

Query: 8   DFLFCKFCGTMLRMES--NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
           D  FC  CG++L +    + V C  C F  NV+D   + +  +V   ++   + +S+ E 
Sbjct: 16  DLDFCSDCGSVLPLPGAQDTVTCIRCGFNINVRDFEGKVVKTSVVFHQLGTAMPMSVEEG 75

Query: 66  PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
           P     E Q   V R C +C +  M Y TRQ RSADEGQT +Y C  C
Sbjct: 76  P-----ECQGPVVDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNC 118

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.

Homo sapiens (taxid: 9606)

>sp|Q56254|RPOM_THECE DNA-directed RNA polymerase subunit M OS=Thermococcus celer GN=rpoM PE=1 SV=1

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 34/107 (31%), Positives = 49/107 (45%), Gaps = 7/107 (6%)

Query: 11  FCKFCGTMLRMESNH--VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQG 68
           FC  CG ++  +      VC SC +++   +  DRE +      + K + GI + EQ   
Sbjct: 3   FCPKCGNLMLPDRKRKVWVCRSCGYEEPFDEEKDREKTVIKQEVKHKPDEGIVVIEQ--- 59

Query: 69  DKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115
                 L   K  C KC N   Y+   QTR+ DE  T +Y C +CGH
Sbjct: 60  --DLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGH 104

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Thermococcus celer (taxid: 2264)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q2M2S7|RPC10_BOVIN DNA-directed RNA polymerase III subunit RPC10 OS=Bos taurus GN=POLR3K PE=3 SV=1

 Score = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 37/118 (31%), Positives = 55/118 (46%), Gaps = 18/118 (15%)

Query: 9   FLFCKFCGTMLRMES----NHVVCSSCKFKKNV-QDVADREISYAVTAEEIKRELGISLF 63
            LFC  CG  L +E     +   C++C +  NV + V +R+       +E+  ELG    
Sbjct: 2   LLFCPGCGNGLIVEEGQRCHRFACNTCPYVHNVTRKVTNRKYP---KLKEVDDELG---- 54

Query: 64  EQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYIC--PRCGHRCQE 119
               G      +      C KC++P  Y+   QTR ADE  TT+Y C   +CGHR ++
Sbjct: 55  ----GAAAWENVDSTAEPCPKCEHPRAYFMQLQTRYADEPMTTFYKCCNAQCGHRWRD 108

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts induce type I interferon and NF- Kappa-B through the RIG-I pathway.

Bos taurus (taxid: 9913)

>sp|O94703|RPA12_SCHPO DNA-directed RNA polymerase I subunit RPA12 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpa12 PE=3 SV=1

 Score = 52.8 bits (125), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 30/110 (27%), Positives = 49/110 (44%), Gaps = 2/110 (1%)

Query: 8   DFLFCKFCGTMLR-MESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQP 66
             +FC  CG +L    +    C  C+     +  A+  +    +A      L +      
Sbjct: 6   SLIFCSECGNLLESTTAQWTTCDQCQSVYPSEQFANLVVETKSSASAFPSALKLK-HSIV 64

Query: 67  QGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
           Q +  + + + ++  C KC N  M + T Q RSADEG T +Y CPRC ++
Sbjct: 65  QVESQKEEAATIEEKCPKCGNDHMTFHTLQLRSADEGSTVFYECPRCAYK 114

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Required for growth at higher temperatures.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q9CQZ7|RPC10_MOUSE DNA-directed RNA polymerase III subunit RPC10 OS=Mus musculus GN=Polr3k PE=2 SV=1

 Score = 52.4 bits (124), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 55/118 (46%), Gaps = 18/118 (15%)

Query: 9   FLFCKFCGTMLRMES----NHVVCSSCKFKKNV-QDVADREISYAVTAEEIKRELGISLF 63
            LFC  CG  L +E     +   C++C +  N+ + V +R+       +E+   LG    
Sbjct: 2   LLFCPGCGNGLIVEEGQRCHRFACNTCPYVHNITRKVTNRKYP---KLKEVDDVLG---- 54

Query: 64  EQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYIC--PRCGHRCQE 119
               G      +      C KC++P  Y+   QTRSADE  TT+Y C   +CGHR ++
Sbjct: 55  ----GAAAWENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD 108

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts induce type I interferon and NF- Kappa-B through the RIG-I pathway.

Mus musculus (taxid: 10090)

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	120
18404735	119	TFIIB zinc-binding protein [Arabidopsis	0.916	0.924	0.575	2e-31
297814818	119	transcription factor S-II domain-contain	0.908	0.915	0.562	6e-30
312281609	119	unnamed protein product [Thellungiella h	0.9	0.907	0.566	7e-29
357465637	115	DNA-directed RNA polymerase I subunit RP	0.916	0.956	0.543	8e-28
449450514	116	PREDICTED: DNA-directed RNA polymerase I	0.958	0.991	0.504	2e-26
168480799	116	TFIIS domain-containing protein [Cucumis	0.9	0.931	0.517	1e-24
224123076	117	predicted protein [Populus trichocarpa]	0.966	0.991	0.471	1e-23
351723413	116	uncharacterized protein LOC100527489 [Gl	0.908	0.939	0.482	2e-23
302142695	126	unnamed protein product [Vitis vinifera]	1.0	0.952	0.456	4e-22
326511037	125	predicted protein [Hordeum vulgare subsp	1.0	0.96	0.467	2e-21

>gi|18404735|ref|NP_566786.1| TFIIB zinc-binding protein [Arabidopsis thaliana] gi|9279599|dbj|BAB01057.1| unnamed protein product [Arabidopsis thaliana] gi|21536551|gb|AAM60883.1| putative RNA polymerase I subunit [Arabidopsis thaliana] gi|88011125|gb|ABD38906.1| At3g25940 [Arabidopsis thaliana] gi|332643572|gb|AEE77093.1| TFIIB zinc-binding protein [Arabidopsis thaliana]

 Score =  139 bits (350), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 65/113 (57%), Positives = 85/113 (75%), Gaps = 3/113 (2%)

Query: 8   DFLFCKFCGTMLRMESN-HVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQP 66
           +FLFC  CGTML ++S  +  C  CK  +N +D+ D+EI+Y V+AE+I+RELGISLF   
Sbjct: 8   EFLFCNLCGTMLVLKSTKYAECPHCKTTRNAKDIIDKEIAYTVSAEDIRRELGISLF--G 65

Query: 67  QGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119
           +  + E +L K+K+ACEKCQ+PE+ Y+TRQTRSADEGQTTYY CP C HR  E
Sbjct: 66  EKTQAEAELPKIKKACEKCQHPELVYTTRQTRSADEGQTTYYTCPNCAHRFTE 118

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297814818|ref|XP_002875292.1| transcription factor S-II domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297321130|gb|EFH51551.1| transcription factor S-II domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  134 bits (337), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 63/112 (56%), Positives = 85/112 (75%), Gaps = 3/112 (2%)

Query: 9   FLFCKFCGTMLRMESN-HVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQ 67
           FLFC +CGTML ++S  +  C  CK  +N +++ +++I+Y VTAE+I+RELGISLF +  
Sbjct: 9   FLFCNWCGTMLVLKSTKYAECPLCKTTRNAKEIINKDIAYTVTAEDIRRELGISLFGEKT 68

Query: 68  GDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119
            +  E +L K+K+ACEKCQ+PE+ Y+TRQTRSADEGQTTYY CP C HR  E
Sbjct: 69  QE--EAELPKIKKACEKCQHPELVYTTRQTRSADEGQTTYYTCPNCAHRFTE 118

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312281609|dbj|BAJ33670.1| unnamed protein product [Thellungiella halophila]

 Score =  130 bits (328), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 64/113 (56%), Positives = 84/113 (74%), Gaps = 5/113 (4%)

Query: 9   FLFCKFCGTMLRMES-NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLF-EQP 66
           FLFC  CGTML ++S     C  C+  +N +++  ++I+Y V+AE+I+RELGISLF E+ 
Sbjct: 9   FLFCNLCGTMLILKSATSAECPLCQTTRNAKEIIGKDIAYTVSAEDIRRELGISLFGEKT 68

Query: 67  QGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119
           Q D    +L K+K+ACEKCQ+PE+ Y+TRQTRSADEGQTTYY CP CGHR  E
Sbjct: 69  QED---AELPKIKKACEKCQHPELVYTTRQTRSADEGQTTYYTCPNCGHRFTE 118

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357465637|ref|XP_003603103.1| DNA-directed RNA polymerase I subunit RPA12 [Medicago truncatula] gi|357470681|ref|XP_003605625.1| DNA-directed RNA polymerase I subunit RPA12 [Medicago truncatula] gi|355492151|gb|AES73354.1| DNA-directed RNA polymerase I subunit RPA12 [Medicago truncatula] gi|355506680|gb|AES87822.1| DNA-directed RNA polymerase I subunit RPA12 [Medicago truncatula]

 Score =  127 bits (319), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 63/116 (54%), Positives = 83/116 (71%), Gaps = 6/116 (5%)

Query: 6   GRDFLFCKFCGTMLRMES-NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFE 64
           GRDFLFC  CGTML + S ++ +C  CK K N++D+  +EISY ++AE+I+RELGI L E
Sbjct: 5   GRDFLFCHLCGTMLTVPSTDYALCPLCKTKCNIKDIKGKEISYTISAEDIRRELGIDLIE 64

Query: 65  QPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES 120
           + +      QLSKV + CEKC + E  + TRQ RSADEGQTT+Y C RCGH+ QE+
Sbjct: 65  EQK-----VQLSKVNKTCEKCGHGEAAFYTRQMRSADEGQTTFYTCTRCGHQFQEN 115

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449450514|ref|XP_004143007.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA12-like isoform 1 [Cucumis sativus] gi|449450516|ref|XP_004143008.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA12-like isoform 2 [Cucumis sativus] gi|449450518|ref|XP_004143009.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA12-like isoform 3 [Cucumis sativus] gi|449500372|ref|XP_004161079.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA12-like isoform 1 [Cucumis sativus] gi|449500375|ref|XP_004161080.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA12-like isoform 2 [Cucumis sativus] gi|449500379|ref|XP_004161081.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA12-like isoform 3 [Cucumis sativus]

 Score =  123 bits (308), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 61/121 (50%), Positives = 84/121 (69%), Gaps = 6/121 (4%)

Query: 1   MADPLGRDFLFCKFCGTMLRM-ESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELG 59
           MA   G DFLFC  CGTML    + +V C SCK +++ +++  REISY VTAEEI+++LG
Sbjct: 1   MAYSRGHDFLFCNLCGTMLSFCSTKYVECPSCKSRRSAKEIVGREISYTVTAEEIRKQLG 60

Query: 60  ISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119
           ISL      D+ + QL+K +R CEKC N E ++ +RQ RSADEGQTT+Y C +C H+ +E
Sbjct: 61  ISLI-----DEEKMQLAKERRRCEKCGNDEAWFESRQMRSADEGQTTFYTCTKCHHQTRE 115

Query: 120 S 120
           +
Sbjct: 116 N 116

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168480799|gb|ACA24493.1| TFIIS domain-containing protein [Cucumis sativus]

 Score =  117 bits (292), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 59/114 (51%), Positives = 77/114 (67%), Gaps = 6/114 (5%)

Query: 1   MADPLGRDFLFCKFCGTMLRM-ESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELG 59
           MA   G DFLFC   GTML    + +V C SCK +++ +++  REISY VTAEEIK++LG
Sbjct: 1   MAYSRGHDFLFCNLGGTMLSFCSTKYVECPSCKSRRSAKEIVGREISYTVTAEEIKKQLG 60

Query: 60  ISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
           ISL      D+   QL+K +R CEKC N E ++ +RQ RSADEGQTT+Y C +C
Sbjct: 61  ISLI-----DENNMQLAKERRRCEKCGNDEAWFESRQMRSADEGQTTFYTCSKC 109

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224123076|ref|XP_002318989.1| predicted protein [Populus trichocarpa] gi|222857365|gb|EEE94912.1| predicted protein [Populus trichocarpa]

 Score =  113 bits (283), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/121 (47%), Positives = 83/121 (68%), Gaps = 5/121 (4%)

Query: 1   MADPLGRDFLFCKFCGTMLRMESN-HVVCSSCKFKKNVQDVADREISYAVTAEEIKRELG 59
           MA   G DF+FC  CGTM+ + S  HV C  CKFKK+ +D+++REISY V++E+++R+LG
Sbjct: 1   MAHARGGDFMFCDLCGTMMFLYSKEHVECPLCKFKKSAKDLSEREISYQVSSEDMRRDLG 60

Query: 60  ISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119
           IS FE     K E +  ++ + CEKC + ++ +STRQ RSADEGQTT++ C  C +   E
Sbjct: 61  ISHFE----GKMEVKDMEINKKCEKCGHTKLKFSTRQMRSADEGQTTFFHCANCSYTFTE 116

Query: 120 S 120
           +
Sbjct: 117 N 117

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351723413|ref|NP_001236766.1| uncharacterized protein LOC100527489 [Glycine max] gi|255632466|gb|ACU16583.1| unknown [Glycine max]

 Score =  113 bits (282), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 55/114 (48%), Positives = 77/114 (67%), Gaps = 5/114 (4%)

Query: 8   DFLFCKFCGTMLRMESN-HVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQP 66
           DFLFC  CGTML + S  +  C  CK ++++QD+ D+EIS+ ++ E+I+RELG+ + E+ 
Sbjct: 7   DFLFCNLCGTMLTVPSTEYAQCPLCKTRRDIQDICDKEISFTISDEDIRRELGMEIIEE- 65

Query: 67  QGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES 120
                  + SKV + CEKC + E  Y TRQ RSADEGQTT+Y C  CGH+ QE+
Sbjct: 66  ---HAVMEYSKVSKKCEKCGHGEATYYTRQMRSADEGQTTFYTCTGCGHQSQEN 116

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302142695|emb|CBI19898.3| unnamed protein product [Vitis vinifera]

 Score =  108 bits (270), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 57/125 (45%), Positives = 81/125 (64%), Gaps = 5/125 (4%)

Query: 1   MADPLGRDFLFCKFCGTMLRMESN-HVVCSSCKFKKNVQDVADREISYAVTAEEIKRELG 59
           MA    RDF+FC  CGTML M S  +  C  CK ++ V+D++ REI Y V+AE+I+REL 
Sbjct: 1   MAYSRQRDFMFCNLCGTMLCMSSTKYAECPLCKSRRKVKDISGREIRYTVSAEDIRRELN 60

Query: 60  ISLFEQPQG---DKGETQLSKVKRACEKCQ-NPEMYYSTRQTRSADEGQTTYYICPRCGH 115
           I  F +  G   ++ E Q +K K  C++C+ +  +YY TRQ RSADEGQT +Y C +CGH
Sbjct: 61  IEPFVKLDGIITEESEAQNAKTKGRCDRCEEDTWLYYYTRQLRSADEGQTIFYECTKCGH 120

Query: 116 RCQES 120
           +  ++
Sbjct: 121 KWSQN 125

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326511037|dbj|BAJ91866.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  105 bits (263), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 58/124 (46%), Positives = 73/124 (58%), Gaps = 4/124 (3%)

Query: 1   MADPLGRDFLFCKFCGTMLRMESN-HVVCSSCKFKKNVQDVADREISYAVTAEEIKRELG 59
           MA    RDFLFC  CGT+L   S+ +  C  C FK+  +D+  +E  YAVTAE+I+REL 
Sbjct: 1   MAFWQARDFLFCGVCGTLLDFNSHRYASCPLCGFKRKAKDIEGKETRYAVTAEDIRRELK 60

Query: 60  ISLF---EQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
           I  F   E         Q S  +RAC KC + E+ Y T+Q RSADEGQT +Y CP CGH 
Sbjct: 61  IKPFVVLESAPNLDIVVQRSLTERACPKCNHHELEYYTKQLRSADEGQTIFYECPECGHA 120

Query: 117 CQES 120
             E+
Sbjct: 121 FNEN 124

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	120
TAIR|locus:2092185	119	AT3G25940 [Arabidopsis thalian	0.916	0.924	0.575	4.1e-33
UNIPROTKB|B6ICU4	123	ZNRD1 "DNA-directed RNA polyme	0.841	0.821	0.361	1.3e-13
UNIPROTKB|Q1RMP0	123	ZNRD1 "DNA-directed RNA polyme	0.841	0.821	0.361	4.4e-13
UNIPROTKB|Q9P1U0	126	ZNRD1 "DNA-directed RNA polyme	0.841	0.801	0.361	9.1e-13
MGI|MGI:1913386	123	Znrd1 "zinc ribbon domain cont	0.841	0.821	0.351	9.1e-13
RGD|1303114	123	Znrd1 "zinc ribbon domain cont	0.841	0.821	0.351	1.9e-12
ZFIN|ZDB-GENE-050320-131	126	znrd1 "zinc ribbon domain cont	0.883	0.841	0.342	3.1e-12
DICTYBASE|DDB_G0278263	324	rpa12 "RNA polymerase I subuni	0.825	0.305	0.339	1.2e-11
CGD|CAL0006382	123	RPA12 [Candida albicans (taxid	0.85	0.829	0.327	3.5e-11
UNIPROTKB|F1PIF7	126	ZNRD1 "DNA-directed RNA polyme	0.875	0.833	0.342	3.5e-11

TAIR|locus:2092185 AT3G25940 [Arabidopsis thaliana (taxid:3702)]

 Score = 361 (132.1 bits), Expect = 4.1e-33, P = 4.1e-33
 Identities = 65/113 (57%), Positives = 85/113 (75%)

Query:     8 DFLFCKFCGTMLRMESN-HVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQP 66
             +FLFC  CGTML ++S  +  C  CK  +N +D+ D+EI+Y V+AE+I+RELGISLF + 
Sbjct:     8 EFLFCNLCGTMLVLKSTKYAECPHCKTTRNAKDIIDKEIAYTVSAEDIRRELGISLFGEK 67

Query:    67 QGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119
                + E +L K+K+ACEKCQ+PE+ Y+TRQTRSADEGQTTYY CP C HR  E
Sbjct:    68 T--QAEAELPKIKKACEKCQHPELVYTTRQTRSADEGQTTYYTCPNCAHRFTE 118

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|B6ICU4 ZNRD1 "DNA-directed RNA polymerase subunit" [Sus scrofa (taxid:9823)]

 Score = 177 (67.4 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 39/108 (36%), Positives = 57/108 (52%)

Query:     8 DFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
             D  FC  CG++L +      V+C+ C F  NV+D   + +  +V  +++   + +S+ E 
Sbjct:    13 DLDFCPDCGSVLPLPGTQDAVICTRCGFSINVRDFEGKVVKTSVVFQKVGTAMPMSMEEG 72

Query:    66 PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
             P     E Q   V R C +C +  M Y TRQ RSADEGQT +Y C  C
Sbjct:    73 P-----EFQGPVVDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNC 115

GO:0005634 "nucleus" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q1RMP0 ZNRD1 "DNA-directed RNA polymerase I subunit RPA12" [Bos taurus (taxid:9913)]

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 39/108 (36%), Positives = 56/108 (51%)

Query:     8 DFLFCKFCGTMLRMES--NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
             D  FC  CG++L +    + V C+ C F  NV+D   + +  +V   ++   + +S+ E 
Sbjct:    13 DLDFCPDCGSVLPLPGVQDAVACTRCGFSINVRDFEGKVVKTSVVFNKLGTAMPLSMEEG 72

Query:    66 PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
             P     E Q   V R C +C +  M Y TRQ RSADEGQT +Y C  C
Sbjct:    73 P-----EFQGPVVDRRCSRCGHEGMAYHTRQMRSADEGQTVFYTCTNC 115

GO:0005730 "nucleolus" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q9P1U0 ZNRD1 "DNA-directed RNA polymerase I subunit RPA12" [Homo sapiens (taxid:9606)]

 Score = 169 (64.5 bits), Expect = 9.1e-13, P = 9.1e-13
 Identities = 39/108 (36%), Positives = 55/108 (50%)

Query:     8 DFLFCKFCGTMLRMES--NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
             D  FC  CG++L +    + V C  C F  NV+D   + +  +V   ++   + +S+ E 
Sbjct:    16 DLDFCSDCGSVLPLPGAQDTVTCIRCGFNINVRDFEGKVVKTSVVFHQLGTAMPMSVEEG 75

Query:    66 PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
             P     E Q   V R C +C +  M Y TRQ RSADEGQT +Y C  C
Sbjct:    76 P-----ECQGPVVDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNC 118

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0006139 "nucleobase-containing compound metabolic process" evidence=TAS

MGI|MGI:1913386 Znrd1 "zinc ribbon domain containing, 1" [Mus musculus (taxid:10090)]

 Score = 169 (64.5 bits), Expect = 9.1e-13, P = 9.1e-13
 Identities = 38/108 (35%), Positives = 57/108 (52%)

Query:     8 DFLFCKFCGTMLRMES--NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
             D  FC  CG++L +    + V+CS C F  +V+D   + +  +V   ++   + +S+ E 
Sbjct:    13 DLDFCPDCGSVLPLPGIQDTVICSRCGFSIDVRDCEGKVVKTSVVFNKLGATIPLSVDEG 72

Query:    66 PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
             P     E Q   + R C +C +  M Y TRQ RSADEGQT +Y C  C
Sbjct:    73 P-----ELQGPVIDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCINC 115

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

RGD|1303114 Znrd1 "zinc ribbon domain containing 1" [Rattus norvegicus (taxid:10116)]

 Score = 166 (63.5 bits), Expect = 1.9e-12, P = 1.9e-12
 Identities = 38/108 (35%), Positives = 57/108 (52%)

Query:     8 DFLFCKFCGTMLRMES--NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
             D  FC  CG++L +    + V+C  C F  +V+D   + +  +V   ++   + +S+ E 
Sbjct:    13 DLDFCPDCGSVLPLPGVQDTVICPRCGFSIDVRDFGGKVVKTSVVFNKLGTVIPMSVDEG 72

Query:    66 PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
             P     E+Q   V R C +C +  M Y TRQ RSADEGQT +Y C  C
Sbjct:    73 P-----ESQGPVVDRRCSRCGHEGMAYYTRQMRSADEGQTVFYTCINC 115

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

ZFIN|ZDB-GENE-050320-131 znrd1 "zinc ribbon domain containing 1" [Danio rerio (taxid:7955)]

 Score = 164 (62.8 bits), Expect = 3.1e-12, P = 3.1e-12
 Identities = 39/114 (34%), Positives = 56/114 (49%)

Query:     8 DFLFCKFCGTMLRMES--NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
             D  FC  CG +L + S  N + C  C FK +VQD   + I  +V    + +   +++   
Sbjct:    15 DVDFCPECGNILPLPSRLNTITCPRCSFKISVQDFTSQVIKSSVMFNPLDQS-NVAV--- 70

Query:    66 PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119
                +  E +   + R C +C    M Y TRQ RSADEGQT ++ C  C  R QE
Sbjct:    71 ESAEDAELKGPVIDRKCSRCNKEGMVYHTRQMRSADEGQTVFFTCIHC--RFQE 122

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

DICTYBASE|DDB_G0278263 rpa12 "RNA polymerase I subunit" [Dictyostelium discoideum (taxid:44689)]

 Score = 163 (62.4 bits), Expect = 1.2e-11, P = 1.2e-11
 Identities = 37/109 (33%), Positives = 55/109 (50%)

Query:    11 FCKFCGTMLRMESN---HVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQ 67
             FC  C   L    N   H+ CS C F K+  D+ +++I   VT    K  L     +  +
Sbjct:   218 FCPQCNAFLNYPKNFSQHITCSLCTFSKSKADLLNKKI---VT----KSSLFNKSIKNKE 270

Query:    68 GDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
              D  E + + +   C +C + +MY+ T QTRSADEGQT +Y C +C  +
Sbjct:   271 EDNEEDRGAIIDEKCPECGHGKMYFKTAQTRSADEGQTIFYDCVKCSFK 319

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006360 "transcription from RNA polymerase I promoter" evidence=ISS

GO:0005736 "DNA-directed RNA polymerase I complex" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS

GO:0044351 "macropinocytosis" evidence=RCA

CGD|CAL0006382 RPA12 [Candida albicans (taxid:5476)]

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 38/116 (32%), Positives = 60/116 (51%)

Query:    10 LFCKFCGTML--RMESNHVVCSSCK--FKK----NVQDVA-DREISYAVTAEEIKRELGI 60
             +FC +CG +L     S+ + C+ C   + K    N++ V    + ++    +  +  +  
Sbjct:     8 IFCNYCGNLLDSHSSSSEIKCTVCSAAYPKSKFANLKVVTKSSDDAFPSKLKSARSVVKT 67

Query:    61 SLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
             SL ++ + D+G T    +K  C KC N EM Y T Q RSADEG T +Y C  CG+R
Sbjct:    68 SL-KKDELDEGAT----IKEKCPKCGNEEMQYHTLQLRSADEGATVFYTCTNCGYR 118

GO:0005829 "cytosol" evidence=IEA

GO:0005736 "DNA-directed RNA polymerase I complex" evidence=IEA

GO:0006363 "termination of RNA polymerase I transcription" evidence=IEA

GO:0042790 "transcription of nuclear large rRNA transcript from RNA polymerase I promoter" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

UNIPROTKB|F1PIF7 ZNRD1 "DNA-directed RNA polymerase subunit" [Canis lupus familiaris (taxid:9615)]

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 39/114 (34%), Positives = 55/114 (48%)

Query:     8 DFLFCKFCGTMLRMES--NHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQ 65
             D  FC  CG++L +    + V C  C F   V+D   + +   +   ++   +   + E+
Sbjct:    16 DLDFCPDCGSVLPLPGAQDAVTCVRCGFGVPVRDFEGKVVRTRIVFNQVGTAVPAPVQEE 75

Query:    66 PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119
             P     E Q   V R C +C +  M Y TRQ RSADEGQT +Y C  C  R QE
Sbjct:    76 P-----ELQGPVVDRRCSRCGHEGMAYHTRQMRSADEGQTVFYTCTSC--RFQE 122

GO:0005634 "nucleus" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" 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)
Q07271	RPOM_SULAC	2, ., 7, ., 7, ., 6	0.3097	0.8583	0.9279	yes	no
P32529	RPA12_YEAST	No assigned EC number	0.3057	0.8416	0.808	yes	no
O27369	RPOM_METTH	2, ., 7, ., 7, ., 6	0.3181	0.825	0.9519	yes	no
Q5TM50	RPA12_MACMU	No assigned EC number	0.3611	0.8416	0.8015	yes	no
Q6MFY5	RPA12_RAT	No assigned EC number	0.3518	0.8416	0.8211	yes	no
Q9P1U0	RPA12_HUMAN	No assigned EC number	0.3611	0.8416	0.8015	yes	no
Q791N7	RPA12_MOUSE	No assigned EC number	0.3518	0.8416	0.8211	yes	no
Q1XHV8	RPA12_PANTR	No assigned EC number	0.3611	0.8416	0.8015	yes	no
Q1RMP0	RPA12_BOVIN	No assigned EC number	0.3611	0.8416	0.8211	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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	AT3G25940	transcription factor S-II (TFIIS) domain-containing protein; transcription factor S-II (TFIIS) domain-containing protein; FUNCTIONS IN- transcription factor activity, transcription regulator activity, DNA binding, zinc ion binding, nucleic acid binding; INVOLVED IN- RNA elongation, regulation of transcription, DNA-dependent, regulation of transcription; LOCATED IN- nucleus; EXPRESSED IN- 21 plant structures; EXPRESSED DURING- 13 growth stages; CONTAINS InterPro DOMAIN/s- Zinc finger, TFIIS-type (InterPro-IPR001222); Has 677 Blast hits to 677 proteins in 189 species- Archae - 101; Bacte [...] (119 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
	emb2742	emb2742 (embryo defective 2742); CTP synthase/ catalytic; embryo defective 2742 (emb2742); FUNC [...] (591 aa)				•		•			0.907
	AT4G13720	inosine triphosphate pyrophosphatase, putative / HAM1 family protein; inosine triphosphate pyro [...] (206 aa)				•		•	•		0.905
	AT5G14580	polyribonucleotide nucleotidyltransferase, putative; polyribonucleotide nucleotidyltransferase, [...] (991 aa)				•		•			0.904
	NDPK1	NDPK1; ATP binding / nucleoside diphosphate kinase; nucleoside diphosphate kinase type 1 (NDPK1 [...] (169 aa)				•		•			0.904
	AT5G66005	Expressed protein; Expressed protein; FUNCTIONS IN- nucleoside-triphosphatase activity, transfe [...] (192 aa)						•			0.899
	AT5G63680	pyruvate kinase, putative; pyruvate kinase, putative; FUNCTIONS IN- pyruvate kinase activity, p [...] (510 aa)						•			0.899
	NDPK2	NDPK2 (NUCLEOSIDE DIPHOSPHATE KINASE 2); ATP binding / nucleoside diphosphate kinase/ protein b [...] (231 aa)						•			0.899
	AT5G56350	pyruvate kinase, putative; pyruvate kinase, putative; FUNCTIONS IN- pyruvate kinase activity, p [...] (498 aa)						•			0.899
	PKP-BETA1	PKP-BETA1 (PLASTIDIC PYRUVATE KINASE BETA SUBUNIT 1); pyruvate kinase; encodes a dominant chlor [...] (579 aa)						•			0.899
	ATAPY2	ATAPY2 (ARABIDOPSIS THALIANA APYRASE 2); ATPase/ nucleotide diphosphatase; Encodes an enzyme wi [...] (630 aa)						•			0.899

---

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	120
COG1594	113	COG1594, RPB9, DNA-directed RNA polymerase, subuni	4e-16
pfam01096	39	pfam01096, TFIIS_C, Transcription factor S-II (TFI	1e-12
TIGR01384	104	TIGR01384, TFS_arch, transcription factor S, archa	8e-11
smart00440	40	smart00440, ZnF_C2C2, C2C2 Zinc finger	3e-09
TIGR01385	299	TIGR01385, TFSII, transcription elongation factor	2e-05

>gnl|CDD|224510 COG1594, RPB9, DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

 Score = 68.3 bits (167), Expect = 4e-16
 Identities = 36/112 (32%), Positives = 49/112 (43%), Gaps = 8/112 (7%)

Query: 9   FLFCKFCGTML----RMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFE 64
             FC  CG++L      E   +VC  C +++   +      S     E+ K  + +   E
Sbjct: 2   MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEASNKKVYRYSVKEAVEKKKEVVLVVEDE 61

Query: 65  QPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
                     L   K  C KC N E YY   QTRSADE +T +Y C RCG+R
Sbjct: 62  TQGA----KTLPTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYR 109

Length = 113

>gnl|CDD|201594 pfam01096, TFIIS_C, Transcription factor S-II (TFIIS)

 Score = 57.2 bits (139), Expect = 1e-12
 Identities = 18/35 (51%), Positives = 23/35 (65%)

Query: 82  CEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
           C KC + E  +   QTRSADE  T +Y+C +CGHR
Sbjct: 3   CPKCGHREAVFFQLQTRSADEPMTLFYVCTKCGHR 37

Length = 39

>gnl|CDD|130451 TIGR01384, TFS_arch, transcription factor S, archaeal

 Score = 54.1 bits (130), Expect = 8e-11
 Identities = 33/109 (30%), Positives = 55/109 (50%), Gaps = 8/109 (7%)

Query: 11  FCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDK 70
           FC  CG+++  ++   VC SC ++K  +   D +++  V   + K +  I + E+     
Sbjct: 2   FCPKCGSLMTPKNGVYVCPSCGYEKEKKPEDDYKVTEKV---KHKIKETIIIREE----- 53

Query: 71  GETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119
               L   +  C KC + E YY   QTR ADE +T +Y C +CG+  +E
Sbjct: 54  DSETLPTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWRE 102

This model describes archaeal transcription factor S, a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase. 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 [Transcription, Transcription factors]. Length = 104

>gnl|CDD|128717 smart00440, ZnF_C2C2, C2C2 Zinc finger

 Score = 48.5 bits (116), Expect = 3e-09
 Identities = 18/37 (48%), Positives = 22/37 (59%)

Query: 80  RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
             C KC N E  +   QTRSADE  T +Y+C +CGH 
Sbjct: 1   AECPKCGNREATFYQLQTRSADEPMTVFYVCTKCGHH 37

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases. Length = 40

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

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 24/65 (36%), Positives = 31/65 (47%), Gaps = 5/65 (7%)

Query: 52  EEIKRELGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICP 111
           EEI +E   +LFE       +         C KC+  +  Y   QTRSADE  TT+  C 
Sbjct: 236 EEITKE---NLFEAQGAKIQKAVTDLFT--CGKCKQKKCTYYQLQTRSADEPMTTFVTCE 290

Query: 112 RCGHR 116
            CG+R
Sbjct: 291 ECGNR 295

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	120
KOG2906	105	consensus RNA polymerase III subunit C11 [Transcri	100.0
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	100.0
KOG2691	113	consensus RNA polymerase II subunit 9 [Transcripti	100.0
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	100.0
KOG2907	116	consensus RNA polymerase I transcription factor TF	100.0
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	99.93
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	99.92
PHA02998	195	RNA polymerase subunit; Provisional	99.85
TIGR01385	299	TFSII transcription elongation factor S-II. This m	99.72
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	99.39
KOG1105	296	consensus Transcription elongation factor TFIIS/Co	99.04
smart00661	52	RPOL9 RNA polymerase subunit 9.	98.79
PRK00432	50	30S ribosomal protein S27ae; Validated	98.21
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	97.24
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	97.24
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	97.2
PF04606	47	Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I	96.98
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	96.98
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	96.88
PHA00626	59	hypothetical protein	96.87
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	96.78
PRK09678	72	DNA-binding transcriptional regulator; Provisional	96.75
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	96.61
TIGR01562	305	FdhE formate dehydrogenase accessory protein FdhE.	96.54
smart00661	52	RPOL9 RNA polymerase subunit 9.	96.42
PHA00626	59	hypothetical protein	96.37
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	96.12
PF12773	50	DZR: Double zinc ribbon	96.08
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	95.95
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	95.9
COG3478	68	Predicted nucleic-acid-binding protein containing	95.89
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	95.74
PF14353	128	CpXC: CpXC protein	95.61
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	95.59
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	95.54
COG4332	203	Uncharacterized protein conserved in bacteria [Fun	95.47
PRK14973	936	DNA topoisomerase I; Provisional	95.43
PF13248	26	zf-ribbon_3: zinc-ribbon domain	95.24
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	95.24
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	95.23
PF11781	36	RRN7: RNA polymerase I-specific transcription init	95.19
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	95.12
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	94.94
PF13453	41	zf-TFIIB: Transcription factor zinc-finger	94.93
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	94.87
PF01396	39	zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc	94.8
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	94.61
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	94.6
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	94.54
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	94.53
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	94.49
PRK04023	1121	DNA polymerase II large subunit; Validated	94.43
PF01396	39	zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc	94.38
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	94.31
PRK07220	740	DNA topoisomerase I; Validated	94.29
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	94.21
COG3478	68	Predicted nucleic-acid-binding protein containing	94.17
COG1779	201	C4-type Zn-finger protein [General function predic	94.06
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	93.99
smart00709	160	Zpr1 Duplicated domain in the epidermal growth fac	93.79
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	93.7
cd00730	50	rubredoxin Rubredoxin; nonheme iron binding domain	93.4
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	93.39
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	93.38
PF00301	47	Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubred	93.37
PRK14714	1337	DNA polymerase II large subunit; Provisional	93.34
TIGR00244	147	transcriptional regulator NrdR. Members of this al	93.09
PRK00241	256	nudC NADH pyrophosphatase; Reviewed	92.98
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	92.94
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	92.89
PF10058	54	DUF2296: Predicted integral membrane metal-binding	92.83
PF09526	71	DUF2387: Probable metal-binding protein (DUF2387);	92.71
PF03367	161	zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004	92.49
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	92.39
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	92.37
COG2816	279	NPY1 NTP pyrophosphohydrolases containing a Zn-fin	92.35
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	92.34
PRK14559	645	putative protein serine/threonine phosphatase; Pro	92.29
TIGR02443	59	conserved hypothetical metal-binding protein. Memb	92.29
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	92.18
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	92.12
COG1773	55	Rubredoxin [Energy production and conversion]	92.03
COG1198	730	PriA Primosomal protein N' (replication factor Y)	91.97
PRK07219	822	DNA topoisomerase I; Validated	91.93
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	91.79
TIGR00595	505	priA primosomal protein N'. All proteins in this f	91.78
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	91.77
TIGR00310	192	ZPR1_znf ZPR1 zinc finger domain.	91.76
KOG3507	62	consensus DNA-directed RNA polymerase, subunit RPB	91.69
PF04032	85	Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; Inte	91.5
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	91.28
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	91.15
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	91.07
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	91.07
COG2023	105	RPR2 RNase P subunit RPR2 [Translation, ribosomal	90.74
COG1592	166	Rubrerythrin [Energy production and conversion]	90.62
PRK00420	112	hypothetical protein; Validated	90.59
PF08772	73	NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon lik	90.52
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	90.48
TIGR00686	109	phnA alkylphosphonate utilization operon protein P	90.3
PRK10220	111	hypothetical protein; Provisional	90.26
PF14353	128	CpXC: CpXC protein	90.21
PF11792	43	Baculo_LEF5_C: Baculoviridae late expression facto	90.03
PF01873	125	eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro:	89.97
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	89.93
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	89.77
COG0551	140	TopA Zn-finger domain associated with topoisomeras	89.59
PF09082	68	DUF1922: Domain of unknown function (DUF1922); Int	89.53
PF14311	55	DUF4379: Domain of unknown function (DUF4379)	89.52
COG1327	156	Predicted transcriptional regulator, consists of a	89.44
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	89.18
PHA02942	383	putative transposase; Provisional	89.09
COG1326	201	Uncharacterized archaeal Zn-finger protein [Genera	89.09
PRK05580	679	primosome assembly protein PriA; Validated	89.06
TIGR00311	133	aIF-2beta translation initiation factor aIF-2, bet	88.67
PF06044	254	DRP: Dam-replacing family; InterPro: IPR010324 Dam	88.4
PRK11827	60	hypothetical protein; Provisional	88.33
PRK11032	160	hypothetical protein; Provisional	88.02
PF07295	146	DUF1451: Protein of unknown function (DUF1451); In	87.96
PRK14873	665	primosome assembly protein PriA; Provisional	87.83
PRK03988	138	translation initiation factor IF-2 subunit beta; V	87.83
PRK12286	57	rpmF 50S ribosomal protein L32; Reviewed	87.76
PRK06319	860	DNA topoisomerase I/SWI domain fusion protein; Val	87.73
PF13408	58	Zn_ribbon_recom: Recombinase zinc beta ribbon doma	87.58
PRK09678	72	DNA-binding transcriptional regulator; Provisional	87.58
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	87.36
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	87.14
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	86.92
PF14205	55	Cys_rich_KTR: Cysteine-rich KTR	86.88
COG0777	294	AccD Acetyl-CoA carboxylase beta subunit [Lipid me	86.84
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	86.84
smart00531	147	TFIIE Transcription initiation factor IIE.	86.78
smart00647	64	IBR In Between Ring fingers. the domains occurs be	86.77
COG2835	60	Uncharacterized conserved protein [Function unknow	86.71
TIGR00515	285	accD acetyl-CoA carboxylase, carboxyl transferase,	86.65
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	86.48
PRK14892	99	putative transcription elongation factor Elf1; Pro	86.43
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	86.37
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	86.33
PF09526	71	DUF2387: Probable metal-binding protein (DUF2387);	86.23
CHL00174	296	accD acetyl-CoA carboxylase beta subunit; Reviewed	86.17
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	85.97
COG4640	465	Predicted membrane protein [Function unknown]	85.86
PF05129	81	Elf1: Transcription elongation factor Elf1 like; I	85.78
PF09151	36	DUF1936: Domain of unknown function (DUF1936); Int	85.5
PF01780	90	Ribosomal_L37ae: Ribosomal L37ae protein family; I	85.19
KOG3084	345	consensus NADH pyrophosphatase I of the Nudix fami	85.18
PRK05654	292	acetyl-CoA carboxylase subunit beta; Validated	84.83
PF02591	56	DUF164: Putative zinc ribbon domain; InterPro: IPR	84.61
smart00653	110	eIF2B_5 domain present in translation initiation f	84.57
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	84.54
PRK09710	64	lar restriction alleviation and modification prote	84.48
COG1571	421	Predicted DNA-binding protein containing a Zn-ribb	84.4
PRK12336	201	translation initiation factor IF-2 subunit beta; P	83.9
PHA02942	383	putative transposase; Provisional	83.7
TIGR03826	137	YvyF flagellar operon protein TIGR03826. This gene	83.65
COG1779	201	C4-type Zn-finger protein [General function predic	83.49
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	83.42
PF03966	68	Trm112p: Trm112p-like protein; InterPro: IPR005651	83.41
COG1571	421	Predicted DNA-binding protein containing a Zn-ribb	83.38
KOG2767	400	consensus Translation initiation factor 5 (eIF-5)	83.32
PF01921	360	tRNA-synt_1f: tRNA synthetases class I (K); InterP	82.79
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	82.36
PRK05452	479	anaerobic nitric oxide reductase flavorubredoxin;	82.32
TIGR01031	55	rpmF_bact ribosomal protein L32. This protein desc	82.28
PF01783	56	Ribosomal_L32p: Ribosomal L32p protein family; Int	82.03
KOG0696	683	consensus Serine/threonine protein kinase [Signal	82.01
cd00674	353	LysRS_core_class_I catalytic core domain of class	81.73
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	81.59
COG0675	364	Transposase and inactivated derivatives [DNA repli	81.45
PF01599	47	Ribosomal_S27: Ribosomal protein S27a; InterPro: I	81.11
PF01927	147	Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 T	80.88
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	80.64
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	80.56
COG4530	129	Uncharacterized protein conserved in bacteria [Fun	80.12

>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]

Probab=100.00  E-value=2.4e-41  Score=218.15  Aligned_cols=101  Identities=34%  Similarity=0.633  Sum_probs=83.6

Q ss_pred             cccCccCCCcccccCCc----EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccccccccc
Q 040426            9 FLFCKFCGTMLRMESNH----VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEK   84 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~~----~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~~Cpk   84 (120)
                      |.|||.|||||.++++.    |.|++|+|..+++.    +|..++.    +..+.+++  ++.+...+++...+++.||+
T Consensus         1 m~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~~----ei~~r~~----~~~Kevd~--vlgg~~a~~nv~~t~~~Cp~   70 (105)
T KOG2906|consen    1 MLFCPTCGNMLIVESGESCNRFSCRTCPYVFPISR----EISSRKY----PKLKEVDD--VLGGDEAWENVDQTEATCPT   70 (105)
T ss_pred             CcccCCCCCEEEEecCCeEeeEEcCCCCceeeEee----eeecccc----Cchhhhhh--hcCCcccccchhhccCcCCC
Confidence            68999999999999764    99999999999975    3332221    22222233  56666678888999999999


Q ss_pred             cCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           85 CQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        85 Cg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      |||++|+|+|+|+||||||||+||+|.+|+|+||+
T Consensus        71 Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wre  105 (105)
T KOG2906|consen   71 CGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWRE  105 (105)
T ss_pred             CCCCceEEEEeeeccCCCcHhHhhhhhcccccccC
Confidence            99999999999999999999999999999999996

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

Probab=100.00  E-value=3.2e-39  Score=217.08  Aligned_cols=108  Identities=33%  Similarity=0.699  Sum_probs=80.3

Q ss_pred             CcccCccCCCcccccCC---c-EEeCCCCCeeeccccccceEEEeeeh-hHHhhhhccccccccCCCccccccccccccc
Q 040426            8 DFLFCKFCGTMLRMESN---H-VVCSSCKFKKNVQDVADREISYAVTA-EEIKRELGISLFEQPQGDKGETQLSKVKRAC   82 (120)
Q Consensus         8 ~~~FCp~CgnlL~~~~~---~-~~C~~C~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~i~~~~~~~~t~~~~~~~C   82 (120)
                      .|.|||+|||||+|+.+   . ++|++|||..++...    .+++... ..++........++ .+....+++++..+.|
T Consensus         1 ~m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~~~----~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~C   75 (113)
T COG1594           1 SMRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEASNK----KVYRYSVKEAVEKKKEVVLVVE-DETQGAKTLPTAKEKC   75 (113)
T ss_pred             CccccCCccCeeEEeEcCCCcEEECCCCCcchhcccc----ceeEEEEeeccCCcceeeeeec-ccccCccccccccccC
Confidence            48999999999999764   2 999999999998863    1221111 11222112111111 1334446777778899


Q ss_pred             cccCCCceEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426           83 EKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES  120 (120)
Q Consensus        83 pkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n  120 (120)
                      |+|||++|+|||+|+||||||||+||+|++|||+||++
T Consensus        76 pkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre~  113 (113)
T COG1594          76 PKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWREY  113 (113)
T ss_pred             CCCCCceeEEEeeehhccCCCceEEEEecccCCEeecC
Confidence            99999999999999999999999999999999999986

>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]

Probab=100.00  E-value=3.5e-38  Score=206.42  Aligned_cols=105  Identities=26%  Similarity=0.543  Sum_probs=90.7

Q ss_pred             CCcccCccCCCcccccCCc------EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCcccccccc-cc
Q 040426            7 RDFLFCKFCGTMLRMESNH------VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSK-VK   79 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~~------~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~-~~   79 (120)
                      ++++||++|||||||++|+      |.||+|.|++.+++    ..+|+....   +...+. ..++.+...|||+|+ .+
T Consensus         2 ~~~rfC~eCNNmLYPkEDked~~L~laCrnCd~ve~A~s----~~vY~~~~~---~e~dE~-t~ii~Dl~~DPTLPrts~   73 (113)
T KOG2691|consen    2 VGIRFCRECNNMLYPKEDKEDRILLLACRNCDYVEEADS----SRVYVNELS---HEHDEL-TQIIMDLASDPTLPRTSD   73 (113)
T ss_pred             CccchhhhhhccccccccccccEEEEEecCCcceEecCC----cceEcCCcc---cchhhH-HHHHHhhccCCCcCcccc
Confidence            5799999999999999984      99999999999988    577776532   222322 337788899999995 78


Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      +.||+|||++|+|||.|+|.|||+|++||+|+.|||+|++
T Consensus        74 ~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h~wte  113 (113)
T KOG2691|consen   74 KHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGHRWTE  113 (113)
T ss_pred             ccCCccCCcceEEEecccccccceEEEEEEeccccccccC
Confidence            9999999999999999999999999999999999999986

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=100.00  E-value=1.8e-37  Score=205.76  Aligned_cols=103  Identities=27%  Similarity=0.577  Sum_probs=79.1

Q ss_pred             ccCccCCCcccccCCcEEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccccccccccCCCc
Q 040426           10 LFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEKCQNPE   89 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~~CpkCg~~e   89 (120)
                      .|||.||+||++.++.+.|+.|+|...+...  ...+++....   .... +++ ++.+ +..+++|++++.||+|||++
T Consensus         1 ~fC~~Cg~~l~~~~~~~~C~~C~~~~~~~~~--~~~v~~~~~~---~~~~-~~~-~~~~-~~~~~~~~~~~~Cp~Cg~~~   72 (104)
T TIGR01384         1 KFCPKCGSLMTPKNGVYVCPSCGYEKEKKPE--DDYKVTEKVK---HKIK-ETI-IIRE-EDSETLPTTRVECPKCGHKE   72 (104)
T ss_pred             CCCcccCcccccCCCeEECcCCCCccccccc--cccEEEEEec---cccc-cce-eecc-ccccCCCcccCCCCCCCCCe
Confidence            4999999999998777999999999876421  1234443321   1111 112 1222 22388998899999999999


Q ss_pred             eEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426           90 MYYSTRQTRSADEGQTTYYICPRCGHRCQES  120 (120)
Q Consensus        90 a~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n  120 (120)
                      |+|||+|+||||||||+||+|++|||+|+++
T Consensus        73 a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~  103 (104)
T TIGR01384        73 AYYWLLQTRRADEPETRFYKCTKCGYVWREY  103 (104)
T ss_pred             eEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence            9999999999999999999999999999985

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.

>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12

Probab=100.00  E-value=1.9e-36  Score=199.93  Aligned_cols=110  Identities=33%  Similarity=0.615  Sum_probs=89.3

Q ss_pred             CCCcccCccCCCcccccCCc--EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCcccccccccccccc
Q 040426            6 GRDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACE   83 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~~Cp   83 (120)
                      ..++.||+.||+||+.+...  ..|..|+..++.+.+....+...+....++.++..+   +  +...+..+|+++++||
T Consensus         4 ~~~~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~~~~~~v~~~~~~~~~~~A~~~~---v--e~~~~~~ga~I~~kCp   78 (116)
T KOG2907|consen    4 NGDLDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQFSGLVVETKSLFDEFTSALAEK---V--ENESSADGAVIKHKCP   78 (116)
T ss_pred             ccCcchhhhhhhhcccccccCceEeccccccCCHHHhCCeeEEEEEeecccchhhhhh---h--cccccccccchhccCc
Confidence            44899999999999998765  889999999999888776666655555444433322   1  1222346789999999


Q ss_pred             ccCCCceEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426           84 KCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES  120 (120)
Q Consensus        84 kCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n  120 (120)
                      ||||++|.|.++||||||||||+||.|++|+|++++|
T Consensus        79 kCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e~  115 (116)
T KOG2907|consen   79 KCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTEN  115 (116)
T ss_pred             ccCCchhhhhhhhcccccCCceEEEEcCccceeeecc
Confidence            9999999999999999999999999999999999986

2/RPA12 [Transcription]

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=99.93  E-value=7.8e-27  Score=130.20  Aligned_cols=40  Identities=50%  Similarity=0.952  Sum_probs=38.4

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      .+||+|||++|+|||+|+||||||||+||+|++|||+|++
T Consensus         1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~~   40 (40)
T smart00440        1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWRE   40 (40)
T ss_pred             CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeCC
Confidence            3699999999999999999999999999999999999986

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

>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=99.92  E-value=1.6e-25  Score=124.24  Aligned_cols=39  Identities=46%  Similarity=0.848  Sum_probs=35.0

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      .+||+|||++|+|+|+|+||||||||+||+|.+|||+||
T Consensus         1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr   39 (39)
T PF01096_consen    1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR   39 (39)
T ss_dssp             S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred             CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence            369999999999999999999999999999999999997

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 ....

>PHA02998 RNA polymerase subunit; Provisional

Probab=99.85  E-value=7.4e-22  Score=140.17  Aligned_cols=45  Identities=24%  Similarity=0.419  Sum_probs=42.6

Q ss_pred             cccc-ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           74 QLSK-VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        74 t~~~-~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      -+|+ ++.+||+|||++|+|+|+|+||||||||+||+|++|||+|+
T Consensus       137 vlpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk  182 (195)
T PHA02998        137 VLDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK  182 (195)
T ss_pred             ccCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence            4665 88999999999999999999999999999999999999997

>TIGR01385 TFSII transcription elongation factor S-II

Probab=99.72  E-value=3.6e-18  Score=131.49  Aligned_cols=42  Identities=40%  Similarity=0.683  Sum_probs=40.0

Q ss_pred             cccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           77 KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +....||+||+++++|||+|+||||||||+||+|++|||+|+
T Consensus       256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~  297 (299)
T TIGR01385       256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK  297 (299)
T ss_pred             cccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence            456799999999999999999999999999999999999997

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

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

Probab=99.39  E-value=1.1e-13  Score=74.86  Aligned_cols=31  Identities=26%  Similarity=0.820  Sum_probs=24.5

Q ss_pred             cccCccCCCcccccCCc---EEeCCCCCeeeccc
Q 040426            9 FLFCKFCGTMLRMESNH---VVCSSCKFKKNVQD   39 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~~---~~C~~C~~~~~~~~   39 (120)
                      |.|||+|||||+|+++.   ..|++|||+++++.
T Consensus         1 m~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~~~~   34 (35)
T PF02150_consen    1 MRFCPECGNLLYPKEDKEKRVACRTCGYEEPISQ   34 (35)
T ss_dssp             --BETTTTSBEEEEEETTTTEEESSSS-EEE-SS
T ss_pred             CeeCCCCCccceEcCCCccCcCCCCCCCccCCCC
Confidence            68999999999999875   68999999999875

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 ....

>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]

Probab=99.04  E-value=1.5e-10  Score=88.86  Aligned_cols=41  Identities=41%  Similarity=0.714  Sum_probs=39.0

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      ....|.+|+.....|+|+|+||||||||.|-.|.+||.+|+
T Consensus       254 d~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~ecgnrWk  294 (296)
T KOG1105|consen  254 DLFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNECGNRWK  294 (296)
T ss_pred             cceeeccccccceeEEeeccCCCCCCcceeeeecccCCccc
Confidence            35789999999999999999999999999999999999996

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=98.79  E-value=7.3e-09  Score=60.05  Aligned_cols=37  Identities=27%  Similarity=0.718  Sum_probs=30.0

Q ss_pred             ccCccCCCcccccCC----cEEeCCCCCeeeccccccceEEEeee
Q 040426           10 LFCKFCGTMLRMESN----HVVCSSCKFKKNVQDVADREISYAVT   50 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~----~~~C~~C~~~~~~~~~~~~~~~~~~~   50 (120)
                      .|||+||+||+++++    .++|+.|||...+..    .++|...
T Consensus         1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~----~~~~~~~   41 (52)
T smart00661        1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQ----KYVYKEK   41 (52)
T ss_pred             CCCCCCCCccccccCCCCCEEECCcCCCeEECCC----cEEEEEE
Confidence            599999999999864    299999999998866    4566543

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=98.21  E-value=8.9e-07  Score=51.36  Aligned_cols=29  Identities=21%  Similarity=0.617  Sum_probs=25.5

Q ss_pred             CcccCccCCC-cccccCCcEEeCCCCCeee
Q 040426            8 DFLFCKFCGT-MLRMESNHVVCSSCKFKKN   36 (120)
Q Consensus         8 ~~~FCp~Cgn-lL~~~~~~~~C~~C~~~~~   36 (120)
                      ...|||.||+ +|.+..+.+.|..|||++-
T Consensus        19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~~   48 (50)
T PRK00432         19 KNKFCPRCGSGFMAEHLDRWHCGKCGYTEF   48 (50)
T ss_pred             ccCcCcCCCcchheccCCcEECCCcCCEEe
Confidence            4569999999 9999888899999999863

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

Probab=97.24  E-value=0.0002  Score=41.10  Aligned_cols=30  Identities=20%  Similarity=0.596  Sum_probs=23.9

Q ss_pred             CcccCccCC--CcccccCCcEEeCCCCCeeec
Q 040426            8 DFLFCKFCG--TMLRMESNHVVCSSCKFKKNV   37 (120)
Q Consensus         8 ~~~FCp~Cg--nlL~~~~~~~~C~~C~~~~~~   37 (120)
                      .-.|||.||  .+|---.++++|-.|||++-.
T Consensus        18 k~~~CPrCG~gvfmA~H~dR~~CGkCgyTe~~   49 (51)
T COG1998          18 KNRFCPRCGPGVFMADHKDRWACGKCGYTEFK   49 (51)
T ss_pred             ccccCCCCCCcchhhhcCceeEeccccceEee
Confidence            457999999  666655667999999998753

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

Probab=97.24  E-value=0.00017  Score=38.49  Aligned_cols=26  Identities=35%  Similarity=0.871  Sum_probs=16.2

Q ss_pred             ccCccCCCccccc---CCc---EEeCCCCCee
Q 040426           10 LFCKFCGTMLRME---SNH---VVCSSCKFKK   35 (120)
Q Consensus        10 ~FCp~CgnlL~~~---~~~---~~C~~C~~~~   35 (120)
                      +|||.||..|...   .+.   ++|..||++.
T Consensus         1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~Ih   32 (34)
T PF14803_consen    1 KFCPQCGGPLERRIPEGDDRERLVCPACGFIH   32 (34)
T ss_dssp             -B-TTT--B-EEE--TT-SS-EEEETTTTEEE
T ss_pred             CccccccChhhhhcCCCCCccceECCCCCCEE
Confidence            5999999999754   232   9999999864

>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []

Probab=97.20  E-value=0.00058  Score=52.48  Aligned_cols=68  Identities=24%  Similarity=0.462  Sum_probs=32.9

Q ss_pred             ccCccCCCc-----ccccC--C-c-EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccccc
Q 040426           10 LFCKFCGTM-----LRMES--N-H-VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKR   80 (120)
Q Consensus        10 ~FCp~Cgnl-----L~~~~--~-~-~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~   80 (120)
                      .+||.||+.     |...+  + + +.|..|++....                                        ...
T Consensus       173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~----------------------------------------~R~  212 (290)
T PF04216_consen  173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRF----------------------------------------VRI  212 (290)
T ss_dssp             SS-TTT---EEEEEEE------EEEEEETTT--EEE------------------------------------------TT
T ss_pred             CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeee----------------------------------------cCC
Confidence            699999986     33333  2 2 999999998753                                        134


Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      .||.||+.+..=+.. +...+++.-..++|.+|+..++
T Consensus       213 ~Cp~Cg~~~~~~l~~-~~~e~~~~~rve~C~~C~~YlK  249 (290)
T PF04216_consen  213 KCPYCGNTDHEKLEY-FTVEGEPAYRVEVCESCGSYLK  249 (290)
T ss_dssp             S-TTT---SS-EEE---------SEEEEEETTTTEEEE
T ss_pred             CCcCCCCCCCcceee-EecCCCCcEEEEECCcccchHH
Confidence            599999976642111 2246777889999999998775

The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.

>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr

Probab=96.98  E-value=0.00076  Score=38.37  Aligned_cols=37  Identities=24%  Similarity=0.561  Sum_probs=26.5

Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCC--CCceecc
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPR--CGHRCQE  119 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~--C~~~w~~  119 (120)
                      .||.||+.-......++  .++--.++|.|.+  |||+|..
T Consensus         1 ~CP~Cg~~a~ir~S~~~--s~~~~~~Y~qC~N~~Cg~tfv~   39 (47)
T PF04606_consen    1 RCPHCGSKARIRTSRQL--SPLTRELYCQCTNPECGHTFVA   39 (47)
T ss_pred             CcCCCCCeeEEEEchhh--CcceEEEEEEECCCcCCCEEEE
Confidence            49999998665544332  3444558999997  9999963

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=96.98  E-value=0.0021  Score=50.17  Aligned_cols=67  Identities=22%  Similarity=0.622  Sum_probs=45.5

Q ss_pred             cccCccCCCcc-----cccC-C--c-EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCcccccccccc
Q 040426            9 FLFCKFCGTML-----RMES-N--H-VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVK   79 (120)
Q Consensus         9 ~~FCp~CgnlL-----~~~~-~--~-~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~   79 (120)
                      -.+||.||+.=     .... +  + +.|..|+.....                                        .+
T Consensus       187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~----------------------------------------~R  226 (309)
T PRK03564        187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHV----------------------------------------VR  226 (309)
T ss_pred             CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccc----------------------------------------cC
Confidence            57999999872     1211 2  2 999999987742                                        24


Q ss_pred             ccccccCCC-ceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           80 RACEKCQNP-EMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        80 ~~CpkCg~~-ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      ..||.||+. +..||.+-   .+++.-..+.|..|+..++
T Consensus       227 ~~C~~Cg~~~~l~y~~~~---~~~~~~r~e~C~~C~~YlK  263 (309)
T PRK03564        227 VKCSNCEQSGKLHYWSLD---SEQAAVKAESCGDCGTYLK  263 (309)
T ss_pred             ccCCCCCCCCceeeeeec---CCCcceEeeecccccccce
Confidence            569999986 44576552   2234567899999987665

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

Probab=96.88  E-value=0.00035  Score=36.28  Aligned_cols=27  Identities=30%  Similarity=0.869  Sum_probs=14.7

Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +||+||....+        .   -...|+|..|+|.|.
T Consensus         4 ~Cp~C~se~~y--------~---D~~~~vCp~C~~ew~   30 (30)
T PF08274_consen    4 KCPLCGSEYTY--------E---DGELLVCPECGHEWN   30 (30)
T ss_dssp             --TTT-----E--------E----SSSEEETTTTEEE-
T ss_pred             CCCCCCCccee--------c---cCCEEeCCcccccCC
Confidence            69999999887        2   223499999999994

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.

>PHA00626 hypothetical protein

Probab=96.87  E-value=0.00078  Score=39.74  Aligned_cols=34  Identities=26%  Similarity=0.656  Sum_probs=23.1

Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      .||+||+.+.+- -...|    .+..-|+|.+|||.++.
T Consensus         2 ~CP~CGS~~Ivr-cg~cr----~~snrYkCkdCGY~ft~   35 (59)
T PHA00626          2 SCPKCGSGNIAK-EKTMR----GWSDDYVCCDCGYNDSK   35 (59)
T ss_pred             CCCCCCCceeee-eceec----ccCcceEcCCCCCeech
Confidence            599999987652 11111    23455999999999863

>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=96.78  E-value=0.0011  Score=34.65  Aligned_cols=27  Identities=26%  Similarity=0.603  Sum_probs=18.9

Q ss_pred             cccCccCCCcccccCCc--EEeCCCCCee
Q 040426            9 FLFCKFCGTMLRMESNH--VVCSSCKFKK   35 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~~--~~C~~C~~~~   35 (120)
                      -+||+.||.-+.+....  ..|..|+...
T Consensus         3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~~   31 (32)
T PF09297_consen    3 HRFCGRCGAPTKPAPGGWARRCPSCGHEH   31 (32)
T ss_dssp             TSB-TTT--BEEE-SSSS-EEESSSS-EE
T ss_pred             CcccCcCCccccCCCCcCEeECCCCcCEe
Confidence            57999999999998775  9999999764

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

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=96.75  E-value=0.0015  Score=40.62  Aligned_cols=36  Identities=22%  Similarity=0.495  Sum_probs=26.6

Q ss_pred             cccccCCCceEEEEeecccCCCCce-EEEEcC--CCCceecc
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQT-TYYICP--RCGHRCQE  119 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T-~fY~C~--~C~~~w~~  119 (120)
                      .||.||+.-.+   .-.|..+++.. ++|.|+  +|||+|..
T Consensus         3 ~CP~Cg~~a~i---rtSr~~s~~~~~~Y~qC~N~eCg~tF~t   41 (72)
T PRK09678          3 HCPLCQHAAHA---RTSRYITDTTKERYHQCQNVNCSATFIT   41 (72)
T ss_pred             cCCCCCCccEE---EEChhcChhhheeeeecCCCCCCCEEEE
Confidence            69999998733   33455565544 889999  89999974

>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=96.61  E-value=0.0038  Score=37.94  Aligned_cols=36  Identities=28%  Similarity=0.525  Sum_probs=21.3

Q ss_pred             cccccCCCceEEEEeecccC------C--CCceEEEEcCCCCce
Q 040426           81 ACEKCQNPEMYYSTRQTRSA------D--EGQTTYYICPRCGHR  116 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSA------D--E~~T~fY~C~~C~~~  116 (120)
                      .|||||+.+...-++|+--.      |  +..-+...|++|||+
T Consensus         2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT   45 (64)
T PF09855_consen    2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT   45 (64)
T ss_pred             CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence            69999998765443332110      1  112245679999997

>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE

Probab=96.54  E-value=0.0064  Score=47.41  Aligned_cols=69  Identities=20%  Similarity=0.484  Sum_probs=46.1

Q ss_pred             cccCccCCCcc-----ccc--CC--c-EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccc
Q 040426            9 FLFCKFCGTML-----RME--SN--H-VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKV   78 (120)
Q Consensus         9 ~~FCp~CgnlL-----~~~--~~--~-~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~   78 (120)
                      -.+||.||+.=     ...  .+  + +.|..|+.....                                        .
T Consensus       184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~----------------------------------------~  223 (305)
T TIGR01562       184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHY----------------------------------------V  223 (305)
T ss_pred             CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccc----------------------------------------c
Confidence            45999999873     221  12  2 999999987742                                        2


Q ss_pred             cccccccCCCc-eEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           79 KRACEKCQNPE-MYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        79 ~~~CpkCg~~e-a~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +..||.||+.+ ..||.+-. ..+++-.....|..|+...+
T Consensus       224 R~~C~~Cg~~~~l~y~~~e~-~~~~~~~r~e~C~~C~~YlK  263 (305)
T TIGR01562       224 RVKCSHCEESKHLAYLSLEH-DAEKAVLKAETCDSCQGYLK  263 (305)
T ss_pred             CccCCCCCCCCceeeEeecC-CCCCcceEEeeccccccchh
Confidence            45699999974 45776522 11245678889999987654

The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=96.42  E-value=0.0038  Score=35.67  Aligned_cols=32  Identities=25%  Similarity=0.686  Sum_probs=19.9

Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES  120 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n  120 (120)
                      -||+||+  +.|    .+ .++ ....|.|..|||.++.+
T Consensus         2 FCp~Cg~--~l~----~~-~~~-~~~~~vC~~Cg~~~~~~   33 (52)
T smart00661        2 FCPKCGN--MLI----PK-EGK-EKRRFVCRKCGYEEPIE   33 (52)
T ss_pred             CCCCCCC--ccc----cc-cCC-CCCEEECCcCCCeEECC
Confidence            4999988  222    12 122 12378999999987653

>PHA00626 hypothetical protein

Probab=96.37  E-value=0.0024  Score=37.65  Aligned_cols=32  Identities=19%  Similarity=0.555  Sum_probs=23.7

Q ss_pred             ccCccCCCcccccC-------CcEEeCCCCCeeeccccc
Q 040426           10 LFCKFCGTMLRMES-------NHVVCSSCKFKKNVQDVA   41 (120)
Q Consensus        10 ~FCp~CgnlL~~~~-------~~~~C~~C~~~~~~~~~~   41 (120)
                      +.||.||+--..+.       +.|.|..|||....+.+.
T Consensus         1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~~   39 (59)
T PHA00626          1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAFG   39 (59)
T ss_pred             CCCCCCCCceeeeeceecccCcceEcCCCCCeechhhhh
Confidence            47999999544442       239999999998776653

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=96.12  E-value=0.0051  Score=33.09  Aligned_cols=32  Identities=31%  Similarity=0.645  Sum_probs=21.4

Q ss_pred             cccccccCCCceEEEEeecccCCC---CceEEEEcCCCCceec
Q 040426           79 KRACEKCQNPEMYYSTRQTRSADE---GQTTYYICPRCGHRCQ  118 (120)
Q Consensus        79 ~~~CpkCg~~ea~y~~~Q~RSADE---~~T~fY~C~~C~~~w~  118 (120)
                      ...||+|+..   |     +-+||   +..+-.+|.+|||.|+
T Consensus         2 ~i~Cp~C~~~---y-----~i~d~~ip~~g~~v~C~~C~~~f~   36 (36)
T PF13717_consen    2 IITCPNCQAK---Y-----EIDDEKIPPKGRKVRCSKCGHVFF   36 (36)
T ss_pred             EEECCCCCCE---E-----eCCHHHCCCCCcEEECCCCCCEeC
Confidence            3568888753   2     22444   4556789999999995

>PF12773 DZR: Double zinc ribbon

Probab=96.08  E-value=0.0033  Score=35.77  Aligned_cols=32  Identities=28%  Similarity=0.592  Sum_probs=24.6

Q ss_pred             CCCCcccCccCCCcccccCC-cEEeCCCCCeee
Q 040426            5 LGRDFLFCKFCGTMLRMESN-HVVCSSCKFKKN   36 (120)
Q Consensus         5 ~~~~~~FCp~CgnlL~~~~~-~~~C~~C~~~~~   36 (120)
                      +..+..|||.||..|..... .+.|..|++...
T Consensus         8 ~~~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~   40 (50)
T PF12773_consen    8 NPDDAKFCPHCGTPLPPPDQSKKICPNCGAENP   40 (50)
T ss_pred             CCccccCChhhcCChhhccCCCCCCcCCcCCCc
Confidence            44568899999999994333 399999999643

>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=95.95  E-value=0.0065  Score=34.25  Aligned_cols=28  Identities=21%  Similarity=0.582  Sum_probs=21.1

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR  116 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~  116 (120)
                      ..||+||+.+++....         ...|+|..|+++
T Consensus        19 ~~CP~Cg~~~~~~~~~---------~~~~~C~~C~~q   46 (46)
T PF12760_consen   19 FVCPHCGSTKHYRLKT---------RGRYRCKACRKQ   46 (46)
T ss_pred             CCCCCCCCeeeEEeCC---------CCeEECCCCCCc
Confidence            5599999995554432         567999999874

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

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=95.90  E-value=0.0094  Score=42.17  Aligned_cols=38  Identities=18%  Similarity=0.427  Sum_probs=22.5

Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +||-||++...-...-.=|--.--+.+|.|.+||.+|.
T Consensus         2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~   39 (154)
T PRK00464          2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFT   39 (154)
T ss_pred             cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcce
Confidence            69999998742111000000001556899999999885

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

Probab=95.89  E-value=0.0063  Score=36.90  Aligned_cols=35  Identities=23%  Similarity=0.586  Sum_probs=23.7

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEE--------E--EcCCCCce
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTY--------Y--ICPRCGHR  116 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~f--------Y--~C~~C~~~  116 (120)
                      .+|||||+++.  .+-+++...++..-+        +  .|.+|||+
T Consensus         5 ~kCpKCgn~~~--~ekei~~tg~~lskifdvq~n~f~~itCk~CgYt   49 (68)
T COG3478           5 FKCPKCGNTNY--EEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYT   49 (68)
T ss_pred             ccCCCcCCcch--hhceeeccCCCcceeEEecccEEEEEEeccCCch
Confidence            35999999875  455556665665433        3  48899986

>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=95.74  E-value=0.013  Score=32.42  Aligned_cols=30  Identities=27%  Similarity=0.642  Sum_probs=20.7

Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      .||.||+.. ..+-        ..+-.++|..||....+
T Consensus         2 ~Cp~Cg~~~-~~~D--------~~~g~~vC~~CG~Vl~e   31 (43)
T PF08271_consen    2 KCPNCGSKE-IVFD--------PERGELVCPNCGLVLEE   31 (43)
T ss_dssp             SBTTTSSSE-EEEE--------TTTTEEEETTT-BBEE-
T ss_pred             CCcCCcCCc-eEEc--------CCCCeEECCCCCCEeec
Confidence            699999988 3332        45566899999986544

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.

>PF14353 CpXC: CpXC protein

Probab=95.61  E-value=0.021  Score=38.59  Aligned_cols=40  Identities=28%  Similarity=0.640  Sum_probs=26.1

Q ss_pred             ccccccCCC-ceEEEEeecccCC--------CCceEEEEcCCCCceecc
Q 040426           80 RACEKCQNP-EMYYSTRQTRSAD--------EGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        80 ~~CpkCg~~-ea~y~~~Q~RSAD--------E~~T~fY~C~~C~~~w~~  119 (120)
                      ..||+||+. ++..|+.=.-+.|        +|.--.|+|..||+..+.
T Consensus         2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~   50 (128)
T PF14353_consen    2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRL   50 (128)
T ss_pred             cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceec
Confidence            469999997 5556654332333        234457899999988653

>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=95.59  E-value=0.0099  Score=39.67  Aligned_cols=39  Identities=23%  Similarity=0.374  Sum_probs=33.5

Q ss_pred             CCCCCCCCcccCccCCCcccccC-CcEEeCCCCCeeeccc
Q 040426            1 MADPLGRDFLFCKFCGTMLRMES-NHVVCSSCKFKKNVQD   39 (120)
Q Consensus         1 ~~~~~~~~~~FCp~CgnlL~~~~-~~~~C~~C~~~~~~~~   39 (120)
                      |+++--+.-+.||.||.-.|=-. +.++|+.||..+++..
T Consensus         1 MakpelGtKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~~   40 (108)
T PF09538_consen    1 MAKPELGTKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPEP   40 (108)
T ss_pred             CCccccCCcccCCCCcchhccCCCCCccCCCCCCccCccc
Confidence            89999999999999999887543 3399999999998873

The function of members of this family is unknown.

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

Probab=95.54  E-value=0.011  Score=49.50  Aligned_cols=42  Identities=21%  Similarity=0.607  Sum_probs=30.6

Q ss_pred             ccccccccCCCc-eEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           78 VKRACEKCQNPE-MYYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        78 ~~~~CpkCg~~e-a~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      -.++||.||+.. ..|-.++--.-..+.+..|+|..||+.|.+
T Consensus       199 ~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e  241 (557)
T PF05876_consen  199 YYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEE  241 (557)
T ss_pred             EEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCH
Confidence            357999999974 455555541111589999999999999875

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 [].

>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.47  E-value=0.014  Score=42.32  Aligned_cols=46  Identities=15%  Similarity=0.438  Sum_probs=33.0

Q ss_pred             cccccccccccccCCCceEEEEeecccCCCCce----EEEEcCCCCceec
Q 040426           73 TQLSKVKRACEKCQNPEMYYSTRQTRSADEGQT----TYYICPRCGHRCQ  118 (120)
Q Consensus        73 ~t~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T----~fY~C~~C~~~w~  118 (120)
                      .++|..-..|++||..+++--.--.|---.|--    ++|+|+.|.++|.
T Consensus        11 ~~~pq~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~tWN   60 (203)
T COG4332          11 VGAPQPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHCDYTWN   60 (203)
T ss_pred             ccCChhhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeeccCCccc
Confidence            355667788999999988744333444444432    6899999999995

>PRK14973 DNA topoisomerase I; Provisional

Probab=95.43  E-value=0.021  Score=50.60  Aligned_cols=32  Identities=22%  Similarity=0.359  Sum_probs=23.4

Q ss_pred             cccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426           79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR  116 (120)
Q Consensus        79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~  116 (120)
                      +..||+||.+.    .+.+|...-|+  |.-|++|.|.
T Consensus       635 ~~~Cp~CG~p~----~~~~r~Gr~g~--fl~CP~C~~~  666 (936)
T PRK14973        635 DEVCPIHHLNH----VRLIRKGARPW--DIGCPLCSHI  666 (936)
T ss_pred             CCCCCCCCCCc----eEEeecCCCcc--cccCccccch
Confidence            55899999972    23346666666  7789999885

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=95.24  E-value=0.0087  Score=29.77  Aligned_cols=24  Identities=29%  Similarity=0.836  Sum_probs=16.9

Q ss_pred             cccCccCCCcccccCCcEEeCCCCCe
Q 040426            9 FLFCKFCGTMLRMESNHVVCSSCKFK   34 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~~~~C~~C~~~   34 (120)
                      ..+||.||..+  +.+.-.|+.||..
T Consensus         2 ~~~Cp~Cg~~~--~~~~~fC~~CG~~   25 (26)
T PF13248_consen    2 EMFCPNCGAEI--DPDAKFCPNCGAK   25 (26)
T ss_pred             cCCCcccCCcC--CcccccChhhCCC
Confidence            46899999843  3334688888864

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=95.24  E-value=0.023  Score=30.45  Aligned_cols=35  Identities=20%  Similarity=0.478  Sum_probs=21.5

Q ss_pred             cccccccCCCceEEEEeecc-cCCCCceEEEEcCCCCceecc
Q 040426           79 KRACEKCQNPEMYYSTRQTR-SADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        79 ~~~CpkCg~~ea~y~~~Q~R-SADE~~T~fY~C~~C~~~w~~  119 (120)
                      ...||.||..    |.++.. -.+++.  -.+|.+||+.|..
T Consensus         2 ~~~CP~C~~~----~~v~~~~~~~~~~--~v~C~~C~~~~~~   37 (38)
T TIGR02098         2 RIQCPNCKTS----FRVVDSQLGANGG--KVRCGKCGHVWYA   37 (38)
T ss_pred             EEECCCCCCE----EEeCHHHcCCCCC--EEECCCCCCEEEe
Confidence            3579999875    222221 223333  6789999999863

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.

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=95.23  E-value=0.009  Score=28.99  Aligned_cols=22  Identities=23%  Similarity=0.757  Sum_probs=15.2

Q ss_pred             cCccCCCcccccCCcEEeCCCCCe
Q 040426           11 FCKFCGTMLRMESNHVVCSSCKFK   34 (120)
Q Consensus        11 FCp~CgnlL~~~~~~~~C~~C~~~   34 (120)
                      |||.||+-|..  +.-.|..||+.
T Consensus         1 ~Cp~CG~~~~~--~~~fC~~CG~~   22 (23)
T PF13240_consen    1 YCPNCGAEIED--DAKFCPNCGTP   22 (23)
T ss_pred             CCcccCCCCCC--cCcchhhhCCc
Confidence            78888887743  23458888863

>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=95.19  E-value=0.012  Score=31.70  Aligned_cols=26  Identities=19%  Similarity=0.529  Sum_probs=22.3

Q ss_pred             ccCccCCCcccccCCc-EEeCCCCCee
Q 040426           10 LFCKFCGTMLRMESNH-VVCSSCKFKK   35 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~-~~C~~C~~~~   35 (120)
                      .=|+.|++.+....+. +.|..||++.
T Consensus         9 ~~C~~C~~~~~~~~dG~~yC~~cG~~~   35 (36)
T PF11781_consen    9 EPCPVCGSRWFYSDDGFYYCDRCGHQS   35 (36)
T ss_pred             CcCCCCCCeEeEccCCEEEhhhCceEc
Confidence            3499999998888777 9999999864

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

Probab=95.12  E-value=0.011  Score=35.32  Aligned_cols=26  Identities=19%  Similarity=0.430  Sum_probs=15.8

Q ss_pred             cccCccCCCcccccCCc--EEeCCCCCe
Q 040426            9 FLFCKFCGTMLRMESNH--VVCSSCKFK   34 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~~--~~C~~C~~~   34 (120)
                      ..-|..||-.|.|.+..  |.|++||.+
T Consensus         9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~   36 (61)
T COG2888           9 PPVCTSCGREIAPGETAVKFPCPNCGEV   36 (61)
T ss_pred             CceeccCCCEeccCCceeEeeCCCCCce
Confidence            44666677666555543  666666643

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

Probab=94.94  E-value=0.021  Score=28.07  Aligned_cols=22  Identities=27%  Similarity=0.786  Sum_probs=18.4

Q ss_pred             CccCCCcccccCC-c-EEeCCCCC
Q 040426           12 CKFCGTMLRMESN-H-VVCSSCKF   33 (120)
Q Consensus        12 Cp~CgnlL~~~~~-~-~~C~~C~~   33 (120)
                      |..||-.|.+.+. . |.|++||+
T Consensus         1 C~sC~~~i~~r~~~v~f~CPnCG~   24 (24)
T PF07754_consen    1 CTSCGRPIAPREQAVPFPCPNCGF   24 (24)
T ss_pred             CccCCCcccCcccCceEeCCCCCC
Confidence            6789999998873 3 99999985

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

>PF13453 zf-TFIIB: Transcription factor zinc-finger

Probab=94.93  E-value=0.048  Score=29.86  Aligned_cols=30  Identities=23%  Similarity=0.600  Sum_probs=21.0

Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      .||+|++. +.=..+       +-...+.|.+|+-.|=
T Consensus         1 ~CP~C~~~-l~~~~~-------~~~~id~C~~C~G~W~   30 (41)
T PF13453_consen    1 KCPRCGTE-LEPVRL-------GDVEIDVCPSCGGIWF   30 (41)
T ss_pred             CcCCCCcc-cceEEE-------CCEEEEECCCCCeEEc
Confidence            49999984 432221       3367799999998884

>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=94.87  E-value=0.016  Score=28.99  Aligned_cols=24  Identities=21%  Similarity=0.605  Sum_probs=18.0

Q ss_pred             cCccCCCcccccCCcEEeCCCCCeee
Q 040426           11 FCKFCGTMLRMESNHVVCSSCKFKKN   36 (120)
Q Consensus        11 FCp~CgnlL~~~~~~~~C~~C~~~~~   36 (120)
                      =||+|+..+...  .-.|+.|||...
T Consensus         2 ~CP~C~~~V~~~--~~~Cp~CG~~F~   25 (26)
T PF10571_consen    2 TCPECGAEVPES--AKFCPHCGYDFE   25 (26)
T ss_pred             cCCCCcCCchhh--cCcCCCCCCCCc
Confidence            399999876333  378999999764

Several members are annotated as putative helicases.

>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i

Probab=94.80  E-value=0.023  Score=31.00  Aligned_cols=29  Identities=28%  Similarity=0.655  Sum_probs=24.1

Q ss_pred             ccCccCCCcccccCCc----EEeCC---CCCeeecc
Q 040426           10 LFCKFCGTMLRMESNH----VVCSS---CKFKKNVQ   38 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~----~~C~~---C~~~~~~~   38 (120)
                      ..||.||..|..+..+    +.|..   |.|+..+.
T Consensus         2 ~~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~~~~~   37 (39)
T PF01396_consen    2 EKCPKCGGPLVLRRGKKGKFLGCSNYPECKYTEPLP   37 (39)
T ss_pred             cCCCCCCceeEEEECCCCCEEECCCCCCcCCeEeCC
Confidence            4699999999988764    89987   99988764

e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=94.61  E-value=0.02  Score=34.10  Aligned_cols=24  Identities=21%  Similarity=0.560  Sum_probs=10.6

Q ss_pred             ccCccCCCcccccCCc--EEeCCCCC
Q 040426           10 LFCKFCGTMLRMESNH--VVCSSCKF   33 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~--~~C~~C~~   33 (120)
                      ..|.-||-.|.+.+..  |.|.+||.
T Consensus         8 ~~CtSCg~~i~~~~~~~~F~CPnCG~   33 (59)
T PRK14890          8 PKCTSCGIEIAPREKAVKFLCPNCGE   33 (59)
T ss_pred             ccccCCCCcccCCCccCEeeCCCCCC
Confidence            3444455444444311  44444444

>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=94.60  E-value=0.036  Score=30.63  Aligned_cols=28  Identities=21%  Similarity=0.617  Sum_probs=18.1

Q ss_pred             ccCccCCCcc-cccC--CcEEeCCCCCeeec
Q 040426           10 LFCKFCGTML-RMES--NHVVCSSCKFKKNV   37 (120)
Q Consensus        10 ~FCp~CgnlL-~~~~--~~~~C~~C~~~~~~   37 (120)
                      ..||.||+-. ....  ..++|..||.+.+-
T Consensus         1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e   31 (43)
T PF08271_consen    1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEE   31 (43)
T ss_dssp             ESBTTTSSSEEEEETTTTEEEETTT-BBEE-
T ss_pred             CCCcCCcCCceEEcCCCCeEECCCCCCEeec
Confidence            3699999854 2222  22999999998653

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.

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=94.54  E-value=0.073  Score=30.77  Aligned_cols=34  Identities=21%  Similarity=0.635  Sum_probs=22.9

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR  116 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~  116 (120)
                      .+||.||.....+.   -+..|-+-.-+|.|.+||+.
T Consensus         2 kPCPfCGg~~~~~~---~~~~~~~~~~~~~C~~Cga~   35 (53)
T TIGR03655         2 KPCPFCGGADVYLR---RGFDPLDLSHYFECSTCGAS   35 (53)
T ss_pred             CCCCCCCCcceeeE---eccCCCCCEEEEECCCCCCC
Confidence            47999999655342   12345556666799999975

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.

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

Probab=94.53  E-value=0.023  Score=29.43  Aligned_cols=26  Identities=27%  Similarity=0.701  Sum_probs=14.3

Q ss_pred             ccCccCCCcccccCCc-EEeCCCCCee
Q 040426           10 LFCKFCGTMLRMESNH-VVCSSCKFKK   35 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~-~~C~~C~~~~   35 (120)
                      .=||.||+-.....+. ++|..|+++.
T Consensus         3 p~Cp~C~se~~y~D~~~~vCp~C~~ew   29 (30)
T PF08274_consen    3 PKCPLCGSEYTYEDGELLVCPECGHEW   29 (30)
T ss_dssp             ---TTT-----EE-SSSEEETTTTEEE
T ss_pred             CCCCCCCCcceeccCCEEeCCcccccC
Confidence            3599999887775554 9999999975

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.

>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, 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

Probab=94.49  E-value=0.029  Score=29.71  Aligned_cols=14  Identities=21%  Similarity=0.693  Sum_probs=10.9

Q ss_pred             ccccccCCCceEEE
Q 040426           80 RACEKCQNPEMYYS   93 (120)
Q Consensus        80 ~~CpkCg~~ea~y~   93 (120)
                      ..||.||++...|.
T Consensus        19 ~~CP~Cg~~~~~F~   32 (34)
T cd00729          19 EKCPICGAPKEKFE   32 (34)
T ss_pred             CcCcCCCCchHHcE
Confidence            36999999877664

In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), 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.

>PRK04023 DNA polymerase II large subunit; Validated

Probab=94.43  E-value=0.025  Score=50.18  Aligned_cols=26  Identities=19%  Similarity=0.278  Sum_probs=20.4

Q ss_pred             CCCCcccCccCCCcccccCCcEEeCCCCCe
Q 040426            5 LGRDFLFCKFCGTMLRMESNHVVCSSCKFK   34 (120)
Q Consensus         5 ~~~~~~FCp~CgnlL~~~~~~~~C~~C~~~   34 (120)
                      ...+.+|||.||..+    ..+.|+.||..
T Consensus       622 VEVg~RfCpsCG~~t----~~frCP~CG~~  647 (1121)
T PRK04023        622 VEIGRRKCPSCGKET----FYRRCPFCGTH  647 (1121)
T ss_pred             ecccCccCCCCCCcC----CcccCCCCCCC
Confidence            345678999999884    23899999986

>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i

Probab=94.38  E-value=0.059  Score=29.36  Aligned_cols=31  Identities=23%  Similarity=0.577  Sum_probs=22.1

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCC---CCceec
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPR---CGHRCQ  118 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~---C~~~w~  118 (120)
                      +.||+|| ..+     .+|.+--|  .|+-|.+   |.++-.
T Consensus         2 ~~CP~Cg-~~l-----v~r~~k~g--~F~~Cs~yP~C~~~~~   35 (39)
T PF01396_consen    2 EKCPKCG-GPL-----VLRRGKKG--KFLGCSNYPECKYTEP   35 (39)
T ss_pred             cCCCCCC-cee-----EEEECCCC--CEEECCCCCCcCCeEe
Confidence            5799999 333     34555556  9999985   988643

e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome

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

Probab=94.31  E-value=0.047  Score=30.60  Aligned_cols=30  Identities=20%  Similarity=0.605  Sum_probs=23.9

Q ss_pred             ccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426           10 LFCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      .=|+.||..+......  +.|+.||......+
T Consensus         4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~   35 (46)
T PRK00398          4 YKCARCGREVELDEYGTGVRCPYCGYRILFKE   35 (46)
T ss_pred             EECCCCCCEEEECCCCCceECCCCCCeEEEcc
Confidence            3599999999887654  99999998766544

>PRK07220 DNA topoisomerase I; Validated

Probab=94.29  E-value=0.11  Score=45.03  Aligned_cols=32  Identities=16%  Similarity=0.340  Sum_probs=19.5

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH  115 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~  115 (120)
                      ++..||+||.+.....    +....+  -||.|.+|.|
T Consensus       634 ~~~~Cp~Cg~~~~k~~----~~g~~~--~~~~Cp~C~~  665 (740)
T PRK07220        634 TDKVCEAHGLNHIRII----NGGKRP--WDLGCPQCNF  665 (740)
T ss_pred             CCCCCCCCCCceEEEE----ecCCcc--ceeeCCCCCC
Confidence            3567999997643111    222112  2889999987

>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases

Probab=94.21  E-value=0.076  Score=28.55  Aligned_cols=35  Identities=26%  Similarity=0.607  Sum_probs=24.2

Q ss_pred             ccccccccccCCCceEEEEeecccCCCCceEEEEcCCCC
Q 040426           76 SKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCG  114 (120)
Q Consensus        76 ~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~  114 (120)
                      +++++.||.|+..+.++---   ....|- .-|.|..|.
T Consensus         2 a~i~v~CP~C~s~~~v~k~G---~~~~G~-qryrC~~C~   36 (36)
T PF03811_consen    2 AKIDVHCPRCQSTEGVKKNG---KSPSGH-QRYRCKDCR   36 (36)
T ss_pred             CcEeeeCCCCCCCCcceeCC---CCCCCC-EeEecCcCC
Confidence            46889999999999776542   233343 348888873

Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated

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

Probab=94.17  E-value=0.034  Score=33.73  Aligned_cols=26  Identities=23%  Similarity=0.669  Sum_probs=19.7

Q ss_pred             CccCCCcccccCC-----------------c---EEeCCCCCeeec
Q 040426           12 CKFCGTMLRMESN-----------------H---VVCSSCKFKKNV   37 (120)
Q Consensus        12 Cp~CgnlL~~~~~-----------------~---~~C~~C~~~~~~   37 (120)
                      ||.|||--+.+..                 .   ..|.+|||++--
T Consensus         7 CpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEfY   52 (68)
T COG3478           7 CPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEFY   52 (68)
T ss_pred             CCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCchhhe
Confidence            9999997665421                 1   899999998753

>COG1779 C4-type Zn-finger protein [General function prediction only]

Probab=94.06  E-value=0.091  Score=38.60  Aligned_cols=42  Identities=19%  Similarity=0.377  Sum_probs=31.0

Q ss_pred             cccccccccCCCceEEEEeecccCCCC--ceEEEEcCCCCceecc
Q 040426           77 KVKRACEKCQNPEMYYSTRQTRSADEG--QTTYYICPRCGHRCQE  119 (120)
Q Consensus        77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~--~T~fY~C~~C~~~w~~  119 (120)
                      ..+..||-||+ .....+....--=.|  +-..+.|.+|||+.++
T Consensus        12 ~~~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~D   55 (201)
T COG1779          12 ETRIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERCGYRSTD   55 (201)
T ss_pred             eeeecCCcccc-eeeEEEeeecCCccceEEEEEEEccccCCcccc
Confidence            45788999999 666666665555555  4466789999999764

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=93.99  E-value=0.034  Score=29.93  Aligned_cols=26  Identities=27%  Similarity=0.603  Sum_probs=21.0

Q ss_pred             cCccCCCcccccCCc-------EEeCCCCCeee
Q 040426           11 FCKFCGTMLRMESNH-------VVCSSCKFKKN   36 (120)
Q Consensus        11 FCp~CgnlL~~~~~~-------~~C~~C~~~~~   36 (120)
                      =||.|+..+.++.+.       +.|..|++.+.
T Consensus         4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~   36 (37)
T PF13719_consen    4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR   36 (37)
T ss_pred             ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence            499999998877541       99999998764

>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1

Probab=93.79  E-value=0.11  Score=37.01  Aligned_cols=38  Identities=21%  Similarity=0.337  Sum_probs=25.1

Q ss_pred             cccccCCCceEEEEeecccCCCCce--EEEEcCCCCceecc
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQT--TYYICPRCGHRCQE  119 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T--~fY~C~~C~~~w~~  119 (120)
                      .||.||++ .......+.--.-+..  .-|.|..|||+..+
T Consensus         2 ~Cp~C~~~-~~~~~~~~~IP~F~evii~sf~C~~CGyk~~e   41 (160)
T smart00709        2 DCPSCGGN-GTTRMLLTSIPYFREVIIMSFECEHCGYRNNE   41 (160)
T ss_pred             cCCCCCCC-CEEEEEEecCCCcceEEEEEEECCCCCCccce
Confidence            59999986 3444445544444433  35889999998764

Also present in archaeal proteins.

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=93.70  E-value=0.038  Score=29.57  Aligned_cols=27  Identities=26%  Similarity=0.498  Sum_probs=20.8

Q ss_pred             cCccCCCcccccCC-----c--EEeCCCCCeeec
Q 040426           11 FCKFCGTMLRMESN-----H--VVCSSCKFKKNV   37 (120)
Q Consensus        11 FCp~CgnlL~~~~~-----~--~~C~~C~~~~~~   37 (120)
                      =||.||....+..+     .  +.|.+|+....+
T Consensus         4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~   37 (38)
T TIGR02098         4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA   37 (38)
T ss_pred             ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence            49999998777643     2  999999987653

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.

>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center

Probab=93.40  E-value=0.048  Score=31.46  Aligned_cols=15  Identities=13%  Similarity=0.392  Sum_probs=12.6

Q ss_pred             cccccccCCCceEEE
Q 040426           79 KRACEKCQNPEMYYS   93 (120)
Q Consensus        79 ~~~CpkCg~~ea~y~   93 (120)
                      ++.||.||..+..|.
T Consensus        34 ~w~CP~C~a~K~~F~   48 (50)
T cd00730          34 DWVCPVCGAGKDDFE   48 (50)
T ss_pred             CCCCCCCCCcHHHcE
Confidence            789999999887664

Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.

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

Probab=93.39  E-value=0.061  Score=37.06  Aligned_cols=29  Identities=31%  Similarity=0.730  Sum_probs=23.3

Q ss_pred             cCccCCCcccccCCcEEeCCCCCeeeccc
Q 040426           11 FCKFCGTMLRMESNHVVCSSCKFKKNVQD   39 (120)
Q Consensus        11 FCp~CgnlL~~~~~~~~C~~C~~~~~~~~   39 (120)
                      -||.||.=|.-+.+.+.|+.|+|......
T Consensus        30 hCp~Cg~PLF~KdG~v~CPvC~~~~~~v~   58 (131)
T COG1645          30 HCPKCGTPLFRKDGEVFCPVCGYREVVVE   58 (131)
T ss_pred             hCcccCCcceeeCCeEECCCCCceEEEee
Confidence            79999999888555599999998765443

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=93.38  E-value=0.059  Score=36.93  Aligned_cols=39  Identities=15%  Similarity=0.067  Sum_probs=33.0

Q ss_pred             CCCCCCCCcccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426            1 MADPLGRDFLFCKFCGTMLRMESNH-VVCSSCKFKKNVQD   39 (120)
Q Consensus         1 ~~~~~~~~~~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~   39 (120)
                      |+++-.+.-+-||.||.-.|--... ++|+.||..++...
T Consensus         1 m~k~elGtKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~   40 (129)
T TIGR02300         1 MAKPDLGTKRICPNTGSKFYDLNRRPAVSPYTGEQFPPEE   40 (129)
T ss_pred             CCchhhCccccCCCcCccccccCCCCccCCCcCCccCcch
Confidence            7888889999999999998865434 99999999987763

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.

>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []

Probab=93.37  E-value=0.075  Score=30.27  Aligned_cols=14  Identities=14%  Similarity=0.539  Sum_probs=11.2

Q ss_pred             EEeCCCCCeeeccc
Q 040426           26 VVCSSCKFKKNVQD   39 (120)
Q Consensus        26 ~~C~~C~~~~~~~~   39 (120)
                      +.|+.|+|+..-..
T Consensus         2 y~C~~CgyvYd~~~   15 (47)
T PF00301_consen    2 YQCPVCGYVYDPEK   15 (47)
T ss_dssp             EEETTTSBEEETTT
T ss_pred             cCCCCCCEEEcCCc
Confidence            78999999986543

The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=93.34  E-value=0.06  Score=48.84  Aligned_cols=14  Identities=21%  Similarity=0.605  Sum_probs=9.9

Q ss_pred             cccccccCCCceEE
Q 040426           79 KRACEKCQNPEMYY   92 (120)
Q Consensus        79 ~~~CpkCg~~ea~y   92 (120)
                      ...||+||.+-..+
T Consensus       709 a~~CP~CGtplv~~  722 (1337)
T PRK14714        709 RVECPRCDVELTPY  722 (1337)
T ss_pred             cccCCCCCCccccc
Confidence            44699999875543

>TIGR00244 transcriptional regulator NrdR

Probab=93.09  E-value=0.093  Score=36.84  Aligned_cols=38  Identities=18%  Similarity=0.301  Sum_probs=21.3

Q ss_pred             cccccCCCceEEEEeecccCCC-CceEEEEcCCCCceecc
Q 040426           81 ACEKCQNPEMYYSTRQTRSADE-GQTTYYICPRCGHRCQE  119 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE-~~T~fY~C~~C~~~w~~  119 (120)
                      .||.|||++-.-.-.-.- .|- ..-+=-+|..||++|+.
T Consensus         2 ~CP~C~~~dtkViDSR~~-~dg~~IRRRReC~~C~~RFTT   40 (147)
T TIGR00244         2 HCPFCQHHNTRVLDSRLV-EDGQSIRRRRECLECHERFTT   40 (147)
T ss_pred             CCCCCCCCCCEeeecccc-CCCCeeeecccCCccCCccce
Confidence            699999987754321000 000 00012469999999873

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.

>PRK00241 nudC NADH pyrophosphatase; Reviewed

Probab=92.98  E-value=0.075  Score=40.35  Aligned_cols=31  Identities=23%  Similarity=0.707  Sum_probs=25.3

Q ss_pred             CCcccCccCCCcccccCCc--EEeCCCCCeeec
Q 040426            7 RDFLFCKFCGTMLRMESNH--VVCSSCKFKKNV   37 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~   37 (120)
                      ...+|||.||.-|....+.  ..|..|+...-.
T Consensus        97 ~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~yp  129 (256)
T PRK00241         97 RSHRFCGYCGHPMHPSKTEWAMLCPHCRERYYP  129 (256)
T ss_pred             hcCccccccCCCCeecCCceeEECCCCCCEECC
Confidence            4578999999999877654  999999987643

>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=92.94  E-value=0.1  Score=31.42  Aligned_cols=31  Identities=19%  Similarity=0.684  Sum_probs=24.1

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +...||.||+....          ......|.|..||+.+-
T Consensus        27 TSq~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~~   57 (69)
T PF07282_consen   27 TSQTCPRCGHRNKK----------RRSGRVFTCPNCGFEMD   57 (69)
T ss_pred             CccCccCccccccc----------ccccceEEcCCCCCEEC
Confidence            56679999998664          24556799999999863

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

>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=92.89  E-value=0.084  Score=32.02  Aligned_cols=26  Identities=23%  Similarity=0.622  Sum_probs=18.8

Q ss_pred             CccCCCcccccC-----------------Cc---EEeCCCCCeeec
Q 040426           12 CKFCGTMLRMES-----------------NH---VVCSSCKFKKNV   37 (120)
Q Consensus        12 Cp~CgnlL~~~~-----------------~~---~~C~~C~~~~~~   37 (120)
                      ||+||+--+-..                 .+   ++|.+|||++--
T Consensus         3 C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~Y   48 (64)
T PF09855_consen    3 CPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEFY   48 (64)
T ss_pred             CCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEEE
Confidence            899998655332                 11   899999998743

>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function []

Probab=92.83  E-value=0.13  Score=30.16  Aligned_cols=37  Identities=24%  Similarity=0.538  Sum_probs=25.8

Q ss_pred             ccccc--cccccccccCCC-ceEEEEeecccCCCCceEEEEcCCCCc
Q 040426           72 ETQLS--KVKRACEKCQNP-EMYYSTRQTRSADEGQTTYYICPRCGH  115 (120)
Q Consensus        72 ~~t~~--~~~~~CpkCg~~-ea~y~~~Q~RSADE~~T~fY~C~~C~~  115 (120)
                      ||+++  +....|++|..+ .++.       ..|...+-|+|..||+
T Consensus        13 d~~~~~~r~aLIC~~C~~hNGla~-------~~~~~~i~y~C~~Cg~   52 (54)
T PF10058_consen   13 DPTSPSNRYALICSKCFSHNGLAP-------KEEFEEIQYRCPYCGA   52 (54)
T ss_pred             CCccccCceeEECcccchhhcccc-------cccCCceEEEcCCCCC
Confidence            34555  345679999665 4432       4567777999999986

>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC

Probab=92.71  E-value=0.17  Score=31.23  Aligned_cols=35  Identities=26%  Similarity=0.612  Sum_probs=23.4

Q ss_pred             ccccccccCCCc-eEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           78 VKRACEKCQNPE-MYYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        78 ~~~~CpkCg~~e-a~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      ....||+|+... ..+|.     -+ + .-.-+|++|||+-+.
T Consensus         7 AGa~CP~C~~~D~i~~~~-----e~-~-ve~vECV~CGy~e~~   42 (71)
T PF09526_consen    7 AGAVCPKCQAMDTIMMWR-----EN-G-VEYVECVECGYTERQ   42 (71)
T ss_pred             cCccCCCCcCccEEEEEE-----eC-C-ceEEEecCCCCeecc
Confidence            457899999864 34443     12 2 455679999998653

Members are found in various proteobacteria.

>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=92.49  E-value=0.15  Score=36.24  Aligned_cols=40  Identities=18%  Similarity=0.330  Sum_probs=20.1

Q ss_pred             ccccccCCCceE-EEEeecccCCCCceEEEEcCCCCceecc
Q 040426           80 RACEKCQNPEMY-YSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        80 ~~CpkCg~~ea~-y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      ..||.||++... .....+=--.|=.-.-|.|..|||+.++
T Consensus         2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~e   42 (161)
T PF03367_consen    2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNE   42 (161)
T ss_dssp             EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEE
T ss_pred             CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeee
Confidence            469999997543 2222221122223455889999999764

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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.

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

Probab=92.39  E-value=0.08  Score=27.68  Aligned_cols=25  Identities=32%  Similarity=0.677  Sum_probs=19.2

Q ss_pred             cCccCCCcccccCCcEEeCCCCCee
Q 040426           11 FCKFCGTMLRMESNHVVCSSCKFKK   35 (120)
Q Consensus        11 FCp~CgnlL~~~~~~~~C~~C~~~~   35 (120)
                      -|+.||.+..+....+.|+.||...
T Consensus         3 ~C~~CGy~y~~~~~~~~CP~Cg~~~   27 (33)
T cd00350           3 VCPVCGYIYDGEEAPWVCPVCGAPK   27 (33)
T ss_pred             ECCCCCCEECCCcCCCcCcCCCCcH
Confidence            3888998877666668999998744

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.

>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=92.37  E-value=0.09  Score=26.63  Aligned_cols=20  Identities=30%  Similarity=0.763  Sum_probs=10.7

Q ss_pred             cCccCCCcccccCCc--EEeCC
Q 040426           11 FCKFCGTMLRMESNH--VVCSS   30 (120)
Q Consensus        11 FCp~CgnlL~~~~~~--~~C~~   30 (120)
                      +||.||+-|.-.++.  +.|.+
T Consensus         1 ~CP~C~s~l~~~~~ev~~~C~N   22 (28)
T PF03119_consen    1 TCPVCGSKLVREEGEVDIRCPN   22 (28)
T ss_dssp             B-TTT--BEEE-CCTTCEEE--
T ss_pred             CcCCCCCEeEcCCCCEeEECCC
Confidence            699999999855553  77753

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.

>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]

Probab=92.35  E-value=0.091  Score=40.53  Aligned_cols=30  Identities=30%  Similarity=0.587  Sum_probs=26.1

Q ss_pred             CCcccCccCCCcccccCCc--EEeCCCCCeee
Q 040426            7 RDFLFCKFCGTMLRMESNH--VVCSSCKFKKN   36 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~   36 (120)
                      ..-+||+.||.-+++....  ..|..|++..-
T Consensus       109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~f  140 (279)
T COG2816         109 RSHRFCGRCGTKTYPREGGWARVCPKCGHEHF  140 (279)
T ss_pred             hhCcCCCCCCCcCccccCceeeeCCCCCCccC
Confidence            4568999999999999876  99999999753

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

Probab=92.34  E-value=0.12  Score=31.50  Aligned_cols=35  Identities=23%  Similarity=0.537  Sum_probs=25.7

Q ss_pred             cccccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426           73 TQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR  116 (120)
Q Consensus        73 ~t~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~  116 (120)
                      |..--.+++||.|||...+|--.|        | --.|..||..
T Consensus        13 p~s~Fl~VkCpdC~N~q~vFshas--------t-~V~C~~CG~~   47 (67)
T COG2051          13 PRSRFLRVKCPDCGNEQVVFSHAS--------T-VVTCLICGTT   47 (67)
T ss_pred             CCceEEEEECCCCCCEEEEeccCc--------e-EEEecccccE
Confidence            333357889999999999996533        3 3678888864

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=92.29  E-value=0.082  Score=45.18  Aligned_cols=12  Identities=17%  Similarity=0.492  Sum_probs=7.4

Q ss_pred             cccccccCCCce
Q 040426           79 KRACEKCQNPEM   90 (120)
Q Consensus        79 ~~~CpkCg~~ea   90 (120)
                      ...||+||+.-.
T Consensus        41 ~~fC~~CG~~~~   52 (645)
T PRK14559         41 EAHCPNCGAETG   52 (645)
T ss_pred             cccccccCCccc
Confidence            345777777644

>TIGR02443 conserved hypothetical metal-binding protein

Probab=92.29  E-value=0.27  Score=29.29  Aligned_cols=35  Identities=20%  Similarity=0.438  Sum_probs=23.9

Q ss_pred             ccccccccCCCce-EEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           78 VKRACEKCQNPEM-YYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        78 ~~~~CpkCg~~ea-~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      ....||+|+.... ..|.       |.-.-.-+|+.|||+-+.
T Consensus         8 AGA~CP~C~~~Dtl~~~~-------e~~~e~vECv~Cg~~~~~   43 (59)
T TIGR02443         8 AGAVCPACSAQDTLAMWK-------ENNIELVECVECGYQEQQ   43 (59)
T ss_pred             ccccCCCCcCccEEEEEE-------eCCceEEEeccCCCcccc
Confidence            4578999998644 4443       223355789999998653

Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=92.18  E-value=0.23  Score=29.15  Aligned_cols=34  Identities=24%  Similarity=0.595  Sum_probs=22.1

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH  115 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~  115 (120)
                      .+||-||.......+  ...-+.++..+-.|..||.
T Consensus         4 kPCPFCG~~~~~~~~--~~~~~~~~~~~V~C~~Cga   37 (61)
T PF14354_consen    4 KPCPFCGSADVLIRQ--DEGFDYGMYYYVECTDCGA   37 (61)
T ss_pred             cCCCCCCCcceEeec--ccCCCCCCEEEEEcCCCCC
Confidence            579999877766554  2333344445555999986

>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=92.12  E-value=0.11  Score=31.22  Aligned_cols=36  Identities=17%  Similarity=0.373  Sum_probs=27.2

Q ss_pred             CCCCCcccCccCCCcccccC-Cc-EEeCCCCCeeeccc
Q 040426            4 PLGRDFLFCKFCGTMLRMES-NH-VVCSSCKFKKNVQD   39 (120)
Q Consensus         4 ~~~~~~~FCp~CgnlL~~~~-~~-~~C~~C~~~~~~~~   39 (120)
                      ....+..=||.||..+.-.. .. +.|..||+..+.+.
T Consensus        23 ~~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD~   60 (69)
T PF07282_consen   23 DEAYTSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRDV   60 (69)
T ss_pred             CCCCCccCccCcccccccccccceEEcCCCCCEECcHH
Confidence            34446778999999988732 33 99999999977654

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

>COG1773 Rubredoxin [Energy production and conversion]

Probab=92.03  E-value=0.1  Score=30.75  Aligned_cols=18  Identities=11%  Similarity=0.266  Sum_probs=14.3

Q ss_pred             ccccccccCCCceEEEEe
Q 040426           78 VKRACEKCQNPEMYYSTR   95 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~   95 (120)
                      .+..||-||..+..|-.+
T Consensus        35 d~w~CP~Cg~~K~~F~~~   52 (55)
T COG1773          35 DDWVCPECGVGKKDFEMI   52 (55)
T ss_pred             CccCCCCCCCCHhHeeec
Confidence            478899999988877554

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=91.97  E-value=0.051  Score=47.00  Aligned_cols=21  Identities=14%  Similarity=0.363  Sum_probs=12.4

Q ss_pred             ccccccCCCceEEEEeecccC
Q 040426           80 RACEKCQNPEMYYSTRQTRSA  100 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSA  100 (120)
                      ..||+||.....++-.-|...
T Consensus       476 ~~Cp~Cgs~~L~~~G~Gteri  496 (730)
T COG1198         476 QSCPECGSEHLRAVGPGTERI  496 (730)
T ss_pred             CCCCCCCCCeeEEecccHHHH
Confidence            347777777666655444433

>PRK07219 DNA topoisomerase I; Validated

Probab=91.93  E-value=0.4  Score=42.07  Aligned_cols=32  Identities=22%  Similarity=0.492  Sum_probs=19.3

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEc---CCCCcee
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYIC---PRCGHRC  117 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C---~~C~~~w  117 (120)
                      +...||+||.+-..   ...|   .|  .|+.|   ..|++..
T Consensus       732 ~~~~CpkCg~~l~~---~k~~---~g--~~~~Cs~~p~C~~~~  766 (822)
T PRK07219        732 TDEKCPECGLPLLR---VKGG---FG--DELGCCNNPKCNYTE  766 (822)
T ss_pred             ccCCCCCCCCeEEE---EecC---CC--ceeeeCCCCCCCccc
Confidence            56789999985322   2222   12  37888   5688643

>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=91.79  E-value=0.07  Score=27.96  Aligned_cols=24  Identities=21%  Similarity=0.760  Sum_probs=18.0

Q ss_pred             CccCCCcccccCCc-EEeCCCCCee
Q 040426           12 CKFCGTMLRMESNH-VVCSSCKFKK   35 (120)
Q Consensus        12 Cp~CgnlL~~~~~~-~~C~~C~~~~   35 (120)
                      |.+||....++... +.|+.|||..
T Consensus         3 C~~Cg~~~~~~~~~~irC~~CG~RI   27 (32)
T PF03604_consen    3 CGECGAEVELKPGDPIRCPECGHRI   27 (32)
T ss_dssp             ESSSSSSE-BSTSSTSSBSSSS-SE
T ss_pred             CCcCCCeeEcCCCCcEECCcCCCeE
Confidence            88999888877554 9999999964

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 ....

>TIGR00595 priA primosomal protein N'

Probab=91.78  E-value=0.18  Score=41.78  Aligned_cols=27  Identities=19%  Similarity=0.630  Sum_probs=14.2

Q ss_pred             CccCCCcccccC-Cc-EEeCCCCCeeecc
Q 040426           12 CKFCGTMLRMES-NH-VVCSSCKFKKNVQ   38 (120)
Q Consensus        12 Cp~CgnlL~~~~-~~-~~C~~C~~~~~~~   38 (120)
                      ||.|+.-|..-. .+ +.|..|||..++.
T Consensus       225 C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~  253 (505)
T TIGR00595       225 CPNCDVSLTYHKKEGKLRCHYCGYQEPIP  253 (505)
T ss_pred             CCCCCCceEEecCCCeEEcCCCcCcCCCC
Confidence            444444443322 22 7777777766543

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria

Probab=91.77  E-value=0.26  Score=27.11  Aligned_cols=12  Identities=25%  Similarity=0.592  Sum_probs=10.0

Q ss_pred             EEeCCCCCeeec
Q 040426           26 VVCSSCKFKKNV   37 (120)
Q Consensus        26 ~~C~~C~~~~~~   37 (120)
                      |.|..||+..++
T Consensus         6 y~C~~Cg~~fe~   17 (42)
T PF09723_consen    6 YRCEECGHEFEV   17 (42)
T ss_pred             EEeCCCCCEEEE
Confidence            899999987754

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.

>TIGR00310 ZPR1_znf ZPR1 zinc finger domain

Probab=91.76  E-value=0.25  Score=36.12  Aligned_cols=39  Identities=28%  Similarity=0.476  Sum_probs=22.8

Q ss_pred             cccccCCC-ceEEEEee-cccCCCCceEEEEcCCCCceecc
Q 040426           81 ACEKCQNP-EMYYSTRQ-TRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        81 ~CpkCg~~-ea~y~~~Q-~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      .||.||.+ .....+.+ +=--.|=.-.-|.|..|||+.++
T Consensus         2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~e   42 (192)
T TIGR00310         2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSND   42 (192)
T ss_pred             cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccce
Confidence            59999976 22233322 11122223456899999998764

>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7

Probab=91.69  E-value=0.093  Score=31.25  Aligned_cols=27  Identities=19%  Similarity=0.668  Sum_probs=22.9

Q ss_pred             cccCccCCCcccccCCc-EEeCCCCCee
Q 040426            9 FLFCKFCGTMLRMESNH-VVCSSCKFKK   35 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~~-~~C~~C~~~~   35 (120)
                      +--|.+||.-+.++... +.||-|||..
T Consensus        20 iYiCgdC~~en~lk~~D~irCReCG~RI   47 (62)
T KOG3507|consen   20 IYICGDCGQENTLKRGDVIRCRECGYRI   47 (62)
T ss_pred             EEEeccccccccccCCCcEehhhcchHH
Confidence            44799999999888765 9999999964

0 [Transcription]

>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast

Probab=91.50  E-value=0.18  Score=31.39  Aligned_cols=22  Identities=32%  Similarity=0.457  Sum_probs=11.5

Q ss_pred             CCCCCCcccCccCCCcccccCC
Q 040426            3 DPLGRDFLFCKFCGTMLRMESN   24 (120)
Q Consensus         3 ~~~~~~~~FCp~CgnlL~~~~~   24 (120)
                      .+....-.||..||++|.|-.+
T Consensus        40 l~~~~kr~~Ck~C~~~liPG~~   61 (85)
T PF04032_consen   40 LPPEIKRTICKKCGSLLIPGVN   61 (85)
T ss_dssp             -STTCCCTB-TTT--B--CTTT
T ss_pred             CChHHhcccccCCCCEEeCCCc
Confidence            3445566799999999998753

Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.

>TIGR01053 LSD1 zinc finger domain, LSD1 subclass

Probab=91.28  E-value=0.2  Score=25.99  Aligned_cols=25  Identities=28%  Similarity=0.586  Sum_probs=20.0

Q ss_pred             cCccCCCcccccCCc--EEeCCCCCee
Q 040426           11 FCKFCGTMLRMESNH--VVCSSCKFKK   35 (120)
Q Consensus        11 FCp~CgnlL~~~~~~--~~C~~C~~~~   35 (120)
                      -|..|+++|..+.+.  +.|..|....
T Consensus         3 ~C~~C~t~L~yP~gA~~vrCs~C~~vt   29 (31)
T TIGR01053         3 VCGGCRTLLMYPRGASSVRCALCQTVN   29 (31)
T ss_pred             CcCCCCcEeecCCCCCeEECCCCCeEe
Confidence            489999999776553  9999998754

This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=91.15  E-value=0.43  Score=26.67  Aligned_cols=27  Identities=26%  Similarity=0.652  Sum_probs=21.4

Q ss_pred             cCccCCCcccccCCc-EEeCCCCCeeec
Q 040426           11 FCKFCGTMLRMESNH-VVCSSCKFKKNV   37 (120)
Q Consensus        11 FCp~CgnlL~~~~~~-~~C~~C~~~~~~   37 (120)
                      -|.+||.-..++... +.|+.||+..-.
T Consensus         4 ~C~~Cg~~~~~~~~~~irC~~CG~rIly   31 (44)
T smart00659        4 ICGECGRENEIKSKDVVRCRECGYRILY   31 (44)
T ss_pred             ECCCCCCEeecCCCCceECCCCCceEEE
Confidence            489999988877544 999999996543

present in RNA polymerase I, II and III

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=91.07  E-value=0.23  Score=29.10  Aligned_cols=29  Identities=28%  Similarity=0.671  Sum_probs=24.1

Q ss_pred             cCccCCCcccccCCc----EEeCCCCCeeeccc
Q 040426           11 FCKFCGTMLRMESNH----VVCSSCKFKKNVQD   39 (120)
Q Consensus        11 FCp~CgnlL~~~~~~----~~C~~C~~~~~~~~   39 (120)
                      =||.||.-+.+..+.    +.|..||....+.+
T Consensus         4 ~CP~CG~~iev~~~~~GeiV~Cp~CGaeleVv~   36 (54)
T TIGR01206         4 ECPDCGAEIELENPELGELVICDECGAELEVVS   36 (54)
T ss_pred             CCCCCCCEEecCCCccCCEEeCCCCCCEEEEEe
Confidence            599999999887642    99999999887644

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.

>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=91.07  E-value=0.17  Score=27.97  Aligned_cols=23  Identities=35%  Similarity=0.739  Sum_probs=18.4

Q ss_pred             ccCccCCCcccccCCc-EEeCCCC
Q 040426           10 LFCKFCGTMLRMESNH-VVCSSCK   32 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~-~~C~~C~   32 (120)
                      .-||.||..|.-..++ ..|..|+
T Consensus        18 ~~Cp~C~~PL~~~k~g~~~Cv~C~   41 (41)
T PF06677_consen   18 EHCPDCGTPLMRDKDGKIYCVSCG   41 (41)
T ss_pred             CccCCCCCeeEEecCCCEECCCCC
Confidence            4799999998874444 9999985

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

>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]

Probab=90.74  E-value=0.18  Score=33.45  Aligned_cols=28  Identities=32%  Similarity=0.496  Sum_probs=23.3

Q ss_pred             ccCccCCCcccccCCc----------EEeCCCCCeeec
Q 040426           10 LFCKFCGTMLRMESNH----------VVCSSCKFKKNV   37 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~----------~~C~~C~~~~~~   37 (120)
                      .||+.|+++|.|..+-          +.|..||+..-.
T Consensus        57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~   94 (105)
T COG2023          57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRY   94 (105)
T ss_pred             HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEe
Confidence            5999999999987641          999999998643

>COG1592 Rubrerythrin [Energy production and conversion]

Probab=90.62  E-value=0.11  Score=37.12  Aligned_cols=14  Identities=21%  Similarity=0.686  Sum_probs=11.3

Q ss_pred             cccccccCCCceEE
Q 040426           79 KRACEKCQNPEMYY   92 (120)
Q Consensus        79 ~~~CpkCg~~ea~y   92 (120)
                      ...||-||+++..|
T Consensus       149 P~~CPiCga~k~~F  162 (166)
T COG1592         149 PEVCPICGAPKEKF  162 (166)
T ss_pred             CCcCCCCCChHHHh
Confidence            35699999998766

>PRK00420 hypothetical protein; Validated

Probab=90.59  E-value=0.23  Score=33.33  Aligned_cols=30  Identities=27%  Similarity=0.393  Sum_probs=23.9

Q ss_pred             ccCccCCCcccc-cCCcEEeCCCCCeeeccc
Q 040426           10 LFCKFCGTMLRM-ESNHVVCSSCKFKKNVQD   39 (120)
Q Consensus        10 ~FCp~CgnlL~~-~~~~~~C~~C~~~~~~~~   39 (120)
                      .-||.||.-|.- +.+...|++||....+++
T Consensus        24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~~   54 (112)
T PRK00420         24 KHCPVCGLPLFELKDGEVVCPVHGKVYIVKS   54 (112)
T ss_pred             CCCCCCCCcceecCCCceECCCCCCeeeecc
Confidence            479999988876 444499999999876655

>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1

Probab=90.52  E-value=0.11  Score=32.39  Aligned_cols=13  Identities=31%  Similarity=0.667  Sum_probs=5.8

Q ss_pred             CCCcccCccCCCc
Q 040426            6 GRDFLFCKFCGTM   18 (120)
Q Consensus         6 ~~~~~FCp~Cgnl   18 (120)
                      .++-.|||.|||-
T Consensus        21 ~~~k~FCp~CGn~   33 (73)
T PF08772_consen   21 DMTKQFCPKCGNA   33 (73)
T ss_dssp             -SS--S-SSS--S
T ss_pred             CCCceeCcccCCC
Confidence            4567899999986

; PDB: 2CON_A.

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=90.48  E-value=0.17  Score=27.06  Aligned_cols=25  Identities=24%  Similarity=0.579  Sum_probs=17.9

Q ss_pred             cCccCCCcccccCCc-------EEeCCCCCee
Q 040426           11 FCKFCGTMLRMESNH-------VVCSSCKFKK   35 (120)
Q Consensus        11 FCp~CgnlL~~~~~~-------~~C~~C~~~~   35 (120)
                      =||.|+.-..++++.       +.|..|+++.
T Consensus         4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence            488888877665431       8888888764

>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA

Probab=90.30  E-value=0.19  Score=33.48  Aligned_cols=31  Identities=19%  Similarity=0.560  Sum_probs=24.7

Q ss_pred             cccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426            9 FLFCKFCGTMLRMESNH-VVCSSCKFKKNVQD   39 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~   39 (120)
                      +.=||.|++-...+... |.|+-|+|.+...+
T Consensus         2 lp~CP~C~seytY~dg~~~iCpeC~~EW~~~~   33 (109)
T TIGR00686         2 LPPCPKCNSEYTYHDGTQLICPSCLYEWNENE   33 (109)
T ss_pred             CCcCCcCCCcceEecCCeeECccccccccccc
Confidence            34699999887776555 99999999986554

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).

>PRK10220 hypothetical protein; Provisional

Probab=90.26  E-value=0.27  Score=32.87  Aligned_cols=32  Identities=22%  Similarity=0.536  Sum_probs=25.8

Q ss_pred             CcccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426            8 DFLFCKFCGTMLRMESNH-VVCSSCKFKKNVQD   39 (120)
Q Consensus         8 ~~~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~   39 (120)
                      .+.=||.|++-...+.+. |.|+-|+|.+...+
T Consensus         2 ~lP~CP~C~seytY~d~~~~vCpeC~hEW~~~~   34 (111)
T PRK10220          2 SLPHCPKCNSEYTYEDNGMYICPECAHEWNDAE   34 (111)
T ss_pred             CCCcCCCCCCcceEcCCCeEECCcccCcCCccc
Confidence            456799999887666555 99999999987655

>PF14353 CpXC: CpXC protein

Probab=90.21  E-value=0.43  Score=32.13  Aligned_cols=14  Identities=14%  Similarity=0.543  Sum_probs=11.3

Q ss_pred             EEeCCCCCeeeccc
Q 040426           26 VVCSSCKFKKNVQD   39 (120)
Q Consensus        26 ~~C~~C~~~~~~~~   39 (120)
                      +.|+.|++...++-
T Consensus         2 itCP~C~~~~~~~v   15 (128)
T PF14353_consen    2 ITCPHCGHEFEFEV   15 (128)
T ss_pred             cCCCCCCCeeEEEE
Confidence            57999999987654

>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain

Probab=90.03  E-value=0.011  Score=32.97  Aligned_cols=30  Identities=27%  Similarity=0.604  Sum_probs=23.2

Q ss_pred             cCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426           85 CQNPEMYYSTRQTRSADEGQTTYYICPRCGH  115 (120)
Q Consensus        85 Cg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~  115 (120)
                      |.|.-. -...|+|+.||.-+.+-.|.+|+.
T Consensus        13 C~H~f~-~~E~Q~RAGDE~VSfI~~C~~C~~   42 (43)
T PF11792_consen   13 CKHKFV-TIEKQLRAGDEAVSFIKYCQKCGQ   42 (43)
T ss_pred             ceeeee-ehhhhhcccchHHHHHHHHHHhCC
Confidence            655544 456799999999888778988875

>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []

Probab=89.97  E-value=0.54  Score=32.07  Aligned_cols=30  Identities=23%  Similarity=0.697  Sum_probs=25.1

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR  116 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~  116 (120)
                      +.||.|++++-.+.--       +-+.|-+|..||.+
T Consensus        94 VlC~~C~spdT~l~k~-------~r~~~l~C~aCGa~  123 (125)
T PF01873_consen   94 VLCPECGSPDTELIKE-------GRLIFLKCKACGAS  123 (125)
T ss_dssp             SSCTSTSSSSEEEEEE-------TTCCEEEETTTSCE
T ss_pred             EEcCCCCCCccEEEEc-------CCEEEEEecccCCc
Confidence            6899999999877542       67799999999975

Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

Probab=89.93  E-value=0.24  Score=36.06  Aligned_cols=28  Identities=21%  Similarity=0.450  Sum_probs=24.1

Q ss_pred             ccCccCCCcccccCCcEEeCCCCCeeec
Q 040426           10 LFCKFCGTMLRMESNHVVCSSCKFKKNV   37 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~~~C~~C~~~~~~   37 (120)
                      --|+.|+..|..+...+.|++||+++..
T Consensus       150 A~CsrC~~~L~~~~~~l~Cp~Cg~tEkR  177 (188)
T COG1096         150 ARCSRCRAPLVKKGNMLKCPNCGNTEKR  177 (188)
T ss_pred             EEccCCCcceEEcCcEEECCCCCCEEee
Confidence            3699999999996666999999998864

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

Probab=89.77  E-value=0.39  Score=30.84  Aligned_cols=31  Identities=26%  Similarity=0.613  Sum_probs=23.4

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      ....||.||.+...      |    -.|=+..|.+||++|.
T Consensus        34 ~~~~Cp~C~~~~Vk------R----~a~GIW~C~kCg~~fA   64 (89)
T COG1997          34 AKHVCPFCGRTTVK------R----IATGIWKCRKCGAKFA   64 (89)
T ss_pred             cCCcCCCCCCccee------e----eccCeEEcCCCCCeec
Confidence            36789999998332      1    2466799999999985

>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]

Probab=89.59  E-value=1.2  Score=30.45  Aligned_cols=35  Identities=20%  Similarity=0.488  Sum_probs=21.0

Q ss_pred             cccccccccCCCceEEEEeecccCCCCceEEEEcC---CCCcee
Q 040426           77 KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICP---RCGHRC  117 (120)
Q Consensus        77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~---~C~~~w  117 (120)
                      .+.+.||+||......     |.+.-| ..||.|.   +|.+.+
T Consensus        58 ~~~~~Cp~C~~~~~~~-----k~~~~~-~~f~~~~~~Pkc~~~~   95 (140)
T COG0551          58 KTGVKCPKCGKGLLVL-----KKGRFG-KNFLGCSNYPKCRFTE   95 (140)
T ss_pred             cCceeCCCCCCCceEE-----EeccCC-ceEEeecCCCcCceee
Confidence            3567899999744432     333222 6788765   566654

>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus

Probab=89.53  E-value=0.23  Score=30.44  Aligned_cols=27  Identities=26%  Similarity=0.551  Sum_probs=19.7

Q ss_pred             cCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426           11 FCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus        11 FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      =| .||+.||.+++.  =.| .||+...++.
T Consensus         5 rC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~   33 (68)
T PF09082_consen    5 RC-DCGRYLYAKEGAKTKKC-VCGKTLKVKE   33 (68)
T ss_dssp             EE-TTS--EEEETT-SEEEE-TTTEEEE--S
T ss_pred             Ee-cCCCEEEecCCcceeEe-cCCCeeeeee
Confidence            37 899999999876  899 9999998877

The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.

>PF14311 DUF4379: Domain of unknown function (DUF4379)

Probab=89.52  E-value=0.41  Score=27.65  Aligned_cols=16  Identities=31%  Similarity=1.142  Sum_probs=9.2

Q ss_pred             CceEEEEcCCCCceec
Q 040426          103 GQTTYYICPRCGHRCQ  118 (120)
Q Consensus       103 ~~T~fY~C~~C~~~w~  118 (120)
                      ...+..+|.+|||.|+
T Consensus        24 ~~~v~W~C~~Cgh~w~   39 (55)
T PF14311_consen   24 NKKVWWKCPKCGHEWK   39 (55)
T ss_pred             CCEEEEECCCCCCeeE
Confidence            3445566666666665

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

Probab=89.44  E-value=0.22  Score=35.20  Aligned_cols=38  Identities=16%  Similarity=0.365  Sum_probs=20.8

Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      .||.|+|++..-.-.-.=..-...-+=-+|.+||++|+
T Consensus         2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFT   39 (156)
T COG1327           2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFT   39 (156)
T ss_pred             CCCCCCCCCCeeeecccccccchhhhhhcccccccccc
Confidence            69999999875442100000000002345999999986

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

Probab=89.18  E-value=0.28  Score=31.48  Aligned_cols=31  Identities=23%  Similarity=0.450  Sum_probs=23.1

Q ss_pred             CcccCccCCCcccccC-Cc--EEeCCCCCeeeccc
Q 040426            8 DFLFCKFCGTMLRMES-NH--VVCSSCKFKKNVQD   39 (120)
Q Consensus         8 ~~~FCp~CgnlL~~~~-~~--~~C~~C~~~~~~~~   39 (120)
                      ...-||.||.- ..+. ..  |.|+.||+..---.
T Consensus        34 ~~~~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAGga   67 (89)
T COG1997          34 AKHVCPFCGRT-TVKRIATGIWKCRKCGAKFAGGA   67 (89)
T ss_pred             cCCcCCCCCCc-ceeeeccCeEEcCCCCCeecccc
Confidence            45679999988 4443 32  99999999986544

>PHA02942 putative transposase; Provisional

Probab=89.09  E-value=0.35  Score=38.83  Aligned_cols=34  Identities=18%  Similarity=0.454  Sum_probs=26.0

Q ss_pred             CCCcccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426            6 GRDFLFCKFCGTMLRMESNH-VVCSSCKFKKNVQD   39 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~   39 (120)
                      ..+..-||.||.......++ |.|..|||..+.+-
T Consensus       322 ~yTSq~Cs~CG~~~~~l~~r~f~C~~CG~~~drD~  356 (383)
T PHA02942        322 SYSSVSCPKCGHKMVEIAHRYFHCPSCGYENDRDV  356 (383)
T ss_pred             CCCCccCCCCCCccCcCCCCEEECCCCCCEeCcHH
Confidence            34678999999876533344 99999999987655

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

Probab=89.09  E-value=0.17  Score=37.10  Aligned_cols=37  Identities=19%  Similarity=0.497  Sum_probs=24.4

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +...||.||..+. -+. =++.  .|...-++|.+||+.|+
T Consensus         5 iy~~Cp~Cg~eev-~hE-Vik~--~g~~~lvrC~eCG~V~~   41 (201)
T COG1326           5 IYIECPSCGSEEV-SHE-VIKE--RGREPLVRCEECGTVHP   41 (201)
T ss_pred             EEEECCCCCcchh-hHH-HHHh--cCCceEEEccCCCcEee
Confidence            4678999994443 111 1222  35558899999999995

>PRK05580 primosome assembly protein PriA; Validated

Probab=89.06  E-value=0.42  Score=41.04  Aligned_cols=12  Identities=17%  Similarity=0.869  Sum_probs=8.3

Q ss_pred             EEeCCCCCeeec
Q 040426           26 VVCSSCKFKKNV   37 (120)
Q Consensus        26 ~~C~~C~~~~~~   37 (120)
                      +.|..|||..+.
T Consensus       409 l~Ch~Cg~~~~~  420 (679)
T PRK05580        409 LRCHHCGYQEPI  420 (679)
T ss_pred             EECCCCcCCCCC
Confidence            777777776544

>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative

Probab=88.67  E-value=0.59  Score=32.25  Aligned_cols=31  Identities=26%  Similarity=0.756  Sum_probs=24.2

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC  117 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w  117 (120)
                      +.||.||+++-.+.-       ++-..|-.|..||++-
T Consensus        98 VlC~~C~sPdT~l~k-------~~r~~~l~C~ACGa~~  128 (133)
T TIGR00311        98 VICRECNRPDTRIIK-------EGRVSLLKCEACGAKA  128 (133)
T ss_pred             EECCCCCCCCcEEEE-------eCCeEEEecccCCCCC
Confidence            689999999987642       2556677999999864

>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements

Probab=88.40  E-value=0.26  Score=37.37  Aligned_cols=31  Identities=23%  Similarity=0.629  Sum_probs=14.8

Q ss_pred             cccCccCCCc-ccccCCc-----EEeCCCCCeeeccc
Q 040426            9 FLFCKFCGTM-LRMESNH-----VVCSSCKFKKNVQD   39 (120)
Q Consensus         9 ~~FCp~Cgnl-L~~~~~~-----~~C~~C~~~~~~~~   39 (120)
                      -.+||.||+. |.--+++     |.|..|+..++.++
T Consensus        31 n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELKS   67 (254)
T PF06044_consen   31 NMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELKS   67 (254)
T ss_dssp             H---TTT--SS-EE--------EEE-TTT--EEEEEE
T ss_pred             CCcCCCCCChhHhhccCCCccceeECCCCchHHhhhh
Confidence            3599999998 5433332     99999999988776

The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.

>PRK11827 hypothetical protein; Provisional

Probab=88.33  E-value=0.38  Score=28.78  Aligned_cols=33  Identities=15%  Similarity=0.451  Sum_probs=27.9

Q ss_pred             CCcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426            7 RDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      ..+.-||.|+.-|....+.  +.|..|+-.+++.+
T Consensus         6 LeILaCP~ckg~L~~~~~~~~Lic~~~~laYPI~d   40 (60)
T PRK11827          6 LEIIACPVCNGKLWYNQEKQELICKLDNLAFPLRD   40 (60)
T ss_pred             HhheECCCCCCcCeEcCCCCeEECCccCeeccccC
Confidence            4577899999988876554  99999999999877

>PRK11032 hypothetical protein; Provisional

Probab=88.02  E-value=0.48  Score=33.73  Aligned_cols=12  Identities=25%  Similarity=0.758  Sum_probs=9.8

Q ss_pred             EEeCCCCCeeec
Q 040426           26 VVCSSCKFKKNV   37 (120)
Q Consensus        26 ~~C~~C~~~~~~   37 (120)
                      ++|..||+...+
T Consensus       125 LvC~~Cg~~~~~  136 (160)
T PRK11032        125 LVCEKCHHHLAF  136 (160)
T ss_pred             EEecCCCCEEEe
Confidence            999999997643

>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length

Probab=87.96  E-value=0.47  Score=33.25  Aligned_cols=12  Identities=25%  Similarity=0.841  Sum_probs=10.0

Q ss_pred             EEeCCCCCeeec
Q 040426           26 VVCSSCKFKKNV   37 (120)
Q Consensus        26 ~~C~~C~~~~~~   37 (120)
                      |+|..||+...+
T Consensus       113 l~C~~Cg~~~~~  124 (146)
T PF07295_consen  113 LVCENCGHEVEL  124 (146)
T ss_pred             EecccCCCEEEe
Confidence            999999997643

Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.

>PRK14873 primosome assembly protein PriA; Provisional

Probab=87.83  E-value=0.54  Score=40.42  Aligned_cols=9  Identities=22%  Similarity=0.408  Sum_probs=5.2

Q ss_pred             EEeCCCCCe
Q 040426           26 VVCSSCKFK   34 (120)
Q Consensus        26 ~~C~~C~~~   34 (120)
                      +.|..|||.
T Consensus       411 l~Ch~CG~~  419 (665)
T PRK14873        411 PRCRWCGRA  419 (665)
T ss_pred             eECCCCcCC
Confidence            556666653

>PRK03988 translation initiation factor IF-2 subunit beta; Validated

Probab=87.83  E-value=0.75  Score=31.93  Aligned_cols=31  Identities=26%  Similarity=0.632  Sum_probs=25.3

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC  117 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w  117 (120)
                      +.||.||+++-.+.-       ++-+.|-.|..||++-
T Consensus       103 VlC~~C~spdT~l~k-------~~r~~~l~C~ACGa~~  133 (138)
T PRK03988        103 VICPECGSPDTKLIK-------EGRIWVLKCEACGAET  133 (138)
T ss_pred             EECCCCCCCCcEEEE-------cCCeEEEEcccCCCCC
Confidence            689999999987642       3668899999999863

>PRK12286 rpmF 50S ribosomal protein L32; Reviewed

Probab=87.76  E-value=0.46  Score=28.08  Aligned_cols=27  Identities=33%  Similarity=0.670  Sum_probs=20.8

Q ss_pred             CCcccCccCCCcccccCCcEEeCCCCCeee
Q 040426            7 RDFLFCKFCGTMLRMESNHVVCSSCKFKKN   36 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~~~~C~~C~~~~~   36 (120)
                      ..+..||.||++..+   ..+|..|||-..
T Consensus        25 ~~l~~C~~CG~~~~~---H~vC~~CG~Y~g   51 (57)
T PRK12286         25 PGLVECPNCGEPKLP---HRVCPSCGYYKG   51 (57)
T ss_pred             CcceECCCCCCccCC---eEECCCCCcCCC
Confidence            446789999988554   389999998654

>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated

Probab=87.73  E-value=0.9  Score=40.15  Aligned_cols=31  Identities=23%  Similarity=0.391  Sum_probs=20.8

Q ss_pred             CcccCccCCC-cccccCCc----EEeCC---CCCeeecc
Q 040426            8 DFLFCKFCGT-MLRMESNH----VVCSS---CKFKKNVQ   38 (120)
Q Consensus         8 ~~~FCp~Cgn-lL~~~~~~----~~C~~---C~~~~~~~   38 (120)
                      ...=||.||. .|..+..+    +.|..   |.|..++.
T Consensus       591 ~~~~CP~Cg~~~L~~k~gr~G~Fl~Cs~yP~C~~t~~~~  629 (860)
T PRK06319        591 TEIDCPKCHKGKLVKIWAKNRYFYGCSEYPECDYKTSEE  629 (860)
T ss_pred             cCcccCCCCCcceeEEecCCCceeeccCCccccccCCcc
Confidence            3456999964 66554332    89976   88876654

>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain

Probab=87.58  E-value=0.37  Score=27.57  Aligned_cols=30  Identities=23%  Similarity=0.445  Sum_probs=22.5

Q ss_pred             CCCcccCccCCCcccccCCc-----EEeCCCCCee
Q 040426            6 GRDFLFCKFCGTMLRMESNH-----VVCSSCKFKK   35 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~~~~~-----~~C~~C~~~~   35 (120)
                      -.++.||+.||.-|......     |.|.+.....
T Consensus         2 l~g~l~C~~CG~~m~~~~~~~~~~yy~C~~~~~~~   36 (58)
T PF13408_consen    2 LSGLLRCGHCGSKMTRRKRKGKYRYYRCSNRRRKG   36 (58)
T ss_pred             CCCcEEcccCCcEeEEEECCCCceEEEcCCCcCCC
Confidence            35789999999999876431     8888776444

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=87.58  E-value=0.44  Score=29.52  Aligned_cols=31  Identities=13%  Similarity=0.446  Sum_probs=23.9

Q ss_pred             cccCccCCCcccccCCc----------EEeC--CCCCeeeccc
Q 040426            9 FLFCKFCGTMLRMESNH----------VVCS--SCKFKKNVQD   39 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~~----------~~C~--~C~~~~~~~~   39 (120)
                      |+.||.||.-......+          ..|.  .||+.+..-.
T Consensus         1 mm~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~e   43 (72)
T PRK09678          1 MFHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITYE   43 (72)
T ss_pred             CccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEEE
Confidence            67999999988665431          8999  8999986543

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

Probab=87.36  E-value=0.71  Score=24.24  Aligned_cols=28  Identities=21%  Similarity=0.363  Sum_probs=21.7

Q ss_pred             cccCccCCCcccc-cCCc-EEeCCCCCeee
Q 040426            9 FLFCKFCGTMLRM-ESNH-VVCSSCKFKKN   36 (120)
Q Consensus         9 ~~FCp~CgnlL~~-~~~~-~~C~~C~~~~~   36 (120)
                      +.-|+.||.-+.. +++. +.|..||.+.+
T Consensus         3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~~   32 (33)
T PF08792_consen    3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSFP   32 (33)
T ss_pred             ceEcCCCCCCeEEEecCCeEEcccCCcEee
Confidence            4568889877766 6555 99999998765

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=87.14  E-value=0.44  Score=27.92  Aligned_cols=27  Identities=26%  Similarity=0.610  Sum_probs=23.7

Q ss_pred             cCccCCCcccccCCcEEeCCCCCeeec
Q 040426           11 FCKFCGTMLRMESNHVVCSSCKFKKNV   37 (120)
Q Consensus        11 FCp~CgnlL~~~~~~~~C~~C~~~~~~   37 (120)
                      -|+.||.-|.+..|.++|..|+.....
T Consensus         7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR   33 (54)
T PF14446_consen    7 KCPVCGKKFKDGDDIVVCPECGAPYHR   33 (54)
T ss_pred             cChhhCCcccCCCCEEECCCCCCcccH
Confidence            599999999888888999999998764

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

Probab=86.92  E-value=0.76  Score=27.46  Aligned_cols=24  Identities=25%  Similarity=0.646  Sum_probs=15.6

Q ss_pred             cCccCCCcccccCCc-------EEeCCCCCe
Q 040426           11 FCKFCGTMLRMESNH-------VVCSSCKFK   34 (120)
Q Consensus        11 FCp~CgnlL~~~~~~-------~~C~~C~~~   34 (120)
                      -||.||+.+..+-.+       |.|.+||+.
T Consensus        29 ~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF~   59 (61)
T COG2888          29 PCPNCGEVEIYRCAKCRKLGNPYRCPKCGFE   59 (61)
T ss_pred             eCCCCCceeeehhhhHHHcCCceECCCcCcc
Confidence            477777666655321       777777775

>PF14205 Cys_rich_KTR: Cysteine-rich KTR

Probab=86.88  E-value=0.46  Score=27.86  Aligned_cols=31  Identities=23%  Similarity=0.849  Sum_probs=23.0

Q ss_pred             CcccCccCCCc--ccccCCc------EEeCCCCCeeecc
Q 040426            8 DFLFCKFCGTM--LRMESNH------VVCSSCKFKKNVQ   38 (120)
Q Consensus         8 ~~~FCp~Cgnl--L~~~~~~------~~C~~C~~~~~~~   38 (120)
                      .+..||.|||-  +..++|.      +.|+.|..+.-+.
T Consensus         3 ~Wi~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~   41 (55)
T PF14205_consen    3 EWILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLID   41 (55)
T ss_pred             eEEECCCCCCccceeeecCceeccccccCCCCCceEEEE
Confidence            46789999975  4555553      9999999876553

>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]

Probab=86.84  E-value=0.22  Score=38.51  Aligned_cols=32  Identities=25%  Similarity=0.542  Sum_probs=26.0

Q ss_pred             CcccCccCCCcccccCC--c-EEeCCCCCeeeccc
Q 040426            8 DFLFCKFCGTMLRMESN--H-VVCSSCKFKKNVQD   39 (120)
Q Consensus         8 ~~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~~   39 (120)
                      -+.=||.|+.|||-++-  + .+|..|+|-..+..
T Consensus        27 lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A   61 (294)
T COG0777          27 LWTKCPSCGEMLYRKELESNLKVCPKCGHHMRISA   61 (294)
T ss_pred             ceeECCCccceeeHHHHHhhhhcccccCcccccCH
Confidence            36679999999998863  2 99999999876554

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=86.84  E-value=0.93  Score=27.03  Aligned_cols=36  Identities=25%  Similarity=0.508  Sum_probs=26.4

Q ss_pred             cccccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426           73 TQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC  117 (120)
Q Consensus        73 ~t~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w  117 (120)
                      |+.--.+++||.|++...+|--.|         .--.|..||..-
T Consensus         5 p~S~F~~VkCp~C~n~q~vFsha~---------t~V~C~~Cg~~L   40 (59)
T PRK00415          5 PRSRFLKVKCPDCGNEQVVFSHAS---------TVVRCLVCGKTL   40 (59)
T ss_pred             CCCeEEEEECCCCCCeEEEEecCC---------cEEECcccCCCc
Confidence            333357889999999999996543         236798898753

>smart00531 TFIIE Transcription initiation factor IIE

Probab=86.78  E-value=0.2  Score=34.81  Aligned_cols=31  Identities=32%  Similarity=0.762  Sum_probs=20.1

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceE-----EEEcCCCCcee
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTT-----YYICPRCGHRC  117 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~-----fY~C~~C~~~w  117 (120)
                      ..-.||+||.   .|.      ++|.+..     -|.|+.||..-
T Consensus        98 ~~Y~Cp~C~~---~y~------~~ea~~~~d~~~~f~Cp~Cg~~l  133 (147)
T smart00531       98 AYYKCPNCQS---KYT------FLEANQLLDMDGTFTCPRCGEEL  133 (147)
T ss_pred             cEEECcCCCC---Eee------HHHHHHhcCCCCcEECCCCCCEE
Confidence            4568999983   222      2333433     49999999764

>smart00647 IBR In Between Ring fingers

Probab=86.77  E-value=0.7  Score=26.77  Aligned_cols=29  Identities=24%  Similarity=0.676  Sum_probs=22.9

Q ss_pred             CCcccCc--cCCCcccccC--C-c-EEeCCCCCee
Q 040426            7 RDFLFCK--FCGTMLRMES--N-H-VVCSSCKFKK   35 (120)
Q Consensus         7 ~~~~FCp--~CgnlL~~~~--~-~-~~C~~C~~~~   35 (120)
                      ..+.+||  .|+.++....  . . +.|..|++..
T Consensus        16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~f   50 (64)
T smart00647       16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSF   50 (64)
T ss_pred             CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeE
Confidence            4678999  9999998873  2 2 9999898865

the domains occurs between pairs og RING fingers

>COG2835 Uncharacterized conserved protein [Function unknown]

Probab=86.71  E-value=0.63  Score=27.82  Aligned_cols=35  Identities=23%  Similarity=0.571  Sum_probs=29.9

Q ss_pred             CCCCcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426            5 LGRDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus         5 ~~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      ....+.-||.|..-|...+.+  +.|+.|+--+++.+
T Consensus         4 ~LLeiLaCP~~kg~L~~~~~~~~L~c~~~~~aYpI~d   40 (60)
T COG2835           4 RLLEILACPVCKGPLVYDEEKQELICPRCKLAYPIRD   40 (60)
T ss_pred             hhheeeeccCcCCcceEeccCCEEEecccCceeeccc
Confidence            446788999999999887665  99999999999877

>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit

Probab=86.65  E-value=0.16  Score=39.27  Aligned_cols=31  Identities=23%  Similarity=0.588  Sum_probs=25.0

Q ss_pred             cccCccCCCcccccCC--c-EEeCCCCCeeeccc
Q 040426            9 FLFCKFCGTMLRMESN--H-VVCSSCKFKKNVQD   39 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~~   39 (120)
                      +.=||.|+.+|+.++-  + ++|+.|||-..+..
T Consensus        26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~a   59 (285)
T TIGR00515        26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMRMDA   59 (285)
T ss_pred             eeECCCCcchhhHHHHHhhCCCCCCCCCcCcCCH
Confidence            6679999999998742  3 99999999876533

The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=86.48  E-value=0.81  Score=31.50  Aligned_cols=13  Identities=15%  Similarity=0.552  Sum_probs=11.6

Q ss_pred             EEeCCCCCeeecc
Q 040426           26 VVCSSCKFKKNVQ   38 (120)
Q Consensus        26 ~~C~~C~~~~~~~   38 (120)
                      +.|+.||+.....
T Consensus        71 ~~C~~CG~~~~~~   83 (135)
T PRK03824         71 LKCRNCGNEWSLK   83 (135)
T ss_pred             EECCCCCCEEecc
Confidence            9999999988775

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=86.43  E-value=0.46  Score=31.20  Aligned_cols=30  Identities=17%  Similarity=0.551  Sum_probs=20.4

Q ss_pred             CcccCccCCCccc-ccCC--c--EEeCCCCCeeec
Q 040426            8 DFLFCKFCGTMLR-MESN--H--VVCSSCKFKKNV   37 (120)
Q Consensus         8 ~~~FCp~CgnlL~-~~~~--~--~~C~~C~~~~~~   37 (120)
                      .+.-||.||+... .+-+  .  .+|++||+....
T Consensus        20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~   54 (99)
T PRK14892         20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEF   54 (99)
T ss_pred             cEeECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence            4567999995322 2222  2  999999998754

>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=86.37  E-value=0.37  Score=27.89  Aligned_cols=30  Identities=23%  Similarity=0.621  Sum_probs=23.4

Q ss_pred             ccCccCCCcccccCC-c---EEeCCCCCeeeccc
Q 040426           10 LFCKFCGTMLRMESN-H---VVCSSCKFKKNVQD   39 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~-~---~~C~~C~~~~~~~~   39 (120)
                      .=|+.||.+|---.+ .   +.|..|+....+..
T Consensus         5 iRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a   38 (51)
T PF10122_consen    5 IRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA   38 (51)
T ss_pred             eeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence            359999999977422 2   99999999887655

>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.33  E-value=0.69  Score=22.86  Aligned_cols=23  Identities=30%  Similarity=0.638  Sum_probs=17.4

Q ss_pred             CccCCCcccccCC-c-EEeCCCCCe
Q 040426           12 CKFCGTMLRMESN-H-VVCSSCKFK   34 (120)
Q Consensus        12 Cp~CgnlL~~~~~-~-~~C~~C~~~   34 (120)
                      |..|..+|..+.+ . ..|..|.++
T Consensus         1 C~~Cr~~L~yp~GA~sVrCa~C~~V   25 (25)
T PF06943_consen    1 CGGCRTLLMYPRGAPSVRCACCHTV   25 (25)
T ss_pred             CCCCCceEEcCCCCCCeECCccCcC
Confidence            6778888866654 3 999999863

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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].

>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC

Probab=86.23  E-value=0.71  Score=28.49  Aligned_cols=30  Identities=27%  Similarity=0.587  Sum_probs=21.8

Q ss_pred             cCccCCCccccc---CCc---EEeCCCCCeeecccc
Q 040426           11 FCKFCGTMLRME---SNH---VVCSSCKFKKNVQDV   40 (120)
Q Consensus        11 FCp~CgnlL~~~---~~~---~~C~~C~~~~~~~~~   40 (120)
                      -||.|+.|=.+.   ++.   ..|-.|||.......
T Consensus        10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~   45 (71)
T PF09526_consen   10 VCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ   45 (71)
T ss_pred             cCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence            599999864332   232   999999999876653

Members are found in various proteobacteria.

>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed

Probab=86.17  E-value=0.17  Score=39.39  Aligned_cols=31  Identities=13%  Similarity=0.445  Sum_probs=25.0

Q ss_pred             cccCccCCCcccccCC--c-EEeCCCCCeeeccc
Q 040426            9 FLFCKFCGTMLRMESN--H-VVCSSCKFKKNVQD   39 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~~   39 (120)
                      +.=||.|+.+|+.+.-  + ++|+.|+|-.....
T Consensus        38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rltA   71 (296)
T CHL00174         38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLKMSS   71 (296)
T ss_pred             eeECCCccchhhHHHHHHcCCCCCCCCCCcCCCH
Confidence            6679999999998853  2 89999999765543

>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []

Probab=85.97  E-value=0.82  Score=35.11  Aligned_cols=35  Identities=26%  Similarity=0.691  Sum_probs=17.9

Q ss_pred             cccccccCCC-ceEEEEeecccCC-CCceEEEEcCCCCceec
Q 040426           79 KRACEKCQNP-EMYYSTRQTRSAD-EGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        79 ~~~CpkCg~~-ea~y~~~Q~RSAD-E~~T~fY~C~~C~~~w~  118 (120)
                      ...||-||.. .+....    ..+ +|. +|..|.-|++.|+
T Consensus       172 ~g~CPvCGs~P~~s~l~----~~~~~G~-R~L~Cs~C~t~W~  208 (290)
T PF04216_consen  172 RGYCPVCGSPPVLSVLR----GGEREGK-RYLHCSLCGTEWR  208 (290)
T ss_dssp             -SS-TTT---EEEEEEE----------E-EEEEETTT--EEE
T ss_pred             CCcCCCCCCcCceEEEe----cCCCCcc-EEEEcCCCCCeee
Confidence            4689999987 444433    322 376 9999999999996

The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.

>COG4640 Predicted membrane protein [Function unknown]

Probab=85.86  E-value=0.41  Score=38.78  Aligned_cols=27  Identities=30%  Similarity=0.727  Sum_probs=19.2

Q ss_pred             cccCccCCCcccccCCcEEeCCCCCeeec
Q 040426            9 FLFCKFCGTMLRMESNHVVCSSCKFKKNV   37 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~~~~C~~C~~~~~~   37 (120)
                      |+|||.||.-  -.++.+.|..||+....
T Consensus         1 M~fC~kcG~q--k~Ed~~qC~qCG~~~t~   27 (465)
T COG4640           1 MKFCPKCGSQ--KAEDDVQCTQCGHKFTS   27 (465)
T ss_pred             CCcccccccc--cccccccccccCCcCCc
Confidence            7999999942  12334669999997543

>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=85.78  E-value=1.6  Score=27.52  Aligned_cols=37  Identities=16%  Similarity=0.305  Sum_probs=19.9

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +.-.||-|||..++--.+.-.    -.+-.-.|..||..|.
T Consensus        21 ~~F~CPfC~~~~sV~v~idkk----~~~~~~~C~~Cg~~~~   57 (81)
T PF05129_consen   21 KVFDCPFCNHEKSVSVKIDKK----EGIGILSCRVCGESFQ   57 (81)
T ss_dssp             S----TTT--SS-EEEEEETT----TTEEEEEESSS--EEE
T ss_pred             ceEcCCcCCCCCeEEEEEEcc----CCEEEEEecCCCCeEE
Confidence            456799999999987776321    3455578999998775

; PDB: 1WII_A.

>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins

Probab=85.50  E-value=0.88  Score=23.70  Aligned_cols=29  Identities=24%  Similarity=0.701  Sum_probs=15.6

Q ss_pred             ccccccCCCce--EEEEeecccCCCCceEEEEcCC--CCc
Q 040426           80 RACEKCQNPEM--YYSTRQTRSADEGQTTYYICPR--CGH  115 (120)
Q Consensus        80 ~~CpkCg~~ea--~y~~~Q~RSADE~~T~fY~C~~--C~~  115 (120)
                      ..|||||-.-.  +|-+       .|....|+|.+  |.+
T Consensus         2 hlcpkcgvgvl~pvy~~-------kgeikvfrcsnpacdy   34 (36)
T PF09151_consen    2 HLCPKCGVGVLEPVYNQ-------KGEIKVFRCSNPACDY   34 (36)
T ss_dssp             -B-TTTSSSBEEEEE-T-------TS-EEEEEES-TT---
T ss_pred             ccCCccCceEEEEeecC-------CCcEEEEEcCCCcccc
Confidence            57999998744  4533       37788899974  765

Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.

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

Probab=85.19  E-value=0.38  Score=31.10  Aligned_cols=31  Identities=23%  Similarity=0.354  Sum_probs=22.0

Q ss_pred             cccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426            9 FLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      -.+||.||..-.-+...  |.|+.|++..---.
T Consensus        35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AGGA   67 (90)
T PF01780_consen   35 KYTCPFCGKTSVKRVATGIWKCKKCGKKFAGGA   67 (90)
T ss_dssp             -BEESSSSSSEEEEEETTEEEETTTTEEEE-BS
T ss_pred             CCcCCCCCCceeEEeeeEEeecCCCCCEEeCCC
Confidence            45899999886444332  99999999875444

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 ....

>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]

Probab=85.18  E-value=0.52  Score=37.12  Aligned_cols=32  Identities=28%  Similarity=0.611  Sum_probs=23.3

Q ss_pred             CcccCccCCCcccccCCc--EEeC--CCC---Ceeeccc
Q 040426            8 DFLFCKFCGTMLRMESNH--VVCS--SCK---FKKNVQD   39 (120)
Q Consensus         8 ~~~FCp~CgnlL~~~~~~--~~C~--~C~---~~~~~~~   39 (120)
                      ..+|||-||+-+.+++.+  ..|+  +|.   +.++..+
T Consensus       149 kykFCp~CG~~tkp~e~g~k~~Cs~~~C~~~n~~yPr~d  187 (345)
T KOG3084|consen  149 KYKFCPGCGSPTKPEEAGTKLQCSDETCPSCNVIYPRTD  187 (345)
T ss_pred             HhccCcccCCCcccccCCccceeecccCCcCCeeccCCC
Confidence            467999999999999875  6666  555   4554444

>PRK05654 acetyl-CoA carboxylase subunit beta; Validated

Probab=84.83  E-value=0.24  Score=38.44  Aligned_cols=30  Identities=23%  Similarity=0.591  Sum_probs=24.9

Q ss_pred             cccCccCCCcccccCC--c-EEeCCCCCeeecc
Q 040426            9 FLFCKFCGTMLRMESN--H-VVCSSCKFKKNVQ   38 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~   38 (120)
                      +.=||.|+.+||-++-  + .+|+.|+|-....
T Consensus        27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~   59 (292)
T PRK05654         27 WTKCPSCGQVLYRKELEANLNVCPKCGHHMRIS   59 (292)
T ss_pred             eeECCCccchhhHHHHHhcCCCCCCCCCCeeCC
Confidence            6789999999998753  2 8999999987654

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

Probab=84.61  E-value=0.42  Score=27.77  Aligned_cols=14  Identities=43%  Similarity=1.213  Sum_probs=11.6

Q ss_pred             CCCcccCccCCCcc
Q 040426            6 GRDFLFCKFCGTML   19 (120)
Q Consensus         6 ~~~~~FCp~CgnlL   19 (120)
                      ...+.|||.||-||
T Consensus        43 ~~~i~~Cp~CgRiL   56 (56)
T PF02591_consen   43 GDEIVFCPNCGRIL   56 (56)
T ss_pred             CCCeEECcCCCccC
Confidence            34688999999887

>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5

Probab=84.57  E-value=1.5  Score=29.33  Aligned_cols=30  Identities=27%  Similarity=0.701  Sum_probs=23.9

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR  116 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~  116 (120)
                      +.||.||+++..+.-       |+-+.|-+|..||.+
T Consensus        81 VlC~~C~spdT~l~k-------~~r~~~l~C~aCGa~  110 (110)
T smart00653       81 VLCPECGSPDTELIK-------ENRLFFLKCEACGAR  110 (110)
T ss_pred             EECCCCCCCCcEEEE-------eCCeEEEEccccCCC
Confidence            689999999986643       256788899999964

>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=84.54  E-value=0.55  Score=27.19  Aligned_cols=30  Identities=20%  Similarity=0.563  Sum_probs=16.2

Q ss_pred             CCCcccCcc--CCCcccccCCc----EEeCCCCCee
Q 040426            6 GRDFLFCKF--CGTMLRMESNH----VVCSSCKFKK   35 (120)
Q Consensus         6 ~~~~~FCp~--CgnlL~~~~~~----~~C~~C~~~~   35 (120)
                      ...+++||.  |+.++......    +.|..|++..
T Consensus        15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f   50 (64)
T PF01485_consen   15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEF   50 (64)
T ss_dssp             ---CC--TTSST---ECS-SSTTS--CCTTSCCSEE
T ss_pred             CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcC
Confidence            345679977  99999887653    7899888864

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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=84.48  E-value=1.8  Score=26.24  Aligned_cols=32  Identities=19%  Similarity=0.364  Sum_probs=23.3

Q ss_pred             cccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426           79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC  117 (120)
Q Consensus        79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w  117 (120)
                      -++||-||.+.+..-+      + +-.-++.|.+|+-.+
T Consensus         6 lKPCPFCG~~~~~v~~------~-~g~~~v~C~~CgA~~   37 (64)
T PRK09710          6 VKPCPFCGCPSVTVKA------I-SGYYRAKCNGCESRT   37 (64)
T ss_pred             ccCCCCCCCceeEEEe------c-CceEEEEcCCCCcCc
Confidence            4679999999887653      1 335568899998654

>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]

Probab=84.40  E-value=0.52  Score=38.39  Aligned_cols=30  Identities=17%  Similarity=0.462  Sum_probs=25.3

Q ss_pred             ccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426           10 LFCKFCGTMLRMESNH-VVCSSCKFKKNVQD   39 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~   39 (120)
                      .-||.||.-|.....+ |.|+.||+..+-..
T Consensus       351 p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~  381 (421)
T COG1571         351 PVCPRCGGRMKSAGRNGFRCKKCGTRARETL  381 (421)
T ss_pred             CCCCccCCchhhcCCCCcccccccccCCccc
Confidence            3699999999988764 99999999887555

>PRK12336 translation initiation factor IF-2 subunit beta; Provisional

Probab=83.90  E-value=1.4  Score=32.30  Aligned_cols=31  Identities=23%  Similarity=0.558  Sum_probs=25.0

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC  117 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w  117 (120)
                      +.||.||+++-.+.-       ++.+.|-.|..||..-
T Consensus        99 V~C~~C~~pdT~l~k-------~~~~~~l~C~aCGa~~  129 (201)
T PRK12336         99 VICSECGLPDTRLVK-------EDRVLMLRCDACGAHR  129 (201)
T ss_pred             EECCCCCCCCcEEEE-------cCCeEEEEcccCCCCc
Confidence            689999999987642       2578888999999753

>PHA02942 putative transposase; Provisional

Probab=83.70  E-value=0.86  Score=36.60  Aligned_cols=29  Identities=28%  Similarity=0.712  Sum_probs=20.8

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC  117 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w  117 (120)
                      +...||.|||...   .        .....|.|.+||+..
T Consensus       324 TSq~Cs~CG~~~~---~--------l~~r~f~C~~CG~~~  352 (383)
T PHA02942        324 SSVSCPKCGHKMV---E--------IAHRYFHCPSCGYEN  352 (383)
T ss_pred             CCccCCCCCCccC---c--------CCCCEEECCCCCCEe
Confidence            4577999999642   1        012479999999975

>TIGR03826 YvyF flagellar operon protein TIGR03826

Probab=83.65  E-value=0.1  Score=36.20  Aligned_cols=28  Identities=25%  Similarity=0.603  Sum_probs=21.1

Q ss_pred             CCcccCccCCCcccccCCcEEeCCCCCee
Q 040426            7 RDFLFCKFCGTMLRMESNHVVCSSCKFKK   35 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~~~~C~~C~~~~   35 (120)
                      +.+.-||.||.+... ...-.|..|....
T Consensus         1 m~l~nC~~CgklF~~-~~~~iCp~C~~~~   28 (137)
T TIGR03826         1 MELANCPKCGRLFVK-TGRDVCPSCYEEE   28 (137)
T ss_pred             CCCccccccchhhhh-cCCccCHHHhHHH
Confidence            467789999997665 3446799998753

This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.

>COG1779 C4-type Zn-finger protein [General function prediction only]

Probab=83.49  E-value=0.54  Score=34.61  Aligned_cols=27  Identities=26%  Similarity=0.696  Sum_probs=20.4

Q ss_pred             cccCccCCCcccccCC--------c-----EEeCCCCCee
Q 040426            9 FLFCKFCGTMLRMESN--------H-----VVCSSCKFKK   35 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~--------~-----~~C~~C~~~~   35 (120)
                      ..=||.||.-|..-.-        .     +.|.+|||..
T Consensus        14 ~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~   53 (201)
T COG1779          14 RIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRS   53 (201)
T ss_pred             eecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcc
Confidence            4469999998765421        1     9999999985

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=83.42  E-value=1  Score=27.72  Aligned_cols=26  Identities=23%  Similarity=0.570  Sum_probs=18.9

Q ss_pred             cCccCCCcccccCCcEEeCCCCCeee
Q 040426           11 FCKFCGTMLRMESNHVVCSSCKFKKN   36 (120)
Q Consensus        11 FCp~CgnlL~~~~~~~~C~~C~~~~~   36 (120)
                      -||.|.+-|.+..+.+.|..|+....
T Consensus         3 ~CP~C~~~L~~~~~~~~C~~C~~~~~   28 (70)
T PF07191_consen    3 TCPKCQQELEWQGGHYHCEACQKDYK   28 (70)
T ss_dssp             B-SSS-SBEEEETTEEEETTT--EEE
T ss_pred             cCCCCCCccEEeCCEEECccccccce
Confidence            49999999999987799999988543

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

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

Probab=83.41  E-value=1.3  Score=26.63  Aligned_cols=34  Identities=21%  Similarity=0.529  Sum_probs=24.2

Q ss_pred             CCCcccCccCCCcc------------------------------cccCCcEEeCCCCCeeeccc
Q 040426            6 GRDFLFCKFCGTML------------------------------RMESNHVVCSSCKFKKNVQD   39 (120)
Q Consensus         6 ~~~~~FCp~CgnlL------------------------------~~~~~~~~C~~C~~~~~~~~   39 (120)
                      -..++-||.|.+=|                              .+.++.+.|+.|+..+++.+
T Consensus         4 llniL~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~eg~L~Cp~c~r~YPI~d   67 (68)
T PF03966_consen    4 LLNILACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIVEGELICPECGREYPIRD   67 (68)
T ss_dssp             GCGTBB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETTTTEEEETTTTEEEEEET
T ss_pred             HHhhhcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhcccccCCEEEcCCCCCEEeCCC
Confidence            45678899999866                              12233399999999998764

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.

>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]

Probab=83.38  E-value=0.55  Score=38.26  Aligned_cols=31  Identities=35%  Similarity=0.890  Sum_probs=23.5

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      .+-.||.||..        +.||  |.+ -|+|.+||++.++
T Consensus       349 ~~p~Cp~Cg~~--------m~S~--G~~-g~rC~kCg~~~~~  379 (421)
T COG1571         349 VNPVCPRCGGR--------MKSA--GRN-GFRCKKCGTRARE  379 (421)
T ss_pred             cCCCCCccCCc--------hhhc--CCC-CcccccccccCCc
Confidence            34479999974        3456  666 8999999998764

>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]

Probab=83.32  E-value=0.42  Score=38.14  Aligned_cols=32  Identities=34%  Similarity=0.650  Sum_probs=26.7

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC  117 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w  117 (120)
                      +.||.|+|+|-.++-.    +  -||+-+.|..||++-
T Consensus        97 VlC~~C~NPETel~it----k--~q~i~~~CkACG~r~  128 (400)
T KOG2767|consen   97 VLCPSCENPETELIIT----K--KQTISLKCKACGFRS  128 (400)
T ss_pred             eeCcCCCCCceeEEec----c--cchhhhHHHHcCCcc
Confidence            5899999999987652    2  589999999999864

>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6

Probab=82.79  E-value=0.76  Score=36.76  Aligned_cols=35  Identities=37%  Similarity=0.700  Sum_probs=20.7

Q ss_pred             ccccccccCC-CceEEEEeecccCC-CCceEEEEcCCCCcee
Q 040426           78 VKRACEKCQN-PEMYYSTRQTRSAD-EGQTTYYICPRCGHRC  117 (120)
Q Consensus        78 ~~~~CpkCg~-~ea~y~~~Q~RSAD-E~~T~fY~C~~C~~~w  117 (120)
                      ....|++||. ....-.     +-| ++-|+.|+|..|||+-
T Consensus       173 f~piC~~cGri~tt~v~-----~~d~~~~~v~Y~c~~cG~~g  209 (360)
T PF01921_consen  173 FLPICEKCGRIDTTEVT-----EYDPEGGTVTYRCEECGHEG  209 (360)
T ss_dssp             EEEEETTTEE--EEEEE-----EE--SSSEEEEE--TTS---
T ss_pred             eeeeccccCCcccceee-----EeecCCCEEEEEecCCCCEE
Confidence            3567999998 544322     334 7899999999999974

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=82.36  E-value=1.2  Score=32.19  Aligned_cols=29  Identities=24%  Similarity=0.560  Sum_probs=24.3

Q ss_pred             cccCccCCCcccccC-CcEEeCCCCCeeec
Q 040426            9 FLFCKFCGTMLRMES-NHVVCSSCKFKKNV   37 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~-~~~~C~~C~~~~~~   37 (120)
                      ..+|+.||..|.|.. +.+.|..|++.+..
T Consensus       149 ~a~~~~~g~~~~~~~~~~~~c~~~~~~e~r  178 (189)
T PRK09521        149 YAMCSRCRTPLVKKGENELKCPNCGNIETR  178 (189)
T ss_pred             EEEccccCCceEECCCCEEECCCCCCEEee
Confidence            348999999998877 55999999988763

>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional

Probab=82.32  E-value=1.2  Score=36.64  Aligned_cols=17  Identities=12%  Similarity=0.317  Sum_probs=14.1

Q ss_pred             cccccccCCCceEEEEe
Q 040426           79 KRACEKCQNPEMYYSTR   95 (120)
Q Consensus        79 ~~~CpkCg~~ea~y~~~   95 (120)
                      ++.||-||..+..|..+
T Consensus       458 ~~~cp~c~~~k~~f~~~  474 (479)
T PRK05452        458 NFLCPECSLGKDVFDEL  474 (479)
T ss_pred             CCcCcCCCCcHHHhEec
Confidence            78999999998877543

>TIGR01031 rpmF_bact ribosomal protein L32

Probab=82.28  E-value=0.91  Score=26.58  Aligned_cols=26  Identities=35%  Similarity=0.792  Sum_probs=19.5

Q ss_pred             CCcccCccCCCcccccCCcEEeCCCCCee
Q 040426            7 RDFLFCKFCGTMLRMESNHVVCSSCKFKK   35 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~~~~C~~C~~~~   35 (120)
                      ..+..||.||.+-.+   ..+|..|||-.
T Consensus        24 p~l~~C~~cG~~~~~---H~vc~~cG~Y~   49 (55)
T TIGR01031        24 PTLVVCPNCGEFKLP---HRVCPSCGYYK   49 (55)
T ss_pred             CcceECCCCCCcccC---eeECCccCeEC
Confidence            346689999986443   38999999865

This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.

>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=82.03  E-value=0.6  Score=27.32  Aligned_cols=26  Identities=31%  Similarity=0.671  Sum_probs=19.7

Q ss_pred             CcccCccCCCcccccCCcEEeCCCCCeee
Q 040426            8 DFLFCKFCGTMLRMESNHVVCSSCKFKKN   36 (120)
Q Consensus         8 ~~~FCp~CgnlL~~~~~~~~C~~C~~~~~   36 (120)
                      .+..||.||.+-.+-   ..|..|||...
T Consensus        25 ~l~~c~~cg~~~~~H---~vc~~cG~y~~   50 (56)
T PF01783_consen   25 NLVKCPNCGEPKLPH---RVCPSCGYYKG   50 (56)
T ss_dssp             SEEESSSSSSEESTT---SBCTTTBBSSS
T ss_pred             ceeeeccCCCEeccc---EeeCCCCeECC
Confidence            577899999765443   78999997654

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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....

>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]

Probab=82.01  E-value=0.28  Score=40.53  Aligned_cols=29  Identities=24%  Similarity=0.653  Sum_probs=23.3

Q ss_pred             CCCcccCccCCCcccccCCc-EEeCCCCCe
Q 040426            6 GRDFLFCKFCGTMLRMESNH-VVCSSCKFK   34 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~~~~~-~~C~~C~~~   34 (120)
                      ++++-||.+||+|||--... +.|.+|.-.
T Consensus       118 YssPTFCDhCGsLLyGl~HQGmKC~~C~mN  147 (683)
T KOG0696|consen  118 YSSPTFCDHCGSLLYGLIHQGMKCDTCDMN  147 (683)
T ss_pred             cCCCchhhhHHHHHHHHHhcccccccccch
Confidence            56789999999999976544 888888753

>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase

Probab=81.73  E-value=1.4  Score=35.06  Aligned_cols=35  Identities=31%  Similarity=0.606  Sum_probs=22.2

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC  117 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w  117 (120)
                      ..-.||+||.-.   ..+ +--..+.-|+.|+| .|||.-
T Consensus       168 ~~p~c~~cg~~~---~~v-~~~d~~~~~v~y~c-~cG~~g  202 (353)
T cd00674         168 FMPYCEKCGKDT---TTV-EAYDAKAGTVTYKC-ECGHEE  202 (353)
T ss_pred             eeeecCCcCcce---eEE-EEEeCCCCeEEEEc-CCCCEE
Confidence            455799999322   111 22233466999999 699964

Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=81.59  E-value=1.9  Score=25.73  Aligned_cols=27  Identities=22%  Similarity=0.704  Sum_probs=18.7

Q ss_pred             cccCccCCCcccccCC-------cEEeCCCCCee
Q 040426            9 FLFCKFCGTMLRMESN-------HVVCSSCKFKK   35 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~-------~~~C~~C~~~~   35 (120)
                      .-.||.||..+..+-.       .|.|..||+.-
T Consensus        25 ~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF~G   58 (59)
T PRK14890         25 KFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGFEG   58 (59)
T ss_pred             EeeCCCCCCeeEeechhHHhcCCceECCCCCCcC
Confidence            4478888887665532       18888888753

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

Probab=81.45  E-value=1.3  Score=33.55  Aligned_cols=26  Identities=27%  Similarity=0.733  Sum_probs=20.7

Q ss_pred             cccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426           77 KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC  117 (120)
Q Consensus        77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w  117 (120)
                      .+...||.||+               -...-|.|..||+.+
T Consensus       307 ~tS~~C~~cg~---------------~~~r~~~C~~cg~~~  332 (364)
T COG0675         307 YTSKTCPCCGH---------------LSGRLFKCPRCGFVH  332 (364)
T ss_pred             CCcccccccCC---------------ccceeEECCCCCCee
Confidence            45678999999               125679999999976

>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=81.11  E-value=1.3  Score=25.16  Aligned_cols=26  Identities=19%  Similarity=0.535  Sum_probs=17.6

Q ss_pred             cccCc--cCCCc--ccccCCcEEeCCCCCe
Q 040426            9 FLFCK--FCGTM--LRMESNHVVCSSCKFK   34 (120)
Q Consensus         9 ~~FCp--~Cgnl--L~~~~~~~~C~~C~~~   34 (120)
                      -..||  +||.-  |---.+++.|-.|+++
T Consensus        18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~T   47 (47)
T PF01599_consen   18 RKECPSPRCGAGVFMAEHKDRHYCGKCGYT   47 (47)
T ss_dssp             SEE-TSTTTTSSSEEEE-SSEEEETTTSS-
T ss_pred             hhcCCCcccCCceEeeecCCCccCCCcccC
Confidence            46899  99983  3334566999999984

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 family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.

>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function

Probab=80.88  E-value=1.5  Score=30.32  Aligned_cols=38  Identities=26%  Similarity=0.579  Sum_probs=20.7

Q ss_pred             cccccccCCCceEEEEeecc-----cCCCCceEEEEcCCCCce
Q 040426           79 KRACEKCQNPEMYYSTRQTR-----SADEGQTTYYICPRCGHR  116 (120)
Q Consensus        79 ~~~CpkCg~~ea~y~~~Q~R-----SADE~~T~fY~C~~C~~~  116 (120)
                      --.|+.|+..-..---.+.+     ..-+....||.|+.||..
T Consensus        91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki  133 (147)
T PF01927_consen   91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI  133 (147)
T ss_pred             CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCE
Confidence            45899999832111000000     011224469999999875

The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=80.64  E-value=1.3  Score=34.48  Aligned_cols=31  Identities=26%  Similarity=0.553  Sum_probs=20.5

Q ss_pred             CCCcccCccCCCc-c-cccCCc-EEeCCCCCeee
Q 040426            6 GRDFLFCKFCGTM-L-RMESNH-VVCSSCKFKKN   36 (120)
Q Consensus         6 ~~~~~FCp~Cgnl-L-~~~~~~-~~C~~C~~~~~   36 (120)
                      ......||+||.- + +-.+.+ ++|..||++-.
T Consensus         8 ~~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~   41 (310)
T PRK00423          8 EEEKLVCPECGSDKLIYDYERGEIVCADCGLVIE   41 (310)
T ss_pred             cccCCcCcCCCCCCeeEECCCCeEeecccCCccc
Confidence            3446789999972 2 111222 99999999754

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]

Probab=80.56  E-value=4.4  Score=32.26  Aligned_cols=27  Identities=33%  Similarity=0.727  Sum_probs=19.1

Q ss_pred             CcccC--ccCCCcccccCCc--EEeCC-CCCe
Q 040426            8 DFLFC--KFCGTMLRMESNH--VVCSS-CKFK   34 (120)
Q Consensus         8 ~~~FC--p~CgnlL~~~~~~--~~C~~-C~~~   34 (120)
                      +-.-|  |-||.=|.++.|.  ..|.. |||.
T Consensus       314 gGVlCP~pgCG~gll~EPD~rkvtC~~gCgf~  345 (446)
T KOG0006|consen  314 GGVLCPRPGCGAGLLPEPDQRKVTCEGGCGFA  345 (446)
T ss_pred             CCEecCCCCCCcccccCCCCCcccCCCCchhH
Confidence            34457  4699888887764  77776 7775

>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.12  E-value=1.2  Score=30.02  Aligned_cols=42  Identities=12%  Similarity=-0.083  Sum_probs=34.5

Q ss_pred             CCCCCCCCcccCccCCCcccccCC-cEEeCCCCCeeecccccc
Q 040426            1 MADPLGRDFLFCKFCGTMLRMESN-HVVCSSCKFKKNVQDVAD   42 (120)
Q Consensus         1 ~~~~~~~~~~FCp~CgnlL~~~~~-~~~C~~C~~~~~~~~~~~   42 (120)
                      ||++-.+.-+-||+||.-.|--.- .++|+.||.+++.+-+..
T Consensus         1 mAk~eLGtKridPetg~KFYDLNrdPiVsPytG~s~P~s~fe~   43 (129)
T COG4530           1 MAKPELGTKRIDPETGKKFYDLNRDPIVSPYTGKSYPRSYFEE   43 (129)
T ss_pred             CCcccccccccCccccchhhccCCCccccCcccccchHHHHHh
Confidence            788888999999999998876543 399999999997666544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	120
3qt1_I	133	Rna Polymerase Ii Variant Containing A Chimeric Rpb		1e-06
1qyp_A	57	Thermococcus Celer Rpb9, Nmr, 25 Structures Length		2e-04

>pdb|3QT1|I Chain I, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11 Subunit Length = 133

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 52/118 (44%), Gaps = 14/118 (11%)
Query: 9   FLFCKFCGTML----RMESNHVV--CSSCKFKKNVQDVADREISYAVTAEEIKRELGISL 62
           F FC+ C  ML      E+N ++  C +C +   V++     +        I    G+  
Sbjct: 24  FRFCRDCNNMLYPREDKENNRLLFECRTCSY---VEEAGSPLVYRHELITNIGETAGVV- 79
Query: 63  FEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES 120
               Q    +  L +  R C KC + E  +   Q RSADE  TT+Y C  CGHR +E+
Sbjct: 80  ----QDIGSDPTLPRSDRECPKCHSRENVFFQLQIRSADEPMTTFYKCVNCGHRWKEN 133

>pdb|1QYP|A Chain A, Thermococcus Celer Rpb9, Nmr, 25 Structures Length = 57

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/41 (43%), Positives = 22/41 (53%)
Query: 75  LSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115
           L   K  C KC N   Y+   QTR+ DE  T +Y C +CGH
Sbjct: 11  LPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGH 51

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	120
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	6e-16
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	5e-15
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	1e-12
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	2e-12
3po3_S	178	Transcription elongation factor S-II; RNA polymera	1e-10
1tfi_A	50	Transcriptional elongation factor SII; transcripti	3e-10
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	2e-09

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 113

 Score = 67.1 bits (163), Expect = 6e-16
 Identities = 20/115 (17%), Positives = 34/115 (29%), Gaps = 14/115 (12%)

Query: 8   DFLFCKFCGTMLRMESNHV------VCSSCKFKKNVQDVADREISYAVTAEEIKRELGIS 61
           +F +C  C  ML    + V       C +C + +              +  E        
Sbjct: 3   NFQYCIECNNMLYPREDKVDRVLRLACRNCDYSEIAATSKVYRHELQSSNVENTTVS--- 59

Query: 62  LFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
                     +  L +  + C +C   E  +    +R  D   T  Y+C  CG  
Sbjct: 60  -----HDASTDPTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFA 109

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae} Length = 133

 Score = 65.2 bits (158), Expect = 5e-15
 Identities = 30/119 (25%), Positives = 41/119 (34%), Gaps = 14/119 (11%)

Query: 4   PLGRDFLFCKFCGTMLRMESN------HVVCSSCKFKKNVQDVADREISYAVTAEEIKRE 57
                F FC+ C  ML    +         C +C + +                 E    
Sbjct: 19  SHMTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGV 78

Query: 58  LGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
           +        Q    +  L +  R C KC + E  +   Q RSADE  TT+Y C  CGHR
Sbjct: 79  V--------QDIGSDPTLPRSDRECPKCHSRENVFFQLQIRSADEPMTTFYKCVNCGHR 129

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1 Length = 57

 Score = 57.1 bits (138), Expect = 1e-12
 Identities = 18/48 (37%), Positives = 24/48 (50%)

Query: 69  DKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
           ++    L   K  C KC N   Y+   QTR+ DE  T +Y C +CGH 
Sbjct: 5   EQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHT 52

>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* ... Length = 122

 Score = 58.7 bits (141), Expect = 2e-12
 Identities = 22/115 (19%), Positives = 34/115 (29%), Gaps = 14/115 (12%)

Query: 8   DFLFCKFCGTMLRMESNHV------VCSSCKFKKNVQDVADREISYAVTAEEIKRELGIS 61
            F FC+ C  ML    +         C +C + +                 E        
Sbjct: 3   TFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETA------ 56

Query: 62  LFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
                Q    +  L +  R C KC + E  +   Q R  D     +++C  C H 
Sbjct: 57  --GVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHI 109

>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A Length = 178

 Score = 54.8 bits (131), Expect = 1e-10
 Identities = 15/35 (42%), Positives = 20/35 (57%)

Query: 82  CEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
           C KC+  ++ Y   QTRSA    TT+  C  CG+R
Sbjct: 140 CGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNR 174

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1 Length = 50

 Score = 50.9 bits (122), Expect = 3e-10
 Identities = 17/35 (48%), Positives = 22/35 (62%)

Query: 82  CEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
           C KC+     Y+  QTRSADE  TT+ +C  CG+R
Sbjct: 12  CGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNR 46

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

 Score = 52.5 bits (124), Expect = 2e-09
 Identities = 17/35 (48%), Positives = 22/35 (62%)

Query: 82  CEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
           C KC+  ++ Y   QTRSADE  TT+  C  CG+R
Sbjct: 271 CGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNR 305

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	120
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	100.0
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	100.0
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	100.0
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	99.93
1tfi_A	50	Transcriptional elongation factor SII; transcripti	99.93
3po3_S	178	Transcription elongation factor S-II; RNA polymera	99.82
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	99.76
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	98.05
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	97.67
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	97.45
1k81_A	36	EIF-2-beta, probable translation initiation factor	96.27
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	95.47
2akl_A	138	PHNA-like protein PA0128; two domains, Zn binding	95.11
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	95.06
1yk4_A	52	Rubredoxin, RD; electron transport; 0.69A {Pyrococ	94.45
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	94.36
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	94.33
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	94.29
2v3b_B	55	Rubredoxin 2, rubredoxin; alkane degradation, iron	94.25
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	94.23
4rxn_A	54	Rubredoxin; electron transfer(iron-sulfur protein)	94.21
2kn9_A	81	Rubredoxin; metalloprotein, ssgcid, structural gen	94.13
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	93.96
1e8j_A	52	Rubredoxin; iron-sulfur-protein, zinc-substitution	93.84
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	93.78
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	93.75
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	93.69
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	93.54
1dx8_A	70	Rubredoxin; electron transport, zinc-substitution;	93.52
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	93.14
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	93.12
1s24_A	87	Rubredoxin 2; electron transport; NMR {Pseudomonas	93.11
2fnf_X	72	Putative RAS effector NORE1; zinc, signal transduc	92.82
3cng_A	189	Nudix hydrolase; structural genomics, APC7497, PSI	92.81
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	92.57
1lko_A	191	Rubrerythrin all-iron(II) form; reduced form, DIIR	92.44
1rfh_A	59	RAS association (ralgds/AF-6) domain family 5; zin	92.07
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	92.02
1x0t_A	120	Ribonuclease P protein component 4; pyrococcus hor	91.89
2k3r_A	123	Ribonuclease P protein component 4; PFU RPP21, RNA	91.49
1vk6_A	269	NADH pyrophosphatase; 1790429, structural genomics	91.25
3pwf_A	170	Rubrerythrin; non heme iron peroxidases, oxidative	91.25
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	91.19
4esj_A	257	Type-2 restriction enzyme DPNI; restriction endonu	91.18
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	90.86
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	90.6
1faq_A	52	RAF-1; transferase, serine/threonine-protein kinas	90.46
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	90.45
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	90.19
1yuz_A	202	Nigerythrin; rubrythrin, rubredoxin, hemerythrin,	90.19
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	89.7
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	89.68
1ptq_A	50	Protein kinase C delta type; phosphotransferase; 1	89.66
2con_A	79	RUH-035 protein, NIN one binding protein; ribosome	89.45
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	88.75
2g2k_A	170	EIF-5, eukaryotic translation initiation factor 5;	88.35
2enz_A	65	NPKC-theta, protein kinase C theta type; zinc bind	87.52
2akl_A	138	PHNA-like protein PA0128; two domains, Zn binding	87.08
3uej_A	65	NPKC-delta, protein kinase C delta type; proteine	87.0
2e9h_A	157	EIF-5, eukaryotic translation initiation factor 5;	86.83
3cc2_Z	116	50S ribosomal protein L37AE, 50S ribosomal protein	86.26
1y8f_A	66	UNC-13 homolog A, MUNC13-1; cysteine-rich domain,	86.06
2yuu_A	83	NPKC-delta, protein kinase C delta type; metal bin	85.73
3ga8_A	78	HTH-type transcriptional regulator MQSA (YGIT/B30;	84.45
3iz5_m	92	60S ribosomal protein L43 (L37AE); eukaryotic ribo	84.23
2eli_A	85	Protein kinase C alpha type; PKC-alpha, PKC-A, str	84.13
3j21_i	83	50S ribosomal protein L37AE; archaea, archaeal, KI	83.67
2enn_A	77	NPKC-theta, protein kinase C theta type; zinc bind	83.46
2jne_A	101	Hypothetical protein YFGJ; zinc fingers, two zinc,	83.21
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	83.09
2qkd_A	404	Zinc finger protein ZPR1; helical hairpins, beta h	82.51
1nee_A	138	EIF-2-beta, probable translation initiation factor	82.22
2row_A	84	RHO-associated protein kinase 2; ATP-binding, coil	81.47
2d74_B	148	Translation initiation factor 2 beta subunit; prot	81.01
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	80.64
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	80.58
3jyw_9	72	60S ribosomal protein L43; eukaryotic ribosome, RA	80.3

>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=100.00  E-value=2.9e-42  Score=233.93  Aligned_cols=106  Identities=22%  Similarity=0.502  Sum_probs=88.5

Q ss_pred             CCcccCccCCCcccccCC----c--EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccccc
Q 040426            7 RDFLFCKFCGTMLRMESN----H--VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKR   80 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~----~--~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~   80 (120)
                      ++|.|||+|||||+|+++    .  |.|++|||.++++.    .++|++...   +..+++.. |+.++..|+++|+++.
T Consensus         2 ~~~~FCp~CgnlL~~~~~~~~~~~~~~C~~C~y~~~~~~----~~v~~~~~~---~~~~e~~~-v~~~~~~~~t~p~t~~   73 (122)
T 1twf_I            2 TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGS----PLVYRHELI---TNIGETAG-VVQDIGSDPTLPRSDR   73 (122)
T ss_dssp             CCCCBCSSSCCBCEEEEETTTTEEEEECSSSSCEEECSC----SEEEEEESS---CCTTSSTT-CCTTGGGCTTSCCCCC
T ss_pred             CCCCcccccCccCcccccCcCCCCEEECCcCCCeeecCc----cEEEEEeec---cccccccc-ccccccccccccccCC
Confidence            579999999999999864    2  99999999999874    567766532   12333333 5566667899999999


Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES  120 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n  120 (120)
                      .||+|||++|+|||+|+||||||||+||+|++|||+|++|
T Consensus        74 ~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~~w~~n  113 (122)
T 1twf_I           74 ECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSD  113 (122)
T ss_dssp             CCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECC
T ss_pred             CCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCCEeccC
Confidence            9999999999999999999999999999999999999986

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

Probab=100.00  E-value=6.7e-42  Score=229.42  Aligned_cols=105  Identities=19%  Similarity=0.487  Sum_probs=87.2

Q ss_pred             CCcccCccCCCcccccCC------cEEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccccc
Q 040426            7 RDFLFCKFCGTMLRMESN------HVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKR   80 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~------~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~   80 (120)
                      ..|.|||+|||||+|+++      .|+|++|||++++++    ..+|+....   +..++. ..|+.++..|+++|+++.
T Consensus         2 ~~m~FCp~Cgn~L~~~~~~~~~~~~~~C~~C~y~~~~~~----~~v~~~~~~---~~~~e~-~~v~~~~~~~~tlp~~~~   73 (113)
T 3h0g_I            2 SNFQYCIECNNMLYPREDKVDRVLRLACRNCDYSEIAAT----SKVYRHELQ---SSNVEN-TTVSHDASTDPTLPRSDK   73 (113)
T ss_dssp             -CCCCCSSSCCCCEECCCTTTCCCCEECSSSCCEECCSC----SEEEECCCC---SCSCTT-CTTCTTSTTCSSSCBCCS
T ss_pred             CcceeCcCCCCEeeEcccCCCCeeEEECCCCCCeEEcCC----CeEEEEEEe---cccccc-cceeccccccccCCCccc
Confidence            468999999999999975      299999999999876    356654321   112222 236777778999999999


Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      .||+|||++|+|||+|+||||||||+||+|++|||+|++
T Consensus        74 ~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~~w~~  112 (113)
T 3h0g_I           74 ECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFAFEE  112 (113)
T ss_dssp             CCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCCCCCC
T ss_pred             CCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCCEEec
Confidence            999999999999999999999999999999999999997

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=100.00  E-value=5.3e-43  Score=240.36  Aligned_cols=107  Identities=30%  Similarity=0.582  Sum_probs=34.0

Q ss_pred             CCCcccCccCCCcccccCCc------EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCcccccccccc
Q 040426            6 GRDFLFCKFCGTMLRMESNH------VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVK   79 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~~~~~------~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~   79 (120)
                      ..+|+|||+|||||+|+++.      |+|++|||++++++    .++|+....   ...+.+ ..++.++..||++|+++
T Consensus        21 ~~~~~FCPeCgNmL~pked~~~~~l~~~CrtCgY~~~~~~----~~v~r~~~~---~~~~e~-~~vv~dv~~dptlp~t~   92 (133)
T 3qt1_I           21 MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGS----PLVYRHELI---TNIGET-AGVVQDIGSDPTLPRSD   92 (133)
T ss_dssp             -CCCCBCTTTCCBCBCCBCTTTCCBCCBCSSSCCBCCCSC----SEEEECCC----------------------------
T ss_pred             ccCCeeCCCCCCEeeECccCCCceeEEECCCCCCcEEcCC----ceEEEEEee---cccccc-ceeEeeccccccCCccc
Confidence            35689999999999999752      99999999998876    467765432   112222 23556667789999999


Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES  120 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n  120 (120)
                      +.||+|||++|+|||+|+||||||||+||+|++|||+|++|
T Consensus        93 ~~CpkCg~~~a~f~q~Q~RsaDE~mT~fy~C~~C~~~w~en  133 (133)
T 3qt1_I           93 RECPKCHSRENVFFQLQIRSADEPMTTFYKCVNCGHRWKEN  133 (133)
T ss_dssp             -----------------------------------------
T ss_pred             CCCCCCCCceEEEEEEeeecCCCCCcEEEEcCCCCCEeCcC
Confidence            99999999999999999999999999999999999999997

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

Probab=99.93  E-value=8e-27  Score=138.66  Aligned_cols=50  Identities=36%  Similarity=0.701  Sum_probs=47.3

Q ss_pred             cccccccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426           71 GETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES  120 (120)
Q Consensus        71 ~~~t~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n  120 (120)
                      .++++|++.++||+|||++|+|+|+|+||||||||+||+|++|||+|++|
T Consensus         7 ~~~~~~~~~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~~~   56 (57)
T 1qyp_A            7 DLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRSY   56 (57)
T ss_dssp             CCSSSCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEECC
T ss_pred             hhhcCCceEeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCEeccC
Confidence            46888888999999999999999999999999999999999999999985

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=99.93  E-value=1.4e-26  Score=134.07  Aligned_cols=43  Identities=40%  Similarity=0.689  Sum_probs=40.7

Q ss_pred             cccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           77 KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      +.+..||+|||++|+|||+|+||||||||+||+|++|||+|+-
T Consensus         7 t~~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~w~~   49 (50)
T 1tfi_A            7 TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWKF   49 (50)
T ss_dssp             CCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEEC
T ss_pred             eCccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCeEEe
Confidence            5678999999999999999999999999999999999999983

>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A

Probab=99.82  E-value=1.9e-21  Score=138.97  Aligned_cols=47  Identities=32%  Similarity=0.616  Sum_probs=42.6

Q ss_pred             ccccc---cccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           72 ETQLS---KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        72 ~~t~~---~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +|+++   +....||+|||++|+|||+|+||||||||+||+|++|||+|+
T Consensus       127 ~~~~~~~~t~~~~Cp~C~~~~a~~~q~Q~rsaDE~mt~f~~C~~C~~~w~  176 (178)
T 3po3_S          127 GATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNRWK  176 (178)
T ss_dssp             CCCCCCCCBSSSCCSSSCCSCEECCCCCCSCTTSCCCCCEEETTTCCEEC
T ss_pred             hccccCCCcCCcCCCCCCCCceEEEEeecccCCCCCcEEEEcCCCCCeec
Confidence            35544   457899999999999999999999999999999999999997

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

Probab=99.76  E-value=3e-19  Score=137.07  Aligned_cols=42  Identities=40%  Similarity=0.735  Sum_probs=39.8

Q ss_pred             cccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           77 KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +....||+|||++++|||+|+||||||||+||+|++|||+|+
T Consensus       266 ~~~~~C~~C~~~~~~~~q~Q~rsaDe~~t~f~~C~~Cg~~w~  307 (309)
T 1pqv_S          266 TDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWK  307 (309)
T ss_pred             cccccCCCCCCCeeEEEEeecccCCCCCcEEEEeCCCCCcee
Confidence            346789999999999999999999999999999999999997

>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=98.05  E-value=3e-06  Score=49.22  Aligned_cols=30  Identities=23%  Similarity=0.677  Sum_probs=23.9

Q ss_pred             CCcccCccCCCccccc--CCcEEeCCCCCeee
Q 040426            7 RDFLFCKFCGTMLRME--SNHVVCSSCKFKKN   36 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~--~~~~~C~~C~~~~~   36 (120)
                      ..+.|||.||+++...  .+++.|.+|||++-
T Consensus        16 ~~~~fCPkCG~~~~ma~~~dr~~C~kCgyt~~   47 (55)
T 2k4x_A           16 RKHRFCPRCGPGVFLAEHADRYSCGRCGYTEF   47 (55)
T ss_dssp             CSSCCCTTTTTTCCCEECSSEEECTTTCCCEE
T ss_pred             EccccCcCCCCceeEeccCCEEECCCCCCEEE
Confidence            3478999999977644  34599999999863

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

Probab=97.67  E-value=2.1e-05  Score=44.77  Aligned_cols=31  Identities=23%  Similarity=0.597  Sum_probs=24.6

Q ss_pred             CCCcccCccCCC--cccccCCcEEeCCCCCeee
Q 040426            6 GRDFLFCKFCGT--MLRMESNHVVCSSCKFKKN   36 (120)
Q Consensus         6 ~~~~~FCp~Cgn--lL~~~~~~~~C~~C~~~~~   36 (120)
                      .....|||.||.  ++.+..++++|..|||++-
T Consensus        16 ~~~~k~CP~CG~~~fm~~~~~R~~C~kCG~t~~   48 (50)
T 3j20_Y           16 IRKNKFCPRCGPGVFMADHGDRWACGKCGYTEW   48 (50)
T ss_dssp             ECSSEECSSSCSSCEEEECSSEEECSSSCCEEE
T ss_pred             EEecccCCCCCCceEEecCCCeEECCCCCCEEE
Confidence            345789999998  6666666699999999863

>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1

Probab=97.45  E-value=0.00028  Score=53.91  Aligned_cols=71  Identities=18%  Similarity=0.465  Sum_probs=48.9

Q ss_pred             CcccCccCCCcccc---c----CCc---EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCcccccccc
Q 040426            8 DFLFCKFCGTMLRM---E----SNH---VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSK   77 (120)
Q Consensus         8 ~~~FCp~CgnlL~~---~----~~~---~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~   77 (120)
                      ...+||.||+.=..   .    .++   +.|..|++....                                        
T Consensus       181 ~~~~CPvCGs~P~~s~l~~~g~~~G~R~l~Cs~C~t~W~~----------------------------------------  220 (309)
T 2fiy_A          181 SRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHY----------------------------------------  220 (309)
T ss_dssp             TCSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEEC----------------------------------------
T ss_pred             cCCCCCCCCCcCceeEEeecCCCCCcEEEEeCCCCCEEee----------------------------------------
Confidence            35799999975322   1    122   999999998743                                        


Q ss_pred             ccccccccCCC-ceEEEEeecccC--CCCceEEEEcCCCCceec
Q 040426           78 VKRACEKCQNP-EMYYSTRQTRSA--DEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        78 ~~~~CpkCg~~-ea~y~~~Q~RSA--DE~~T~fY~C~~C~~~w~  118 (120)
                      ....||.||+. ...||++-.-++  +++....+.|.+|++.++
T Consensus       221 ~R~~C~~Cg~~~~l~y~~~e~~~~~~~~~~~r~e~C~~C~~YlK  264 (309)
T 2fiy_A          221 VRIKCSHCEESKHLAYLSLEHDGQPAEKAVLRAETCPSCQGYLK  264 (309)
T ss_dssp             CTTSCSSSCCCSCCEEECCCC-CCCSTTCSEEEEEETTTTEEEE
T ss_pred             cCcCCcCCCCCCCeeEEEecCccccCCCcceEEEEcccccchHh
Confidence            24569999996 456765521111  457789999999998775

>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1

Probab=96.27  E-value=0.0049  Score=32.41  Aligned_cols=32  Identities=25%  Similarity=0.595  Sum_probs=26.5

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +.||.||+++-.+.-       +.-.+|.+|..||+++.
T Consensus         1 VlC~~C~~peT~l~~-------~~~~~~l~C~aCG~~~~   32 (36)
T 1k81_A            1 VICRECGKPDTKIIK-------EGRVHLLKCMACGAIRP   32 (36)
T ss_dssp             CCCSSSCSCEEEEEE-------ETTEEEEEEETTTEEEE
T ss_pred             CCCcCCCCCCcEEEE-------eCCcEEEEhhcCCCccc
Confidence            469999999997654       35789999999999875

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

Probab=95.47  E-value=0.0092  Score=33.08  Aligned_cols=15  Identities=20%  Similarity=0.472  Sum_probs=12.6

Q ss_pred             cccccccCCCceEEE
Q 040426           79 KRACEKCQNPEMYYS   93 (120)
Q Consensus        79 ~~~CpkCg~~ea~y~   93 (120)
                      ++.||.||+.+..|-
T Consensus        30 dw~CP~Cg~~k~~F~   44 (46)
T 6rxn_A           30 DWCCPVCGVSKDQFS   44 (46)
T ss_dssp             TCBCTTTCCBGGGEE
T ss_pred             CCcCcCCCCcHHHcE
Confidence            578999999987764

>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=95.11  E-value=0.0086  Score=40.25  Aligned_cols=28  Identities=32%  Similarity=0.923  Sum_probs=21.1

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      -.||+|+..-.|-        | |.  .|+|+.|+|.|.
T Consensus        28 P~CP~C~seytYe--------D-g~--l~vCPeC~hEW~   55 (138)
T 2akl_A           28 PPCPQCNSEYTYE--------D-GA--LLVCPECAHEWS   55 (138)
T ss_dssp             CCCTTTCCCCCEE--------C-SS--SEEETTTTEEEC
T ss_pred             CCCCCCCCcceEe--------c-CC--eEECCccccccC
Confidence            4699999876652        1 11  299999999996

>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=95.06  E-value=0.0098  Score=35.94  Aligned_cols=29  Identities=31%  Similarity=0.607  Sum_probs=25.0

Q ss_pred             ccCccCCCcccccCCc--EEeCCCCCeeecccc
Q 040426           10 LFCKFCGTMLRMESNH--VVCSSCKFKKNVQDV   40 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~~   40 (120)
                      .=|| ||++++.+...  -.|+ ||....++..
T Consensus         5 v~C~-C~~~~~~~~~~kT~~C~-CG~~~~~~k~   35 (71)
T 1gh9_A            5 FRCD-CGRALYSREGAKTRKCV-CGRTVNVKDR   35 (71)
T ss_dssp             EEET-TSCCEEEETTCSEEEET-TTEEEECCSS
T ss_pred             EECC-CCCEEEEcCCCcEEECC-CCCeeeeceE
Confidence            3599 99999999875  9998 9999988773

>1yk4_A Rubredoxin, RD; electron transport; 0.69A {Pyrococcus abyssi} PDB: 2pya_A 1yk5_A 1bq8_A 1bq9_A* 3kyu_A 3kyv_A 3kyw_A 3kyx_A 3kyy_A 3ryg_A 3rz6_A 3rzt_A 3ss2_A 1brf_A 1caa_A 1cad_A 1vcx_A 1zrp_A 1iu5_A 1iu6_A ...

Probab=94.45  E-value=0.052  Score=30.68  Aligned_cols=17  Identities=18%  Similarity=0.491  Sum_probs=14.0

Q ss_pred             ccccccccCCCceEEEE
Q 040426           78 VKRACEKCQNPEMYYST   94 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~   94 (120)
                      .++.||.||..+..|..
T Consensus        34 ~dw~CP~Cg~~K~~F~~   50 (52)
T 1yk4_A           34 DDWVCPLCGAPKSEFER   50 (52)
T ss_dssp             TTCBCTTTCCBGGGEEE
T ss_pred             CCCcCCCCCCCHHHcEE
Confidence            46789999999887764

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

Probab=94.36  E-value=0.038  Score=32.97  Aligned_cols=36  Identities=17%  Similarity=0.231  Sum_probs=30.0

Q ss_pred             CCCCCcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426            4 PLGRDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus         4 ~~~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      .....+.-||.|+.-|......  +.|..|+..+++.+
T Consensus         3 ~~LL~iL~CP~ck~~L~~~~~~~~LiC~~cg~~YPI~d   40 (68)
T 2jr6_A            3 KKFLDILVCPVTKGRLEYHQDKQELWSRQAKLAYPIKD   40 (68)
T ss_dssp             CSSSCCCBCSSSCCBCEEETTTTEEEETTTTEEEEEET
T ss_pred             hHHhhheECCCCCCcCeEeCCCCEEEcCCCCcEecCCC
Confidence            3456788999999999887543  99999999999877

>3a43_A HYPD, hydrogenase nickel incorporation protein HYPA; [NIFE] hydrogenase maturation, zinc-finger, nickel binding, metal-binding; HET: FME; 2.30A {Pyrococcus kodakaraensis} PDB: 3a44_A*

Probab=94.33  E-value=0.032  Score=37.66  Aligned_cols=14  Identities=14%  Similarity=0.774  Sum_probs=12.3

Q ss_pred             EEeCCCCCeeeccc
Q 040426           26 VVCSSCKFKKNVQD   39 (120)
Q Consensus        26 ~~C~~C~~~~~~~~   39 (120)
                      +.|+.|||....+.
T Consensus        71 ~~C~~CG~~~~~~~   84 (139)
T 3a43_A           71 FKCRNCNYEWKLKE   84 (139)
T ss_dssp             EEETTTCCEEEGGG
T ss_pred             EECCCCCCEEeccc
Confidence            99999999987655

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

Probab=94.29  E-value=0.037  Score=33.21  Aligned_cols=36  Identities=25%  Similarity=0.497  Sum_probs=30.2

Q ss_pred             CCCCCcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426            4 PLGRDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus         4 ~~~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      .....+.-||.|+.-|......  +.|..|+..+++.+
T Consensus         3 ~~LL~iL~CP~ck~~L~~~~~~~~LiC~~cg~~YPI~d   40 (70)
T 2js4_A            3 SRLLDILVCPVCKGRLEFQRAQAELVCNADRLAFPVRD   40 (70)
T ss_dssp             CCCCCCCBCTTTCCBEEEETTTTEEEETTTTEEEEEET
T ss_pred             hHHhhheECCCCCCcCEEeCCCCEEEcCCCCceecCCC
Confidence            3456788999999999877543  99999999999877

>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=94.25  E-value=0.053  Score=31.01  Aligned_cols=18  Identities=11%  Similarity=0.381  Sum_probs=14.9

Q ss_pred             ccccccccCCCceEEEEe
Q 040426           78 VKRACEKCQNPEMYYSTR   95 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~   95 (120)
                      .++.||.||..+..|..+
T Consensus        35 ~dw~CP~Cga~K~~F~~~   52 (55)
T 2v3b_B           35 ADWVCPDCGVGKIDFEMI   52 (55)
T ss_dssp             TTCCCTTTCCCGGGEEEC
T ss_pred             CCCcCCCCCCCHHHceec
Confidence            367899999999888654

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

Probab=94.23  E-value=0.03  Score=31.06  Aligned_cols=29  Identities=21%  Similarity=0.553  Sum_probs=21.4

Q ss_pred             cccCccCCC-cccccCC-c-EEeCCCCCeeec
Q 040426            9 FLFCKFCGT-MLRMESN-H-VVCSSCKFKKNV   37 (120)
Q Consensus         9 ~~FCp~Cgn-lL~~~~~-~-~~C~~C~~~~~~   37 (120)
                      ...||.||. -|..... . ++|..||...+.
T Consensus         5 ~~~CP~C~~~~l~~d~~~gelvC~~CG~v~~e   36 (50)
T 1pft_A            5 QKVCPACESAELIYDPERGEIVCAKCGYVIEE   36 (50)
T ss_dssp             CCSCTTTSCCCEEEETTTTEEEESSSCCBCCC
T ss_pred             cEeCcCCCCcceEEcCCCCeEECcccCCcccc
Confidence            457999998 5554433 3 999999997753

>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=94.21  E-value=0.039  Score=31.53  Aligned_cols=17  Identities=12%  Similarity=0.245  Sum_probs=13.9

Q ss_pred             ccccccccCCCceEEEE
Q 040426           78 VKRACEKCQNPEMYYST   94 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~   94 (120)
                      .++.||.||..+..|..
T Consensus        35 ~dw~CP~Cg~~K~~F~~   51 (54)
T 4rxn_A           35 DDWVCPLCGVGKDEFEE   51 (54)
T ss_dssp             TTCBCTTTCCBGGGEEE
T ss_pred             CCCcCcCCCCcHHHceE
Confidence            36899999999887754

>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle structural genomics center for infectious electron transport, iron; NMR {Mycobacterium tuberculosis}

Probab=94.13  E-value=0.079  Score=32.70  Aligned_cols=19  Identities=11%  Similarity=0.361  Sum_probs=15.6

Q ss_pred             ccccccccCCCceEEEEee
Q 040426           78 VKRACEKCQNPEMYYSTRQ   96 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q   96 (120)
                      .++.||.||..+..|..+.
T Consensus        59 ddW~CPvCga~K~~F~~i~   77 (81)
T 2kn9_A           59 DDWSCPDCGAAKSDFEMVE   77 (81)
T ss_dssp             TTCCCTTTCCCGGGEEEEC
T ss_pred             CCCcCCCCCCCHHHcEEcc
Confidence            3689999999999887653

>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=93.96  E-value=0.061  Score=30.98  Aligned_cols=33  Identities=12%  Similarity=0.214  Sum_probs=22.6

Q ss_pred             CCCCCcccCccCCC-cccccCC-c-EEeCCCCCeee
Q 040426            4 PLGRDFLFCKFCGT-MLRMESN-H-VVCSSCKFKKN   36 (120)
Q Consensus         4 ~~~~~~~FCp~Cgn-lL~~~~~-~-~~C~~C~~~~~   36 (120)
                      +.....+.||+||+ -|..... + ++|..||.+..
T Consensus         6 ~~ll~~~~Cp~C~~~~lv~D~~~ge~vC~~CGlVl~   41 (58)
T 1dl6_A            6 LDALPRVTCPNHPDAILVEDYRAGDMICPECGLVVG   41 (58)
T ss_dssp             CCCCSCCSBTTBSSSCCEECSSSCCEECTTTCCEEC
T ss_pred             hhccccccCcCCCCCceeEeCCCCeEEeCCCCCEEe
Confidence            44455668999987 3333322 3 99999999864

>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=93.84  E-value=0.049  Score=30.82  Aligned_cols=16  Identities=19%  Similarity=0.410  Sum_probs=13.0

Q ss_pred             ccccccccCCCceEEE
Q 040426           78 VKRACEKCQNPEMYYS   93 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~   93 (120)
                      .++.||.||..+..|.
T Consensus        35 ~dw~CP~Cg~~K~~F~   50 (52)
T 1e8j_A           35 DDWACPVCGASKDAFE   50 (52)
T ss_dssp             TTCCCSSSCCCTTSCE
T ss_pred             CCCcCCCCCCcHHHcE
Confidence            3678999999987664

>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=93.78  E-value=0.043  Score=32.84  Aligned_cols=35  Identities=17%  Similarity=0.419  Sum_probs=29.2

Q ss_pred             CCCCcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426            5 LGRDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus         5 ~~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      ....+.-||.|+.-|......  +.|..|+..+++.+
T Consensus         4 ~LLeiL~CP~ck~~L~~~~~~~~LiC~~cg~~YPI~d   40 (69)
T 2pk7_A            4 KLLDILACPICKGPLKLSADKTELISKGAGLAYPIRD   40 (69)
T ss_dssp             CGGGTCCCTTTCCCCEECTTSSEEEETTTTEEEEEET
T ss_pred             HHHhheeCCCCCCcCeEeCCCCEEEcCCCCcEecCcC
Confidence            345678999999999876543  99999999999877

>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=93.75  E-value=0.037  Score=33.03  Aligned_cols=35  Identities=17%  Similarity=0.468  Sum_probs=29.2

Q ss_pred             CCCCcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426            5 LGRDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus         5 ~~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      ....+.-||.|+.-|......  +.|..|+..+++.+
T Consensus         4 ~LL~iL~CP~ck~~L~~~~~~~~LiC~~cg~~YPI~d   40 (68)
T 2hf1_A            4 KFLEILVCPLCKGPLVFDKSKDELICKGDRLAFPIKD   40 (68)
T ss_dssp             CCEEECBCTTTCCBCEEETTTTEEEETTTTEEEEEET
T ss_pred             HHhhheECCCCCCcCeEeCCCCEEEcCCCCcEecCCC
Confidence            345678999999998876543  99999999999877

>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=93.69  E-value=0.062  Score=33.14  Aligned_cols=29  Identities=24%  Similarity=0.591  Sum_probs=21.8

Q ss_pred             CcccCccCCCcccccCCc--EEeCCCCCeee
Q 040426            8 DFLFCKFCGTMLRMESNH--VVCSSCKFKKN   36 (120)
Q Consensus         8 ~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~   36 (120)
                      .+.+||.|++++....+.  +.|..|++..=
T Consensus        24 ~~~wCP~C~~~~~~~~~~~~v~C~~C~~~FC   54 (86)
T 2ct7_A           24 KFLWCAQCSFGFIYEREQLEATCPQCHQTFC   54 (86)
T ss_dssp             CEECCSSSCCCEECCCSCSCEECTTTCCEEC
T ss_pred             CEeECcCCCchheecCCCCceEeCCCCCccc
Confidence            456899999987665443  88988888753

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

Probab=93.54  E-value=0.083  Score=29.16  Aligned_cols=33  Identities=24%  Similarity=0.760  Sum_probs=22.7

Q ss_pred             cccccccCCCceEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426           79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES  120 (120)
Q Consensus        79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n  120 (120)
                      ...||.||.....|-         +.+--.+|..||..+.++
T Consensus         5 ~~~CP~C~~~~l~~d---------~~~gelvC~~CG~v~~e~   37 (50)
T 1pft_A            5 QKVCPACESAELIYD---------PERGEIVCAKCGYVIEEN   37 (50)
T ss_dssp             CCSCTTTSCCCEEEE---------TTTTEEEESSSCCBCCCC
T ss_pred             cEeCcCCCCcceEEc---------CCCCeEECcccCCccccc
Confidence            457999999666552         122238999999977653

>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A

Probab=93.52  E-value=0.074  Score=31.90  Aligned_cols=18  Identities=17%  Similarity=0.501  Sum_probs=15.1

Q ss_pred             ccccccccCCCceEEEEe
Q 040426           78 VKRACEKCQNPEMYYSTR   95 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~   95 (120)
                      .++.||.||..+..|..+
T Consensus        39 ddw~CP~Cga~K~~F~~~   56 (70)
T 1dx8_A           39 DSFMCPACRSPKNQFKSI   56 (70)
T ss_dssp             TTCBCTTTCCBGGGEEEC
T ss_pred             CCCcCCCCCCCHHHceEc
Confidence            367999999999988764

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

Probab=93.14  E-value=0.074  Score=31.63  Aligned_cols=36  Identities=19%  Similarity=0.206  Sum_probs=29.9

Q ss_pred             CCCCCcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426            4 PLGRDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus         4 ~~~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      .....+.-||.|+.-|......  +.|..|+..+++.+
T Consensus         5 ~~LLeiL~CP~ck~~L~~~~~~g~LvC~~c~~~YPI~d   42 (67)
T 2jny_A            5 PQLLEVLACPKDKGPLRYLESEQLLVNERLNLAYRIDD   42 (67)
T ss_dssp             GGGTCCCBCTTTCCBCEEETTTTEEEETTTTEEEEEET
T ss_pred             HHHHHHhCCCCCCCcCeEeCCCCEEEcCCCCccccCCC
Confidence            4456788999999988876543  99999999999876

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=93.12  E-value=0.067  Score=34.92  Aligned_cols=12  Identities=17%  Similarity=0.487  Sum_probs=10.0

Q ss_pred             EEeCCCCCeeec
Q 040426           26 VVCSSCKFKKNV   37 (120)
Q Consensus        26 ~~C~~C~~~~~~   37 (120)
                      +.|+.||+....
T Consensus        74 ~~C~~CG~~~e~   85 (119)
T 2kdx_A           74 LECKDCSHVFKP   85 (119)
T ss_dssp             EECSSSSCEECS
T ss_pred             EEcCCCCCEEeC
Confidence            999999997754

>1s24_A Rubredoxin 2; electron transport; NMR {Pseudomonas oleovorans} SCOP: g.41.5.1

Probab=93.11  E-value=0.08  Score=33.11  Aligned_cols=18  Identities=17%  Similarity=0.342  Sum_probs=14.8

Q ss_pred             ccccccccCCCceEEEEe
Q 040426           78 VKRACEKCQNPEMYYSTR   95 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~   95 (120)
                      .++.||-||..+..|..+
T Consensus        67 ddW~CPvCga~K~~F~~i   84 (87)
T 1s24_A           67 DDWCCPDCGATKEDYVLY   84 (87)
T ss_dssp             TTCCCSSSCCCGGGEEEC
T ss_pred             CCCCCCCCCCCHHHhhhc
Confidence            367999999999888654

>2fnf_X Putative RAS effector NORE1; zinc, signal transduction, apoptosis, cysteine rich domain; NMR {Mus musculus}

Probab=92.82  E-value=0.091  Score=31.46  Aligned_cols=31  Identities=26%  Similarity=0.630  Sum_probs=24.5

Q ss_pred             CCCCcccCccCCCcccccCCcEEeCCCCCeeec
Q 040426            5 LGRDFLFCKFCGTMLRMESNHVVCSSCKFKKNV   37 (120)
Q Consensus         5 ~~~~~~FCp~CgnlL~~~~~~~~C~~C~~~~~~   37 (120)
                      ....+.||..||++|  -..++.|..|+|....
T Consensus        31 ~~~~pt~C~~C~~~l--~~qG~kC~~C~~~cHk   61 (72)
T 2fnf_X           31 LRGGPGWCDLCGREV--LRQALRCANCKFTCHS   61 (72)
T ss_dssp             CCSSCCBCTTTSSBC--SSCCEECTTSSCEECT
T ss_pred             cCCCCcchhhhhHHH--HhCcCccCCCCCeech
Confidence            356788999999999  3334999999998653

>3cng_A Nudix hydrolase; structural genomics, APC7497, PSI-2, protei structure initiative; 2.00A {Nitrosomonas europaea atcc 19718}

Probab=92.81  E-value=0.054  Score=37.36  Aligned_cols=28  Identities=21%  Similarity=0.662  Sum_probs=21.1

Q ss_pred             CcccCccCCCcccccC-C-----cEEeCCCCCee
Q 040426            8 DFLFCKFCGTMLRMES-N-----HVVCSSCKFKK   35 (120)
Q Consensus         8 ~~~FCp~CgnlL~~~~-~-----~~~C~~C~~~~   35 (120)
                      .++|||.||..|.... +     ...|..|++..
T Consensus         2 ~~~~C~~CG~~~~~~~~~G~~~~~~~~~~~~~~~   35 (189)
T 3cng_A            2 HMKFCSQCGGEVILRIPEGDTLPRYICPKCHTIH   35 (189)
T ss_dssp             -CCBCTTTCCBCEEECCTTCSSCEEEETTTTEEE
T ss_pred             CcccCchhCCccccccccCCCCcceECCCCCCcc
Confidence            4789999999997642 1     28999999543

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=92.57  E-value=0.071  Score=37.26  Aligned_cols=29  Identities=21%  Similarity=0.436  Sum_probs=25.0

Q ss_pred             cccCccCCCcccccCCcEEeCCCCCeeec
Q 040426            9 FLFCKFCGTMLRMESNHVVCSSCKFKKNV   37 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~~~~C~~C~~~~~~   37 (120)
                      ...|++||+.|.|..+.+.|+.||..+..
T Consensus       140 ~a~~~~~g~~m~~~~~~~~cp~~g~~e~R  168 (179)
T 3m7n_A          140 RALCSNCKTEMVREGDILKCPECGRVEKR  168 (179)
T ss_dssp             ECBCTTTCCBCEECSSSEECSSSCCEECC
T ss_pred             EecccccCCceEECCCEEECCCCCCEEEE
Confidence            45899999999998755999999998864

>1lko_A Rubrerythrin all-iron(II) form; reduced form, DIIRON, four-helix bundle, rubre like, electron transport; 1.63A {Desulfovibrio vulgaris} SCOP: a.25.1.1 g.41.5.1 PDB: 1dvb_A 1jyb_A 1b71_A 1lkm_A 1lkp_A 1qyb_A 1s2z_A 1s30_A 1ryt_A

Probab=92.44  E-value=0.056  Score=38.18  Aligned_cols=14  Identities=21%  Similarity=0.757  Sum_probs=11.7

Q ss_pred             cccccCCCceEEEE
Q 040426           81 ACEKCQNPEMYYST   94 (120)
Q Consensus        81 ~CpkCg~~ea~y~~   94 (120)
                      .||.||+++..|-.
T Consensus       173 ~CP~C~~~k~~f~~  186 (191)
T 1lko_A          173 LCPACAHPKAHFEL  186 (191)
T ss_dssp             BCTTTCCBGGGEEE
T ss_pred             CCCCCcCCHHHHHh
Confidence            79999999887743

>1rfh_A RAS association (ralgds/AF-6) domain family 5; zinc, signal transduction, apoptosis, cysteine rich domain, metal binding protein; NMR {Mus musculus}

Probab=92.07  E-value=0.1  Score=29.89  Aligned_cols=30  Identities=27%  Similarity=0.662  Sum_probs=23.8

Q ss_pred             CCCCcccCccCCCcccccCCcEEeCCCCCeee
Q 040426            5 LGRDFLFCKFCGTMLRMESNHVVCSSCKFKKN   36 (120)
Q Consensus         5 ~~~~~~FCp~CgnlL~~~~~~~~C~~C~~~~~   36 (120)
                      ....+.||..||++|  -..++.|..|++...
T Consensus        18 ~~~~pt~C~~C~~~i--~kqg~kC~~C~~~cH   47 (59)
T 1rfh_A           18 LRGGPGWCDLCGREV--LRQALRCANCKFTCH   47 (59)
T ss_dssp             CSSCCEECTTTCSEE--CSCCEECTTTSCEEC
T ss_pred             ccCCCeEchhcchhh--hhCccEeCCCCCeEe
Confidence            346688999999999  233499999999764

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

Probab=92.02  E-value=0.21  Score=28.56  Aligned_cols=36  Identities=22%  Similarity=0.482  Sum_probs=30.7

Q ss_pred             CCCCCcccCccCCCcccccCCcEEeC--CCCCeeeccc
Q 040426            4 PLGRDFLFCKFCGTMLRMESNHVVCS--SCKFKKNVQD   39 (120)
Q Consensus         4 ~~~~~~~FCp~CgnlL~~~~~~~~C~--~C~~~~~~~~   39 (120)
                      .....+.-||.|+.-|....+.+.|.  .|+..+++.+
T Consensus         5 ~~lL~iL~CP~c~~~L~~~~~~L~C~~~~c~~~YPI~d   42 (56)
T 2kpi_A            5 AGLLEILACPACHAPLEERDAELICTGQDCGLAYPVRD   42 (56)
T ss_dssp             CSCTTSCCCSSSCSCEEEETTEEEECSSSCCCEEEEET
T ss_pred             HHHHhheeCCCCCCcceecCCEEEcCCcCCCcEEeeEC
Confidence            44567889999999998887669999  9999999876

>1x0t_A Ribonuclease P protein component 4; pyrococcus horikoshii OT3, hydrolase; 1.60A {Pyrococcus horikoshii} PDB: 2zae_B

Probab=91.89  E-value=0.19  Score=33.04  Aligned_cols=35  Identities=29%  Similarity=0.533  Sum_probs=26.6

Q ss_pred             CCCCCCcccCccCCCcccccCC-----------c--EEeCCCCCeeec
Q 040426            3 DPLGRDFLFCKFCGTMLRMESN-----------H--VVCSSCKFKKNV   37 (120)
Q Consensus         3 ~~~~~~~~FCp~CgnlL~~~~~-----------~--~~C~~C~~~~~~   37 (120)
                      .+....-.||..||++|.|-.+           .  +.|-.||++.-.
T Consensus        59 lp~~~KR~~Ck~C~s~LiPG~t~~vri~~~~~~~vv~tCl~Cg~~kR~  106 (120)
T 1x0t_A           59 IPRKWKRRYCKRCHTFLIPGVNARVRLRTKRMPHVVITCLECGYIMRY  106 (120)
T ss_dssp             CCTTTTTSBCTTTCCBCCBTTTEEEEEECSSSCEEEEEETTTCCEEEE
T ss_pred             CCHHHHHHhccCCCCEeECCCceEEEEecCCccEEEEECCCCCCEEEE
Confidence            3444556799999999998753           1  789999998654

>2k3r_A Ribonuclease P protein component 4; PFU RPP21, RNAse P, hydrolase, tRNA processing; NMR {Pyrococcus furiosus} PDB: 2ki7_B

Probab=91.49  E-value=0.19  Score=33.24  Aligned_cols=35  Identities=26%  Similarity=0.383  Sum_probs=26.7

Q ss_pred             CCCCCCcccCccCCCcccccCCc-------------EEeCCCCCeeec
Q 040426            3 DPLGRDFLFCKFCGTMLRMESNH-------------VVCSSCKFKKNV   37 (120)
Q Consensus         3 ~~~~~~~~FCp~CgnlL~~~~~~-------------~~C~~C~~~~~~   37 (120)
                      .+....-.||..||++|.|-.+.             +.|-.||++.-.
T Consensus        54 lp~~~KR~~Ck~C~s~LIPG~t~~vri~~~~k~~vv~tCl~Cg~~kR~  101 (123)
T 2k3r_A           54 IPRKWKRRYCKKCHAFLVPGINARVRLRQKRMPHIVVKCLECGHIMRY  101 (123)
T ss_dssp             CSSTTTTSBCTTTCCBCCBTTTEEEEEECSSSCEEEEEETTTTEEEEE
T ss_pred             CCHHHHHHhccCCCCEeECCCceEEEEecCCccEEEEECCCCCCEEEE
Confidence            34445567999999999987531             889999998654

>1vk6_A NADH pyrophosphatase; 1790429, structural genomics, JCSG, PS protein structure initiative, joint center for structural G hydrolase; HET: MSE; 2.20A {Escherichia coli} SCOP: d.113.1.4 d.113.1.4 g.41.14.1 PDB: 2gb5_A

Probab=91.25  E-value=0.12  Score=38.21  Aligned_cols=30  Identities=23%  Similarity=0.729  Sum_probs=24.6

Q ss_pred             CCcccCccCCCcccccCCc--EEeCCCCCeee
Q 040426            7 RDFLFCKFCGTMLRMESNH--VVCSSCKFKKN   36 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~   36 (120)
                      ..++|||.||.-+....+.  ..|..|++..-
T Consensus       105 ~~~~fC~~CG~~~~~~~~~~~~~C~~C~~~~y  136 (269)
T 1vk6_A          105 RSHKYCGYCGHEMYPSKTEWAMLCSHCRERYY  136 (269)
T ss_dssp             HTTSBCTTTCCBEEECSSSSCEEESSSSCEEC
T ss_pred             hcCCccccCCCcCccCCCceeeeCCCCCCEec
Confidence            3578999999999776554  99999999754

>3pwf_A Rubrerythrin; non heme iron peroxidases, oxidative stress, oxidoreductase; 1.64A {Pyrococcus furiosus} PDB: 3mps_A 3pza_A 3qvd_A 1nnq_A 2hr5_A

Probab=91.25  E-value=0.096  Score=36.43  Aligned_cols=14  Identities=21%  Similarity=0.622  Sum_probs=11.6

Q ss_pred             cccccCCCceEEEE
Q 040426           81 ACEKCQNPEMYYST   94 (120)
Q Consensus        81 ~CpkCg~~ea~y~~   94 (120)
                      .||-||+++..|-.
T Consensus       155 ~CP~Cg~~~~~F~~  168 (170)
T 3pwf_A          155 YCPVCGAPKEKFVV  168 (170)
T ss_dssp             BCTTTCCBGGGCEE
T ss_pred             CCCCCCCCHHHcee
Confidence            79999999887653

>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=91.19  E-value=0.073  Score=32.96  Aligned_cols=31  Identities=23%  Similarity=0.302  Sum_probs=22.4

Q ss_pred             cccCccCCCcccccC-Cc-EEeCCCCCeeeccc
Q 040426            9 FLFCKFCGTMLRMES-NH-VVCSSCKFKKNVQD   39 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~-~~-~~C~~C~~~~~~~~   39 (120)
                      ...||.||.-+.... .. |.|+.|++...--.
T Consensus        27 ~y~Cp~CG~~~v~r~atGiW~C~~Cg~~~agga   59 (83)
T 1vq8_Z           27 DHACPNCGEDRVDRQGTGIWQCSYCDYKFTGGS   59 (83)
T ss_dssp             CEECSSSCCEEEEEEETTEEEETTTCCEEECCS
T ss_pred             cCcCCCCCCcceeccCCCeEECCCCCCEecCCE
Confidence            358999998554433 33 99999999876543

>4esj_A Type-2 restriction enzyme DPNI; restriction endonuclease-DNA complex, type IIM, type IIE, RE enzyme, DPNI; HET: DNA 6MA; 2.05A {Streptococcus pneumoniae}

Probab=91.18  E-value=0.1  Score=38.40  Aligned_cols=32  Identities=25%  Similarity=0.620  Sum_probs=22.7

Q ss_pred             cccCccCCCc-c-cccCCc----EEeCCCCCeeecccc
Q 040426            9 FLFCKFCGTM-L-RMESNH----VVCSSCKFKKNVQDV   40 (120)
Q Consensus         9 ~~FCp~Cgnl-L-~~~~~~----~~C~~C~~~~~~~~~   40 (120)
                      -.+||.||+. | ..+.++    |.|..|+-..+.++.
T Consensus        34 n~yCPnCG~~~l~~f~nN~PVaDF~C~~C~EeyELKSk   71 (257)
T 4esj_A           34 QSYCPNCGNNPLNHFENNRPVADFYCNHCSEEFELKSK   71 (257)
T ss_dssp             HCCCTTTCCSSCEEC----CCCEEECTTTCCEEEEEEE
T ss_pred             CCcCCCCCChhhhhccCCCcccccccCCcchhheeccc
Confidence            4699999994 4 444443    999999999887763

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

Probab=90.86  E-value=0.13  Score=33.48  Aligned_cols=33  Identities=18%  Similarity=0.366  Sum_probs=21.5

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      .-||+||+--.      .+..++.-.+.|.|..|+|.+-
T Consensus         5 ~FCp~Cgn~L~------~~~~~~~~~~~~~C~~C~y~~~   37 (113)
T 3h0g_I            5 QYCIECNNMLY------PREDKVDRVLRLACRNCDYSEI   37 (113)
T ss_dssp             CCCSSSCCCCE------ECCCTTTCCCCEECSSSCCEEC
T ss_pred             eeCcCCCCEee------EcccCCCCeeEEECCCCCCeEE
Confidence            45999998622      2333333456788999998763

>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=90.60  E-value=0.07  Score=30.11  Aligned_cols=25  Identities=24%  Similarity=0.574  Sum_probs=19.4

Q ss_pred             CcccCccCCCcccccCCcEEeCCCCCe
Q 040426            8 DFLFCKFCGTMLRMESNHVVCSSCKFK   34 (120)
Q Consensus         8 ~~~FCp~CgnlL~~~~~~~~C~~C~~~   34 (120)
                      ...-||.||..+.+  ..+.|+.|||.
T Consensus        13 ~k~iCpkC~a~~~~--gaw~CrKCG~~   37 (51)
T 3j21_g           13 KKYVCLRCGATNPW--GAKKCRKCGYK   37 (51)
T ss_dssp             SEEECTTTCCEECT--TCSSCSSSSSC
T ss_pred             CCccCCCCCCcCCC--CceecCCCCCc
Confidence            45689999998332  23999999998

>1faq_A RAF-1; transferase, serine/threonine-protein kinase, proto- oncogene, zinc, ATP-binding, phorbol-ester binding; NMR {Homo sapiens} SCOP: g.49.1.1 PDB: 1far_A

Probab=90.46  E-value=0.17  Score=27.85  Aligned_cols=29  Identities=28%  Similarity=0.647  Sum_probs=23.6

Q ss_pred             CCCcccCccCCCcccccCCcEEeCCCCCeeec
Q 040426            6 GRDFLFCKFCGTMLRMESNHVVCSSCKFKKNV   37 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~~~~~~~C~~C~~~~~~   37 (120)
                      ...+.||..|+.+|.   .++.|+.|++....
T Consensus        11 ~~~pt~C~~C~~~l~---qG~~C~~C~~~~H~   39 (52)
T 1faq_A           11 FLKLAFCDICQKFLL---NGFRCQTCGYKFHE   39 (52)
T ss_dssp             CSSCEECTTSSSEEC---SEEECTTTTCCBCS
T ss_pred             CCCCcCCCCcccccc---cCCEeCCCCCeECh
Confidence            345789999999997   45999999987643

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=90.45  E-value=0.082  Score=35.51  Aligned_cols=34  Identities=24%  Similarity=0.479  Sum_probs=23.7

Q ss_pred             cccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           79 KRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        79 ~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      -.-||+||+-      |..+...+.-.+.|.|.+|+|.+.
T Consensus        24 ~~FCPeCgNm------L~pked~~~~~l~~~CrtCgY~~~   57 (133)
T 3qt1_I           24 FRFCRDCNNM------LYPREDKENNRLLFECRTCSYVEE   57 (133)
T ss_dssp             CCBCTTTCCB------CBCCBCTTTCCBCCBCSSSCCBCC
T ss_pred             CeeCCCCCCE------eeECccCCCceeEEECCCCCCcEE
Confidence            4569999984      233444444577899999999753

>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=90.19  E-value=0.17  Score=30.29  Aligned_cols=26  Identities=23%  Similarity=0.614  Sum_probs=19.4

Q ss_pred             cCccCCCcccccCC-cEEeCCCCCeee
Q 040426           11 FCKFCGTMLRMESN-HVVCSSCKFKKN   36 (120)
Q Consensus        11 FCp~CgnlL~~~~~-~~~C~~C~~~~~   36 (120)
                      -|++||....+... .+.|+.||+..-
T Consensus        30 ~C~~CG~~~e~~~~d~irCp~CG~RIL   56 (70)
T 1twf_L           30 ICAECSSKLSLSRTDAVRCKDCGHRIL   56 (70)
T ss_dssp             ECSSSCCEECCCTTSTTCCSSSCCCCC
T ss_pred             ECCCCCCcceeCCCCCccCCCCCceEe
Confidence            59999988655543 389999999543

>1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron transfer, DIIR center, oxidoreductase; 1.40A {Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1 PDB: 1yv1_A 1yux_A

Probab=90.19  E-value=0.12  Score=36.80  Aligned_cols=14  Identities=21%  Similarity=0.681  Sum_probs=11.7

Q ss_pred             ccccccCCCceEEE
Q 040426           80 RACEKCQNPEMYYS   93 (120)
Q Consensus        80 ~~CpkCg~~ea~y~   93 (120)
                      +.||-||+++..|.
T Consensus       187 ~~CP~C~~~k~~F~  200 (202)
T 1yuz_A          187 EKCPICFRPKDTFT  200 (202)
T ss_dssp             SBCTTTCCBGGGCE
T ss_pred             CCCCCCCCChHHhe
Confidence            67999999987664

>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=89.70  E-value=0.29  Score=28.07  Aligned_cols=30  Identities=23%  Similarity=0.605  Sum_probs=20.9

Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      .||.||....+|=      .+.|.   ++|..||....+
T Consensus        13 ~Cp~C~~~~lv~D------~~~ge---~vC~~CGlVl~e   42 (58)
T 1dl6_A           13 TCPNHPDAILVED------YRAGD---MICPECGLVVGD   42 (58)
T ss_dssp             SBTTBSSSCCEEC------SSSCC---EECTTTCCEECC
T ss_pred             cCcCCCCCceeEe------CCCCe---EEeCCCCCEEec
Confidence            6999999776551      11222   889999987654

>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=89.68  E-value=0.25  Score=30.54  Aligned_cols=31  Identities=19%  Similarity=0.448  Sum_probs=22.6

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      ....||.||.+ ++|-.         .+-...|..||+.+.
T Consensus        26 ~~y~Cp~CG~~-~v~r~---------atGiW~C~~Cg~~~a   56 (83)
T 1vq8_Z           26 EDHACPNCGED-RVDRQ---------GTGIWQCSYCDYKFT   56 (83)
T ss_dssp             SCEECSSSCCE-EEEEE---------ETTEEEETTTCCEEE
T ss_pred             ccCcCCCCCCc-ceecc---------CCCeEECCCCCCEec
Confidence            46789999974 44533         234799999999864

>1ptq_A Protein kinase C delta type; phosphotransferase; 1.95A {Mus musculus} SCOP: g.49.1.1 PDB: 1ptr_A*

Probab=89.66  E-value=0.35  Score=26.25  Aligned_cols=31  Identities=23%  Similarity=0.560  Sum_probs=24.2

Q ss_pred             CCCcccCccCCCcccc-cCCcEEeCCCCCeee
Q 040426            6 GRDFLFCKFCGTMLRM-ESNHVVCSSCKFKKN   36 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~-~~~~~~C~~C~~~~~   36 (120)
                      ...+.||..|+.+|.- ....+.|..|++...
T Consensus         8 ~~~pt~C~~C~~~l~g~~~qg~~C~~C~~~~H   39 (50)
T 1ptq_A            8 YMSPTFCDHCGSLLWGLVKQGLKCEDCGMNVH   39 (50)
T ss_dssp             CSSCCBCTTTCCBCCSSSSCEEEETTTCCEEC
T ss_pred             CCCCCCcCCCCceeeccCCccCEeCCCCCeEC
Confidence            4568899999999963 234499999998754

>2con_A RUH-035 protein, NIN one binding protein; ribosome, RNA binding protein, unknown function, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.41.15.1

Probab=89.45  E-value=0.12  Score=31.77  Aligned_cols=14  Identities=29%  Similarity=0.752  Sum_probs=10.9

Q ss_pred             CCCCcccCccCCCc
Q 040426            5 LGRDFLFCKFCGTM   18 (120)
Q Consensus         5 ~~~~~~FCp~Cgnl   18 (120)
                      ..++-.|||.|||-
T Consensus        26 ~~~~k~FCp~CGn~   39 (79)
T 2con_A           26 SDMNRVFCGHCGNK   39 (79)
T ss_dssp             SCSSCCSCSSSCCS
T ss_pred             CCcccccccccCcc
Confidence            34567899999984

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=88.75  E-value=0.32  Score=28.53  Aligned_cols=30  Identities=17%  Similarity=0.534  Sum_probs=23.9

Q ss_pred             ccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426           10 LFCKFCGTMLRMESNH-VVCSSCKFKKNVQD   39 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~   39 (120)
                      --|.+||....++... +.|+.|||..-.+.
T Consensus        22 Y~C~~Cg~~~~l~~~~~iRC~~CG~RILyK~   52 (63)
T 3h0g_L           22 YLCADCGARNTIQAKEVIRCRECGHRVMYKM   52 (63)
T ss_dssp             CBCSSSCCBCCCCSSSCCCCSSSCCCCCBCC
T ss_pred             EECCCCCCeeecCCCCceECCCCCcEEEEEe
Confidence            4699999998887654 99999999765444

>2g2k_A EIF-5, eukaryotic translation initiation factor 5; EIF125 fold; NMR {Homo sapiens}

Probab=88.35  E-value=0.44  Score=33.23  Aligned_cols=32  Identities=34%  Similarity=0.648  Sum_probs=26.6

Q ss_pred             ccccccCCCceEEEEeecccCC-CCceEEEEcCCCCcee
Q 040426           80 RACEKCQNPEMYYSTRQTRSAD-EGQTTYYICPRCGHRC  117 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSAD-E~~T~fY~C~~C~~~w  117 (120)
                      +.|+.|++++..+.-      | +.-.+|-.|..||++-
T Consensus        97 VlC~~C~sPdT~L~k------~~~~r~~~l~C~ACGa~~  129 (170)
T 2g2k_A           97 VLCPECENPETDLHV------NPKKQTIGNSCKACGYRG  129 (170)
T ss_dssp             HSCTTTSSSCEEEEE------ETTTTEEEEEETTTCCCC
T ss_pred             EECCCCCCCccEEEE------ecCCCEEEEEccccCCcc
Confidence            689999999997753      3 5788999999999864

>2enz_A NPKC-theta, protein kinase C theta type; zinc binding, DAG/PE-binding protein, diacylglycerol, phorbol ester, TCR, T-cell, structural genomics; NMR {Homo sapiens}

Probab=87.52  E-value=0.61  Score=26.92  Aligned_cols=32  Identities=25%  Similarity=0.611  Sum_probs=24.6

Q ss_pred             CCCcccCccCCCcccc-cCCcEEeCCCCCeeec
Q 040426            6 GRDFLFCKFCGTMLRM-ESNHVVCSSCKFKKNV   37 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~-~~~~~~C~~C~~~~~~   37 (120)
                      ...+.||..|+.+|.- -...+.|..|++....
T Consensus        20 ~~~pt~C~~C~~~l~Gl~~qg~~C~~C~~~~Hk   52 (65)
T 2enz_A           20 YKSPTFCEHCGTLLWGLARQGLKCDACGMNVHH   52 (65)
T ss_dssp             CCSCCBCSSSCCBCCCSSSCSEEESSSCCEECT
T ss_pred             CCCCcCchhcChhheecCCcccccCCCCCccCH
Confidence            4567899999999974 2334999999997653

>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=87.08  E-value=0.43  Score=31.98  Aligned_cols=30  Identities=20%  Similarity=0.490  Sum_probs=24.8

Q ss_pred             CcccCccCCCcccccCCc-EEeCCCCCeeec
Q 040426            8 DFLFCKFCGTMLRMESNH-VVCSSCKFKKNV   37 (120)
Q Consensus         8 ~~~FCp~CgnlL~~~~~~-~~C~~C~~~~~~   37 (120)
                      .+.=||.|++-...+.+. |+|+-|++.+..
T Consensus        26 ~lP~CP~C~seytYeDg~l~vCPeC~hEW~~   56 (138)
T 2akl_A           26 TLPPCPQCNSEYTYEDGALLVCPECAHEWSP   56 (138)
T ss_dssp             CSCCCTTTCCCCCEECSSSEEETTTTEEECT
T ss_pred             cCCCCCCCCCcceEecCCeEECCccccccCC
Confidence            467899999987777655 999999999953

>3uej_A NPKC-delta, protein kinase C delta type; proteine kinase cdelta, phosphotransferase, anesthetic bindi metal binding protein; 1.30A {Mus musculus} PDB: 3ugi_A 3ugl_A 3uey_A 3ugd_A 3uff_A 1ptq_A 1ptr_A*

Probab=87.00  E-value=0.65  Score=26.78  Aligned_cols=31  Identities=23%  Similarity=0.550  Sum_probs=24.1

Q ss_pred             CCCcccCccCCCccccc-CCcEEeCCCCCeee
Q 040426            6 GRDFLFCKFCGTMLRME-SNHVVCSSCKFKKN   36 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~~-~~~~~C~~C~~~~~   36 (120)
                      ...+.||..|+.+|.-- ...+.|..|++...
T Consensus        17 ~~~pt~C~~C~~~l~Gl~~qg~~C~~C~~~~H   48 (65)
T 3uej_A           17 YMSPTFCDHCGSLLWGLVKQGLKCEDCGMNVH   48 (65)
T ss_dssp             CSSCCBCTTTCCBCCSSSSCEEEETTTCCEEC
T ss_pred             CCCCCcccccChhhhccCceeeECCCCCCeEc
Confidence            35678999999999642 33499999998764

>2e9h_A EIF-5, eukaryotic translation initiation factor 5; zinc binding, C4 type zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=86.83  E-value=0.66  Score=31.93  Aligned_cols=33  Identities=33%  Similarity=0.596  Sum_probs=26.7

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC  117 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w  117 (120)
                      +.|+.|++++..+.-     ..|.-+.|-.|..||++-
T Consensus       104 VlC~~C~sPdT~L~~-----~~~~r~~~l~C~ACGa~~  136 (157)
T 2e9h_A          104 VLCPECENPETDLHV-----NPKKQTIGNSCKACGYRG  136 (157)
T ss_dssp             TSCTTTCCSCCEEEE-----ETTTTEEEEECSSSCCEE
T ss_pred             EECCCCCCCccEEEE-----ecCCCEEEEEccCCCCCC
Confidence            689999999987643     135778999999999864

>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=86.26  E-value=0.32  Score=31.88  Aligned_cols=30  Identities=27%  Similarity=0.490  Sum_probs=21.2

Q ss_pred             cccCccCCCccccc--CCc-EEeCCCCCeeeccc
Q 040426            9 FLFCKFCGTMLRME--SNH-VVCSSCKFKKNVQD   39 (120)
Q Consensus         9 ~~FCp~CgnlL~~~--~~~-~~C~~C~~~~~~~~   39 (120)
                      -.+||.||.. .+.  ... |.|+.|++..---.
T Consensus        60 kytCPfCGk~-~vKR~avGIW~C~~Cgk~fAGGA   92 (116)
T 3cc2_Z           60 DHACPNCGED-RVDRQGTGIWQCSYCDYKFTGGS   92 (116)
T ss_dssp             CEECSSSCCE-EEEEEETTEEEETTTCCEEECCS
T ss_pred             CCcCCCCCCc-eeEecCceeEECCCCCCEEECCC
Confidence            4589999973 332  223 99999999975443

>1y8f_A UNC-13 homolog A, MUNC13-1; cysteine-rich domain, C1-domain, zinc-binding domain, endocytosis/exocytosis,signaling protein complex; NMR {Rattus norvegicus}

Probab=86.06  E-value=0.74  Score=26.67  Aligned_cols=31  Identities=19%  Similarity=0.424  Sum_probs=23.7

Q ss_pred             CCCcccCccCCCcccccCC-cEEeCCCCCeee
Q 040426            6 GRDFLFCKFCGTMLRMESN-HVVCSSCKFKKN   36 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~~~~-~~~C~~C~~~~~   36 (120)
                      ...+.||..|+.+|.--.. .+.|..|++...
T Consensus        21 ~~~pt~C~~C~~~l~Gl~~qg~~C~~C~~~~H   52 (66)
T 1y8f_A           21 ATTPTYCYECEGLLWGIARQGMRCTECGVKCH   52 (66)
T ss_dssp             CSSCCCCTTTCCCCCSSCCEEEEETTTCCEEC
T ss_pred             CCCCcChhhcChhhcccCcceeEcCCCCCeeC
Confidence            3467899999999964322 399999999754

>2yuu_A NPKC-delta, protein kinase C delta type; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=85.73  E-value=0.75  Score=27.88  Aligned_cols=32  Identities=16%  Similarity=0.345  Sum_probs=24.7

Q ss_pred             CCCcccCccCCCcccc-cCCcEEeCCCCCeeec
Q 040426            6 GRDFLFCKFCGTMLRM-ESNHVVCSSCKFKKNV   37 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~-~~~~~~C~~C~~~~~~   37 (120)
                      ...+.||..|+.+|.- -...|.|..|++....
T Consensus        25 ~~~pt~C~~C~~~lwGl~kqg~~C~~C~~~~Hk   57 (83)
T 2yuu_A           25 FGQPTFCSVCKDFVWGLNKQGYKCRQCNAAIHK   57 (83)
T ss_dssp             CSSCCCCSSSCCCCCSSSCCEEEETTTCCEECT
T ss_pred             CCCCcChhhcChhhccccccccccCCcCCeeCh
Confidence            3567899999999963 3344999999998654

>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=84.45  E-value=1.4  Score=26.26  Aligned_cols=38  Identities=16%  Similarity=0.266  Sum_probs=22.2

Q ss_pred             ccccccCCCceEEEE--eecccCCCCce----EEEEcCCCCcee
Q 040426           80 RACEKCQNPEMYYST--RQTRSADEGQT----TYYICPRCGHRC  117 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~--~Q~RSADE~~T----~fY~C~~C~~~w  117 (120)
                      .+||-||..++..-.  +...-..+-.+    -.+.|..||-.|
T Consensus         3 m~Cp~Cg~~~l~~~~~~~~~~~~G~~~~I~~Vp~~~C~~CGE~~   46 (78)
T 3ga8_A            3 MKCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESI   46 (78)
T ss_dssp             CBCTTTSSSBEEEEEEEEEEEETTEEEEEEEEEEEEETTTCCEE
T ss_pred             eECCCCCCCeeEeEEEEEEEEECCEEEEEcCceeEECCCCCCEE
Confidence            479999988664322  22222222121    357899999876

>2eli_A Protein kinase C alpha type; PKC-alpha, PKC-A, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=84.13  E-value=0.89  Score=27.73  Aligned_cols=32  Identities=22%  Similarity=0.545  Sum_probs=24.7

Q ss_pred             CCCcccCccCCCccccc-CCcEEeCCCCCeeec
Q 040426            6 GRDFLFCKFCGTMLRME-SNHVVCSSCKFKKNV   37 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~~-~~~~~C~~C~~~~~~   37 (120)
                      ...+.||..|+.+|.-- ...+.|..|++....
T Consensus        25 ~~~pt~C~~C~~~l~Gl~kqG~~C~~C~~~~Hk   57 (85)
T 2eli_A           25 YGSPTFCDHCGSLLYGLIHQGMKCDTCDMNVHK   57 (85)
T ss_dssp             CSSCCBCSSSCCBCCCSSSCEEECSSSCCEEET
T ss_pred             CCCCcCCcccCccccccccCCCcCCCcCCccCH
Confidence            35678999999999643 234999999998654

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

Probab=83.67  E-value=0.46  Score=29.37  Aligned_cols=30  Identities=17%  Similarity=0.286  Sum_probs=21.7

Q ss_pred             cccCccCCCcccccCC--c-EEeCCCCCeeeccc
Q 040426            9 FLFCKFCGTMLRMESN--H-VVCSSCKFKKNVQD   39 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~~   39 (120)
                      ...||.||.. .++..  . |.|+.|++..---.
T Consensus        35 ky~CpfCGk~-~vkR~a~GIW~C~kCg~~~AGGA   67 (83)
T 3j21_i           35 KHTCPVCGRK-AVKRISTGIWQCQKCGATFAGGA   67 (83)
T ss_dssp             CBCCSSSCSS-CEEEEETTEEEETTTCCEEECCS
T ss_pred             ccCCCCCCCc-eeEecCcCeEEcCCCCCEEeCCc
Confidence            4589999987 44432  2 99999999875433

>2enn_A NPKC-theta, protein kinase C theta type; zinc binding, DAG/PE-binding protein, diacylglycerol, phorbol ester, TCR, T-cell, structural genomics; NMR {Homo sapiens}

Probab=83.46  E-value=0.85  Score=27.30  Aligned_cols=32  Identities=16%  Similarity=0.306  Sum_probs=24.6

Q ss_pred             CCCcccCccCCCccccc-CCcEEeCCCCCeeec
Q 040426            6 GRDFLFCKFCGTMLRME-SNHVVCSSCKFKKNV   37 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~~-~~~~~C~~C~~~~~~   37 (120)
                      ...+.||..|+.+|.-- ...+.|..|++....
T Consensus        31 f~~pt~C~~C~~~lwGl~kqG~~C~~C~~~~Hk   63 (77)
T 2enn_A           31 FPQPTFCSVCHEFVWGLNKQGYQCRQCNAAIHK   63 (77)
T ss_dssp             CSSCEECSSSCCEECCTTCCEEECSSSCCEEES
T ss_pred             CCCCcCccccChhhccccccccCcCCCCCcCCH
Confidence            34678999999999743 234999999997653

>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural genomics, PSI-2, protein structure initiative; NMR {Escherichia coli} SCOP: g.41.18.1

Probab=83.21  E-value=0.9  Score=28.92  Aligned_cols=27  Identities=30%  Similarity=0.621  Sum_probs=22.1

Q ss_pred             ccCccCCCcccccCCcEEeCCCCCeee
Q 040426           10 LFCKFCGTMLRMESNHVVCSSCKFKKN   36 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~~~C~~C~~~~~   36 (120)
                      ..||.|.+-|......+.|..|+....
T Consensus        33 ~~CP~Cq~eL~~~g~~~hC~~C~~~f~   59 (101)
T 2jne_A           33 LHCPQCQHVLDQDNGHARCRSCGEFIE   59 (101)
T ss_dssp             CBCSSSCSBEEEETTEEEETTTCCEEE
T ss_pred             ccCccCCCcceecCCEEECccccchhh
Confidence            599999999998755588999998543

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

Probab=83.09  E-value=0.72  Score=32.58  Aligned_cols=30  Identities=23%  Similarity=0.459  Sum_probs=20.9

Q ss_pred             CCcccCccCCC---cccc--cCCcEEeCCCCCeee
Q 040426            7 RDFLFCKFCGT---MLRM--ESNHVVCSSCKFKKN   36 (120)
Q Consensus         7 ~~~~FCp~Cgn---lL~~--~~~~~~C~~C~~~~~   36 (120)
                      .....||+||.   -|..  ....++|..||.+..
T Consensus        19 n~~~~CPECGs~~t~IV~D~erGE~VCsdCGLVLE   53 (197)
T 3k1f_M           19 NIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLS   53 (197)
T ss_dssp             CCCCCCTTTCCSSCCEEEEGGGTEEEETTTCBBCC
T ss_pred             ccCeECcCCCCcCCeEEEeCCCCEEEEcCCCCCcC
Confidence            34558999997   2333  233399999999864

>2qkd_A Zinc finger protein ZPR1; helical hairpins, beta helix, anti-parrallel beta sheet, double straded anti-parallel beta helix, metal binding protein; 2.00A {Mus musculus}

Probab=82.51  E-value=1.4  Score=34.67  Aligned_cols=42  Identities=26%  Similarity=0.471  Sum_probs=25.9

Q ss_pred             ccccccccCCCceE-EEEeecccCCCCceEEEEcCCCCceecc
Q 040426           78 VKRACEKCQNPEMY-YSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        78 ~~~~CpkCg~~ea~-y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      ....||.||++... .....+=--.|=.-.-|.|..|||+..+
T Consensus       219 ~~s~Cp~C~~~~~t~~~~~~IP~F~eViims~~C~~CGyr~ne  261 (404)
T 2qkd_A          219 FNTNCPECNAPAQTNMKLVQIPHFKEVIIMATNCENCGHRTNE  261 (404)
T ss_dssp             EEECCTTTCCTTCEEEEEECCTTSCCEEEEEEECSSSCCEEEE
T ss_pred             ecccCccCCCccEEEEEEEeCCCCCcEEEEEEECCCCCCcccc
Confidence            45689999987442 2222221123334556899999998753

>1nee_A EIF-2-beta, probable translation initiation factor 2 beta subunit; two domain protein, mixed alpha-beta structure; NMR {Methanothermobacterthermautotrophicus} SCOP: d.241.1.1 g.59.1.1

Probab=82.22  E-value=0.36  Score=32.55  Aligned_cols=31  Identities=26%  Similarity=0.746  Sum_probs=25.1

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC  117 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w  117 (120)
                      +.||.|++++..+.-       |+-..|-.|..||++-
T Consensus       103 VlC~~C~sPdT~l~k-------~~r~~~l~C~ACGa~~  133 (138)
T 1nee_A          103 VICHECNRPDTRIIR-------EGRISLLKCEACGAKA  133 (138)
T ss_dssp             HHHTCCSSCSSCCEE-------ETTTTEEECSTTSCCC
T ss_pred             EECCCCCCcCcEEEE-------cCCeEEEEccCCCCCc
Confidence            689999999986542       4577999999999863

>2row_A RHO-associated protein kinase 2; ATP-binding, coiled coil, cytoplasm, membrane, metal-binding, nucleotide-binding, phorbol-ester binding; NMR {Rattus norvegicus}

Probab=81.47  E-value=1.2  Score=27.36  Aligned_cols=31  Identities=19%  Similarity=0.220  Sum_probs=24.3

Q ss_pred             CCCcccCccCCCcccccC-C--cEEeCCCCCeee
Q 040426            6 GRDFLFCKFCGTMLRMES-N--HVVCSSCKFKKN   36 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~~~-~--~~~C~~C~~~~~   36 (120)
                      ...+-||..|+++|.--. .  .|.|+.|++...
T Consensus        32 ~~~PT~Cd~C~~~lWGl~kqp~G~~C~~C~~~~H   65 (84)
T 2row_A           32 YHFPTNCEACMKPLWHMFKPPPALECRRCHIKCH   65 (84)
T ss_dssp             CSSCEECSSSSSEECCSSSCCCEEEESSSCCEEE
T ss_pred             CCCCcchhhcCHhhhccccCCCCCEecCCCCccc
Confidence            345689999999998643 2  599999998764

>2d74_B Translation initiation factor 2 beta subunit; protein complex; 2.80A {Pyrococcus furiosus} PDB: 2dcu_B*

Probab=81.01  E-value=0.3  Score=33.33  Aligned_cols=32  Identities=19%  Similarity=0.557  Sum_probs=25.6

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +.||.||+++....       -|+-..|-.|..||.+..
T Consensus       105 VlC~~C~sPdT~L~-------k~~r~~~l~C~ACGa~~~  136 (148)
T 2d74_B          105 VICPVCGSPDTKII-------KRDRFHFLKCEACGAETP  136 (148)
T ss_dssp             SSCSSSCCTTCCCC-------BSSSSBCCCCSSSCCCCC
T ss_pred             EECCCCCCcCcEEE-------EeCCEEEEEecCCCCCcc
Confidence            68999999997543       145788999999998764

>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1

Probab=80.64  E-value=1.6  Score=33.08  Aligned_cols=39  Identities=21%  Similarity=0.447  Sum_probs=24.8

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      ....||-||..-..=. +..+ .+++=.+|..|.-|++.|+
T Consensus       181 ~~~~CPvCGs~P~~s~-l~~~-g~~~G~R~l~Cs~C~t~W~  219 (309)
T 2fiy_A          181 SRTLCPACGSPPMAGM-IRQG-GKETGLRYLSCSLCACEWH  219 (309)
T ss_dssp             TCSSCTTTCCCEEEEE-EEC-----CCEEEEEETTTCCEEE
T ss_pred             cCCCCCCCCCcCceeE-Eeec-CCCCCcEEEEeCCCCCEEe
Confidence            4568999999744321 2222 2334456899999999996

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=80.58  E-value=1.5  Score=26.92  Aligned_cols=27  Identities=19%  Similarity=0.541  Sum_probs=21.0

Q ss_pred             ccCccCCCcccccCCcEEeCCCCCeee
Q 040426           10 LFCKFCGTMLRMESNHVVCSSCKFKKN   36 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~~~~C~~C~~~~~   36 (120)
                      ..||+|++.|......+.|..|+....
T Consensus         3 ~~CP~C~~~l~~~~~~~~C~~C~~~~~   29 (81)
T 2jrp_A            3 ITCPVCHHALERNGDTAHCETCAKDFS   29 (81)
T ss_dssp             CCCSSSCSCCEECSSEEECTTTCCEEE
T ss_pred             CCCCCCCCccccCCCceECccccccCC
Confidence            579999999887655577999987543

>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=80.30  E-value=0.78  Score=27.57  Aligned_cols=28  Identities=29%  Similarity=0.554  Sum_probs=20.6

Q ss_pred             cccCccCCCcccccCC--c-EEeCCCCCeeec
Q 040426            9 FLFCKFCGTMLRMESN--H-VVCSSCKFKKNV   37 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~   37 (120)
                      ...||.||.. .++..  . +.|+.|++..--
T Consensus        26 ky~C~fCgk~-~vkR~a~GIW~C~~C~~~~AG   56 (72)
T 3jyw_9           26 RYDCSFCGKK-TVKRGAAGIWTCSCCKKTVAG   56 (72)
T ss_dssp             CBCCSSCCSS-CBSBCSSSCBCCSSSCCCCCC
T ss_pred             CccCCCCCCc-eeEecCCCeEECCCCCCEEeC
Confidence            4589999976 44432  2 999999998654

---

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	120
d1qypa_	57	g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {A	3e-12
d1tfia_	50	g.41.3.1 (A:) Transcriptional factor SII, C-termin	5e-11
d1twfi2	72	g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase	6e-11

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]} Length = 57

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

 Score = 54.8 bits (132), Expect = 3e-12
 Identities = 18/51 (35%), Positives = 25/51 (49%)

Query: 69  DKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE 119
           ++    L   K  C KC N   Y+   QTR+ DE  T +Y C +CGH  + 
Sbjct: 5   EQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS 55

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 50

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (124), Expect = 5e-11
 Identities = 17/35 (48%), Positives = 22/35 (62%)

Query: 82  CEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
           C KC+     Y+  QTRSADE  TT+ +C  CG+R
Sbjct: 12  CGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNR 46

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 72

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]

 Score = 52.2 bits (125), Expect = 6e-11
 Identities = 12/42 (28%), Positives = 18/42 (42%)

Query: 75  LSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
           L +  R C KC + E  +   Q R  D     +++C  C H 
Sbjct: 19  LPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHI 60

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	120
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	99.96
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	99.95
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	99.9
d1twfi1	49	RBP9 subunit of RNA polymerase II {Baker's yeast (	99.55
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	96.76
d1lkoa2	44	Rubrerythrin, C-terminal domain {Desulfovibrio vul	96.61
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	96.57
d1dx8a_	70	Rubredoxin {Guillardia theta [TaxId: 55529]}	96.51
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	96.03
d2dsxa1	52	Rubredoxin {Desulfovibrio gigas [TaxId: 879]}	95.46
d1iroa_	53	Rubredoxin {Clostridium pasteurianum [TaxId: 1501]	95.36
d1brfa_	53	Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2	95.17
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	95.01
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	94.77
d6rxna_	45	Rubredoxin {Desulfovibrio desulfuricans, strain 27	94.68
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	94.66
d1s24a_	56	Two-iron rubredoxin {Pseudomonas oleovorans [TaxId	94.62
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	94.38
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	94.23
d2hf1a1	59	Hypothetical protein CV3345 {Chromobacterium viola	92.56
d2cona1	66	RNA-binding protein NOB1 (Nin one binding) {Mouse	92.14
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	92.04
d2pk7a1	59	Uncharacterized protein PFL1779 {Pseudomonas fluor	91.02
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	90.5
d1twfl_	46	RBP12 subunit of RNA polymerase II {Baker's yeast	90.15
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	88.95
d2f9yb1	263	Acetyl-coenzyme A carboxylase carboxyl transferase	88.06
d2ayja1	56	Ribosomal protein L40e {Sulfolobus solfataricus [T	86.3
d1pfva3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch	85.81
d1vqoz1	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	85.16
d1ptqa_	50	Protein kinase C-delta (PKCdelta) {Mouse (Mus musc	84.71
d1tbna_	66	Protein kinase c-gamma {Rat (Rattus rattus) [TaxId	84.15
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	84.04
d1x6ha1	37	Transcriptional repressor CTCF {Human (Homo sapien	83.57
d1pvma3	36	Hypothetical protein Ta0289 C-terminal domain {Arc	83.45
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	83.38
d1k3xa3	40	Endonuclease VIII {Escherichia coli [TaxId: 562]}	82.79
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	82.62
d1k81a_	36	Zinc-binding domain of translation initiation fact	82.37
d1rqga3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro	82.16
d1jj2y_	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	81.58
d1faqa_	52	RAF-1 {Human (Homo sapiens) [TaxId: 9606]}	81.46
d1vk6a4	29	NADH pyrophosphatase intervening domain {Escherich	80.64

>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=99.96  E-value=2.1e-30  Score=158.64  Aligned_cols=57  Identities=23%  Similarity=0.497  Sum_probs=54.3

Q ss_pred             cccCCCccccccccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426           64 EQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES  120 (120)
Q Consensus        64 ~i~~~~~~~~t~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n  120 (120)
                      .|+.|+..||+||++++.||+|||++|+|||+|+||||||||+||+|++|||+||+|
T Consensus         8 ~v~~d~~~DPtlp~t~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~C~h~Wr~~   64 (72)
T d1twfi2           8 GVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSD   64 (72)
T ss_dssp             TCCTTGGGCTTSCCCCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECC
T ss_pred             ccccccccCCCCCccCCCCCCCCCCeEEEEEeecCccCCCceEEEEcCCCCCCcccc
Confidence            378888899999999999999999999999999999999999999999999999976

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

Probab=99.95  E-value=8.2e-29  Score=145.27  Aligned_cols=48  Identities=38%  Similarity=0.743  Sum_probs=46.3

Q ss_pred             ccccccccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceecc
Q 040426           72 ETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQE  119 (120)
Q Consensus        72 ~~t~~~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~  119 (120)
                      .+++|+++..||+|||++|+|+|+|+||||||||+||+|.+|||+||+
T Consensus         8 ~~~~pt~~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~Cg~~wre   55 (57)
T d1qypa_           8 LKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             CSSSCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred             cccCCcccCCCCCCCCCceEEEEeecccccCCCeEEEEeCCCCCccee
Confidence            478899999999999999999999999999999999999999999997

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=4.9e-25  Score=125.55  Aligned_cols=42  Identities=40%  Similarity=0.736  Sum_probs=40.0

Q ss_pred             cccccccccCCCceEEEEeecccCCCCceEEEEcCCCCceec
Q 040426           77 KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +...+||+||++++.|+++|+||||||||+||.|.+|||+||
T Consensus         7 T~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~Cg~~Wr   48 (50)
T d1tfia_           7 TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK   48 (50)
T ss_dssp             CCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEE
T ss_pred             cCCEECCCCCCCccEEEEEEccCCCCCceEEEEccccCCeee
Confidence            455699999999999999999999999999999999999997

>d1twfi1 g.41.3.1 (I:1-49) 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=99.55  E-value=1e-15  Score=85.27  Aligned_cols=40  Identities=23%  Similarity=0.628  Sum_probs=36.0

Q ss_pred             CCcccCccCCCcccccCCc------EEeCCCCCeeeccccccceEEEeee
Q 040426            7 RDFLFCKFCGTMLRMESNH------VVCSSCKFKKNVQDVADREISYAVT   50 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~~------~~C~~C~~~~~~~~~~~~~~~~~~~   50 (120)
                      .+++|||+|+|||||++|+      |.||+|+|++.+++    .+||+++
T Consensus         2 s~~rFC~eCnNmLYPKEDk~~~~L~yaCR~C~y~e~A~~----~cVYrn~   47 (49)
T d1twfi1           2 TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGS----PLVYRHE   47 (49)
T ss_dssp             CCCCBCSSSCCBCEEEEETTTTEEEEECSSSSCEEECSC----SEEEEEE
T ss_pred             CceecChhcccccccCCccccCEEEEEccCCCceeEcCC----CeEEecc
Confidence            5789999999999999874      99999999999987    6899875

>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=96.76  E-value=0.00024  Score=36.64  Aligned_cols=29  Identities=28%  Similarity=0.857  Sum_probs=21.1

Q ss_pred             cccccCCCceEEEEeecccCCCCceEEEEcCCCCceeccC
Q 040426           81 ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES  120 (120)
Q Consensus        81 ~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w~~n  120 (120)
                      .||+|+..-.+  +      |   -..|+|..|+|.|..+
T Consensus         5 ~CP~C~seytY--e------d---g~l~vCPeC~hEW~~~   33 (38)
T d2akla2           5 PCPQCNSEYTY--E------D---GALLVCPECAHEWSPN   33 (38)
T ss_dssp             CCTTTCCCCCE--E------C---SSSEEETTTTEEECTT
T ss_pred             cCCCCCCcceE--c------C---CCEEECCcccCcCCcc
Confidence            59999987553  1      1   2238999999999753

>d1lkoa2 g.41.5.1 (A:148-191) Rubrerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=96.61  E-value=0.00057  Score=36.36  Aligned_cols=14  Identities=21%  Similarity=0.757  Sum_probs=11.9

Q ss_pred             cccccCCCceEEEE
Q 040426           81 ACEKCQNPEMYYST   94 (120)
Q Consensus        81 ~CpkCg~~ea~y~~   94 (120)
                      .||.|||+.++|-.
T Consensus        26 ~CPvC~~p~~~Fe~   39 (44)
T d1lkoa2          26 LCPACAHPKAHFEL   39 (44)
T ss_dssp             BCTTTCCBGGGEEE
T ss_pred             cCCCCCCcHHHHee
Confidence            69999999998843

>d2fiya1 e.59.1.1 (A:19-308) FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId: 287]}

class: Multi-domain proteins (alpha and beta)
fold: FdhE-like
superfamily: FdhE-like
family: FdhE-like
domain: FdhE homolog PA4809
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=96.57  E-value=0.0018  Score=47.23  Aligned_cols=70  Identities=20%  Similarity=0.474  Sum_probs=43.7

Q ss_pred             cccCccCCCccccc-------CC--c-EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccc
Q 040426            9 FLFCKFCGTMLRME-------SN--H-VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKV   78 (120)
Q Consensus         9 ~~FCp~CgnlL~~~-------~~--~-~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~   78 (120)
                      ..+||.||+.=...       .+  + +.|..|++....                                        .
T Consensus       164 ~~~CPvCGs~P~~s~l~~~~~~~G~R~l~C~~C~teW~~----------------------------------------~  203 (290)
T d2fiya1         164 RTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHY----------------------------------------V  203 (290)
T ss_dssp             CSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEEC----------------------------------------C
T ss_pred             CCcCCCCCCcchhheeeccCCCCCceEEECCCCCCcccc----------------------------------------c
Confidence            46899999852211       12  2 999999998753                                        1


Q ss_pred             cccccccCCCce-EEEEee--cccCCCCceEEEEcCCCCceec
Q 040426           79 KRACEKCQNPEM-YYSTRQ--TRSADEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        79 ~~~CpkCg~~ea-~y~~~Q--~RSADE~~T~fY~C~~C~~~w~  118 (120)
                      +..||.||+.+. .|+.+-  .-..+++-.....|..|+..++
T Consensus       204 R~~C~~Cg~~~~~~~~~~~~~~~~~~~~~~r~e~C~~C~~Y~K  246 (290)
T d2fiya1         204 RIKCSHCEESKHLAYLSLEHDGQPAEKAVLRAETCPSCQGYLK  246 (290)
T ss_dssp             TTSCSSSCCCSCCEEECCCC-CCCSTTCSEEEEEETTTTEEEE
T ss_pred             cccCCCCCCCCCcceEEEecCCCcccccceEEEEcCCcCCeEE
Confidence            445999988754 343332  1122233467888999977654

>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=96.51  E-value=0.0021  Score=37.36  Aligned_cols=57  Identities=19%  Similarity=0.438  Sum_probs=34.2

Q ss_pred             ccCCcEEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccccccccccCCCceEEEEeecc
Q 040426           21 MESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTR   98 (120)
Q Consensus        21 ~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~~CpkCg~~ea~y~~~Q~R   98 (120)
                      +...+|.|+.|+|++.-..- +             ...+     |..+. ....|| .++.||.||..+..|..++-.
T Consensus         3 ~~~~ky~C~~CgyiYDp~~G-D-------------~~~g-----I~pGT-~F~dLP-~dW~CP~Cga~K~~F~~~~~~   59 (70)
T d1dx8a_           3 IDEGKYECEACGYIYEPEKG-D-------------KFAG-----IPPGT-PFVDLS-DSFMCPACRSPKNQFKSIKKV   59 (70)
T ss_dssp             CCSSCEEETTTCCEECTTTC-C-------------TTTT-----CCSSC-CGGGSC-TTCBCTTTCCBGGGEEECCCB
T ss_pred             ccCCeEEcCCCCeEECcccC-C-------------cccC-----CCCCC-ChHHCC-CCCCCcCCCCcHHHheEcccc
Confidence            34445999999999864321 0             0011     11111 123344 578999999999999876543

>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=96.03  E-value=0.0023  Score=32.74  Aligned_cols=32  Identities=19%  Similarity=0.495  Sum_probs=26.6

Q ss_pred             CcccCccCCCcccccCCc-EEeCCCCCeeeccc
Q 040426            8 DFLFCKFCGTMLRMESNH-VVCSSCKFKKNVQD   39 (120)
Q Consensus         8 ~~~FCp~CgnlL~~~~~~-~~C~~C~~~~~~~~   39 (120)
                      ++--||+|++-...+.+. |+|.-|+|......
T Consensus         2 ~lP~CP~C~seytYedg~l~vCPeC~hEW~~~~   34 (38)
T d2akla2           2 TLPPCPQCNSEYTYEDGALLVCPECAHEWSPNE   34 (38)
T ss_dssp             CSCCCTTTCCCCCEECSSSEEETTTTEEECTTT
T ss_pred             CCCcCCCCCCcceEcCCCEEECCcccCcCCccc
Confidence            466799999998777666 99999999987654

>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=95.46  E-value=0.008  Score=32.82  Aligned_cols=20  Identities=20%  Similarity=0.415  Sum_probs=15.2

Q ss_pred             cccccccccccccCCCceEEE
Q 040426           73 TQLSKVKRACEKCQNPEMYYS   93 (120)
Q Consensus        73 ~t~~~~~~~CpkCg~~ea~y~   93 (120)
                      ..|| .++.||.||..+..|-
T Consensus        31 ~~LP-~~w~CP~C~a~K~~F~   50 (52)
T d2dsxa1          31 EDLP-DDWACPVCGASKDAFE   50 (52)
T ss_dssp             GGSC-TTCBCTTTCCBGGGEE
T ss_pred             HHCC-CCCCCcCCCCcHHHhc
Confidence            3444 5789999999988764

>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=95.36  E-value=0.011  Score=32.32  Aligned_cols=48  Identities=19%  Similarity=0.385  Sum_probs=28.6

Q ss_pred             EEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccccccccccCCCceEEEE
Q 040426           26 VVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYST   94 (120)
Q Consensus        26 ~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~~CpkCg~~ea~y~~   94 (120)
                      |.|+.|||++.-..- +             ...+     |..+. ....|| .++.||.||..+..|-.
T Consensus         4 y~C~~CgyiYd~~~G-d-------------~~~g-----i~pGT-~F~~LP-~dw~CP~C~a~K~~F~~   51 (53)
T d1iroa_           4 YTCTVCGYIYNPEDG-D-------------PDNG-----VNPGT-DFKDIP-DDWVCPLCGVGKDQFEE   51 (53)
T ss_dssp             EEETTTCCEECTTTC-B-------------GGGT-----BCTTC-CGGGSC-TTCBCTTTCCBGGGEEE
T ss_pred             eEcCCCCcEECcccC-C-------------cccC-----CCCCC-CHHHCC-CCCCCcCCCCcHHHcEE
Confidence            899999999864331 0             0011     11111 123344 46899999999887754

>d1brfa_ g.41.5.1 (A:) Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.17  E-value=0.014  Score=31.87  Aligned_cols=50  Identities=20%  Similarity=0.396  Sum_probs=29.8

Q ss_pred             cEEeCCCCCeeeccccccceEEEeeehhHHhhhhccccccccCCCccccccccccccccccCCCceEEEEe
Q 040426           25 HVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTR   95 (120)
Q Consensus        25 ~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~t~~~~~~~CpkCg~~ea~y~~~   95 (120)
                      +|.|+.|||++.-..- +             ...+     |..+. ....|| .++.||-||..+..|..+
T Consensus         2 ky~C~~CgyiYd~~~G-d-------------~~~g-----i~pGT-~f~dLP-~dw~CP~C~a~K~~F~~~   51 (53)
T d1brfa_           2 KWVCKICGYIYDEDAG-D-------------PDNG-----ISPGT-KFEELP-DDWVCPICGAPKSEFEKL   51 (53)
T ss_dssp             EEEETTTCCEEETTTC-B-------------GGGT-----BCTTC-CGGGSC-TTCBCTTTCCBGGGEEES
T ss_pred             ceECCCCCcEECcccC-C-------------cccC-----CCCCC-CHHHCC-CCCCCcCCCCcHHHceEc
Confidence            3899999999864321 0             0011     11111 123444 478999999998887653

>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Nigerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=95.01  E-value=0.0057  Score=30.93  Aligned_cols=13  Identities=23%  Similarity=0.723  Sum_probs=10.8

Q ss_pred             cccccCCCceEEE
Q 040426           81 ACEKCQNPEMYYS   93 (120)
Q Consensus        81 ~CpkCg~~ea~y~   93 (120)
                      .||-||++...|.
T Consensus        22 ~CPvCg~~~~~F~   34 (36)
T d1yuza2          22 KCPICFRPKDTFT   34 (36)
T ss_dssp             BCTTTCCBGGGCE
T ss_pred             cCCCCCCcHHHcC
Confidence            4999999988764

>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=94.77  E-value=0.013  Score=33.73  Aligned_cols=29  Identities=24%  Similarity=0.602  Sum_probs=23.1

Q ss_pred             CCcccCccCCCcccccCCc--EEeCCCCCee
Q 040426            7 RDFLFCKFCGTMLRMESNH--VVCSSCKFKK   35 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~   35 (120)
                      ..+.+||.|++.+....+.  +.|..|++..
T Consensus        16 ~~~k~CP~C~~~~~~~~~~~~~~C~~C~~~f   46 (73)
T d2ct7a1          16 PKFLWCAQCSFGFIYEREQLEATCPQCHQTF   46 (73)
T ss_dssp             CCEECCSSSCCCEECCCSCSCEECTTTCCEE
T ss_pred             CCCCCCCCCCCEeEECCCCCEEEcCCCCCeE
Confidence            3578999999987766543  9999999875

>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=94.68  E-value=0.013  Score=30.96  Aligned_cols=16  Identities=19%  Similarity=0.382  Sum_probs=13.1

Q ss_pred             ccccccccCCCceEEE
Q 040426           78 VKRACEKCQNPEMYYS   93 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~   93 (120)
                      .++.||.||.++..|.
T Consensus        28 ~dw~CP~C~a~K~~F~   43 (45)
T d6rxna_          28 DDWCCPVCGVSKDQFS   43 (45)
T ss_dssp             TTCBCTTTCCBGGGEE
T ss_pred             CCCCCcCCCCcHHHcc
Confidence            3789999999987663

>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=94.66  E-value=0.018  Score=31.60  Aligned_cols=33  Identities=24%  Similarity=0.666  Sum_probs=24.7

Q ss_pred             CCcccCccCCC--cccccCCcEEeCCCCCeeeccc
Q 040426            7 RDFLFCKFCGT--MLRMESNHVVCSSCKFKKNVQD   39 (120)
Q Consensus         7 ~~~~FCp~Cgn--lL~~~~~~~~C~~C~~~~~~~~   39 (120)
                      .--.+||.||.  +|---.|++.|-.|||++-.+.
T Consensus        16 r~~k~CP~CG~GvFmA~H~dR~~CGKCgyTefkk~   50 (55)
T d2k4xa1          16 RKHRFCPRCGPGVFLAEHADRYSCGRCGYTEFKKA   50 (55)
T ss_dssp             CSSCCCTTTTTTCCCEECSSEEECTTTCCCEECCC
T ss_pred             EecCcCcCCCCcEEeeecCCCccccCCcccEEecc
Confidence            33579999966  5555566799999999986544

>d1s24a_ g.41.5.1 (A:) Two-iron rubredoxin {Pseudomonas oleovorans [TaxId: 301]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Two-iron rubredoxin
species: Pseudomonas oleovorans [TaxId: 301]

Probab=94.62  E-value=0.018  Score=31.77  Aligned_cols=18  Identities=17%  Similarity=0.342  Sum_probs=14.9

Q ss_pred             ccccccccCCCceEEEEe
Q 040426           78 VKRACEKCQNPEMYYSTR   95 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~   95 (120)
                      .++.||.||..+..|..+
T Consensus        36 ~dw~CP~C~a~K~~F~~~   53 (56)
T d1s24a_          36 DDWCCPDCGATKEDYVLY   53 (56)
T ss_dssp             TTCCCSSSCCCGGGEEEC
T ss_pred             CCCCCcCCCCcHHHceEc
Confidence            468999999999888654

>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=94.38  E-value=0.0098  Score=30.19  Aligned_cols=14  Identities=21%  Similarity=0.622  Sum_probs=11.6

Q ss_pred             cccccCCCceEEEE
Q 040426           81 ACEKCQNPEMYYST   94 (120)
Q Consensus        81 ~CpkCg~~ea~y~~   94 (120)
                      .||-||++...|-.
T Consensus        22 ~CPvCg~~~~~F~~   35 (37)
T d1nnqa2          22 YCPVCGAPKEKFVV   35 (37)
T ss_dssp             BCTTTCCBGGGSEE
T ss_pred             cCCCCCCcHHHcEE
Confidence            59999999887754

>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=94.23  E-value=0.018  Score=32.14  Aligned_cols=35  Identities=17%  Similarity=0.140  Sum_probs=29.0

Q ss_pred             CCCCcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426            5 LGRDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus         5 ~~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      ....+.-||.|+.=|...+..  ++|+.|+..+++.+
T Consensus         6 ~LL~iL~CP~ck~~L~~~~~~~~Lvc~~~~~~YPI~d   42 (59)
T d2jnya1           6 QLLEVLACPKDKGPLRYLESEQLLVNERLNLAYRIDD   42 (59)
T ss_dssp             GGTCCCBCTTTCCBCEEETTTTEEEETTTTEEEEEET
T ss_pred             HHHHHhcCCCCCCEeEEeCCCCEEEcCccCccccccC
Confidence            445678899999999876554  99999999998866

>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=92.56  E-value=0.035  Score=30.85  Aligned_cols=34  Identities=18%  Similarity=0.503  Sum_probs=28.6

Q ss_pred             CCCcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426            6 GRDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus         6 ~~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      ...+.-||.|+.-|...++.  ++|..|+..+++.+
T Consensus         4 LL~iL~CP~ck~~L~~~~~~~~Lvc~~~~l~YPI~d   39 (59)
T d2hf1a1           4 FLEILVCPLCKGPLVFDKSKDELICKGDRLAFPIKD   39 (59)
T ss_dssp             CEEECBCTTTCCBCEEETTTTEEEETTTTEEEEEET
T ss_pred             HhhhhcCCCCCCeeeEeCCCCEEecCCcCccccccC
Confidence            44677899999999886554  99999999999876

>d2cona1 g.41.15.1 (A:8-73) RNA-binding protein NOB1 (Nin one binding) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: NOB1 zinc finger-like
family: NOB1 zinc finger-like
domain: RNA-binding protein NOB1 (Nin one binding)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.14  E-value=0.022  Score=32.43  Aligned_cols=14  Identities=29%  Similarity=0.752  Sum_probs=10.8

Q ss_pred             CCCCcccCccCCCc
Q 040426            5 LGRDFLFCKFCGTM   18 (120)
Q Consensus         5 ~~~~~~FCp~Cgnl   18 (120)
                      ..++-.|||.|||-
T Consensus        19 ~~~~k~FCpkCGn~   32 (66)
T d2cona1          19 SDMNRVFCGHCGNK   32 (66)
T ss_dssp             SCSSCCSCSSSCCS
T ss_pred             CCcccccCcccCCC
Confidence            34567899999983

>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=92.04  E-value=0.039  Score=30.53  Aligned_cols=28  Identities=14%  Similarity=0.375  Sum_probs=20.0

Q ss_pred             cccCccCCCcccccC--Cc-EEeCCCCCeee
Q 040426            9 FLFCKFCGTMLRMES--NH-VVCSSCKFKKN   36 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~--~~-~~C~~C~~~~~   36 (120)
                      -.=||+||+--....  .+ ++|..||++..
T Consensus        11 ~~~Cp~Cgs~~ii~D~~~Ge~vC~~CG~Vle   41 (58)
T d1dl6a_          11 RVTCPNHPDAILVEDYRAGDMICPECGLVVG   41 (58)
T ss_dssp             CCSBTTBSSSCCEECSSSCCEECTTTCCEEC
T ss_pred             ccCCCCCCCCCEEEECCCCcEecccCCCEec
Confidence            347999998744322  22 99999999753

>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=91.02  E-value=0.079  Score=29.35  Aligned_cols=33  Identities=18%  Similarity=0.510  Sum_probs=28.2

Q ss_pred             CCcccCccCCCcccccCCc--EEeCCCCCeeeccc
Q 040426            7 RDFLFCKFCGTMLRMESNH--VVCSSCKFKKNVQD   39 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~~--~~C~~C~~~~~~~~   39 (120)
                      ..+.-||.|+.-|...++.  ++|..|+..+++.+
T Consensus         4 L~iL~CP~ck~~L~~~~~~~~Lvc~~~~laYPI~d   38 (59)
T d2pk7a1           4 LDILACPICKGPLKLSADKTELISKGAGLAYPIRD   38 (59)
T ss_dssp             GGTCCCTTTCCCCEECTTSSEEEETTTTEEEEEET
T ss_pred             HhheECCCCCCcceEeCCCCEEecCCcCccccccC
Confidence            3567899999999887664  99999999999876

>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=90.50  E-value=0.088  Score=29.01  Aligned_cols=30  Identities=23%  Similarity=0.574  Sum_probs=21.6

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR  116 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~  116 (120)
                      .+.+||.||....++-      ...|.   ++|.+||..
T Consensus        10 ~~~~Cp~Cgs~~ii~D------~~~Ge---~vC~~CG~V   39 (58)
T d1dl6a_          10 PRVTCPNHPDAILVED------YRAGD---MICPECGLV   39 (58)
T ss_dssp             SCCSBTTBSSSCCEEC------SSSCC---EECTTTCCE
T ss_pred             cccCCCCCCCCCEEEE------CCCCc---EecccCCCE
Confidence            4678999999876552      12244   789999975

>d1twfl_ g.41.9.2 (L:) RBP12 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: RNA polymerase subunits
family: RBP12 subunit of RNA polymerase II
domain: RBP12 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.15  E-value=0.091  Score=27.62  Aligned_cols=28  Identities=21%  Similarity=0.624  Sum_probs=22.7

Q ss_pred             cCccCCCcccccCCc-EEeCCCCCeeecc
Q 040426           11 FCKFCGTMLRMESNH-VVCSSCKFKKNVQ   38 (120)
Q Consensus        11 FCp~CgnlL~~~~~~-~~C~~C~~~~~~~   38 (120)
                      -|.+||.-..++... +.|+.||+..--+
T Consensus         6 iCgeCg~~~~l~~~d~irCreCG~RIlYK   34 (46)
T d1twfl_           6 ICAECSSKLSLSRTDAVRCKDCGHRILLK   34 (46)
T ss_dssp             ECSSSCCEECCCTTSTTCCSSSCCCCCBC
T ss_pred             EcccCCCceEeCCCCcEEeccCCcEEEEe
Confidence            599999988887665 9999999975433

>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=88.95  E-value=0.091  Score=28.05  Aligned_cols=27  Identities=22%  Similarity=0.623  Sum_probs=18.4

Q ss_pred             cccCccCCCc-ccccCC-c-EEeCCCCCee
Q 040426            9 FLFCKFCGTM-LRMESN-H-VVCSSCKFKK   35 (120)
Q Consensus         9 ~~FCp~Cgnl-L~~~~~-~-~~C~~C~~~~   35 (120)
                      -.-||.||+- |..... + ++|..||.+.
T Consensus         5 ~~~Cp~Cgs~~iv~D~~~Ge~vC~~CG~Vi   34 (50)
T d1pfta_           5 QKVCPACESAELIYDPERGEIVCAKCGYVI   34 (50)
T ss_dssp             CCSCTTTSCCCEEEETTTTEEEESSSCCBC
T ss_pred             cccCcCCCCCcEEEECCCCeEecccCCcEe
Confidence            3469999875 322222 2 9999999865

>d2f9yb1 c.14.1.4 (B:23-285) Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, AccD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Biotin dependent carboxylase carboxyltransferase domain
domain: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, AccD
species: Escherichia coli [TaxId: 562]

Probab=88.06  E-value=0.041  Score=38.96  Aligned_cols=29  Identities=24%  Similarity=0.572  Sum_probs=23.0

Q ss_pred             ccCccCCCcccccCC--c-EEeCCCCCeeecc
Q 040426           10 LFCKFCGTMLRMESN--H-VVCSSCKFKKNVQ   38 (120)
Q Consensus        10 ~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~   38 (120)
                      .=||.|++||+-+.-  + ++|..|+|-....
T Consensus         3 ~~C~~C~~~~~~~~l~~~~~vC~~C~~h~~lt   34 (263)
T d2f9yb1           3 TKCDSCGQVLYRAELERNLEVCPKCDHHMRMT   34 (263)
T ss_dssp             ECCTTTCCCEETTHHHHTTTBCTTTCCBCCCC
T ss_pred             CcCCCCcceeeHHHHHHhCCCCcCCCCCCCcC
Confidence            459999999998753  2 8999999976543

>d2ayja1 g.41.8.7 (A:1-56) Ribosomal protein L40e {Sulfolobus solfataricus [TaxId: 2287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L40e
domain: Ribosomal protein L40e
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=86.30  E-value=0.24  Score=26.93  Aligned_cols=31  Identities=16%  Similarity=0.405  Sum_probs=23.2

Q ss_pred             CCCCCCcccCccCCCcccccCCcEEeCCCCCee
Q 040426            3 DPLGRDFLFCKFCGTMLRMESNHVVCSSCKFKK   35 (120)
Q Consensus         3 ~~~~~~~~FCp~CgnlL~~~~~~~~C~~C~~~~   35 (120)
                      ....-...-|-.|+-.|.+...+  ||.|||..
T Consensus        13 ~k~~~~k~ICrkC~AR~p~rAt~--CRKCg~~n   43 (56)
T d2ayja1          13 QQRVFLKKVCRKCGALNPIRATK--CRRCHSTN   43 (56)
T ss_dssp             TTCSCCCEEETTTCCEECTTCSS--CTTTCCCC
T ss_pred             HHHhhhhHHHhhccccCCccccc--cccCCCCC
Confidence            34445567899999988888764  89999865

>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=85.81  E-value=0.14  Score=25.31  Aligned_cols=13  Identities=46%  Similarity=1.229  Sum_probs=10.6

Q ss_pred             cccccccCCCceE
Q 040426           79 KRACEKCQNPEMY   91 (120)
Q Consensus        79 ~~~CpkCg~~ea~   91 (120)
                      .-.||+||+.+|+
T Consensus         2 ~G~CP~C~~~~a~   14 (35)
T d1pfva3           2 KGTCPKCKSPDQY   14 (35)
T ss_dssp             EEECTTTCCSSEE
T ss_pred             eeECCCCCCcccc
Confidence            4579999999884

>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=85.16  E-value=0.18  Score=29.05  Aligned_cols=30  Identities=27%  Similarity=0.485  Sum_probs=21.6

Q ss_pred             cccCccCCCcccccCC--c-EEeCCCCCeeeccc
Q 040426            9 FLFCKFCGTMLRMESN--H-VVCSSCKFKKNVQD   39 (120)
Q Consensus         9 ~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~~   39 (120)
                      -..||.||.. .++..  . |.|+.|++..--..
T Consensus        27 ky~Cp~Cgk~-~vkR~a~GIW~C~kC~~~~AGGA   59 (73)
T d1vqoz1          27 DHACPNCGED-RVDRQGTGIWQCSYCDYKFTGGS   59 (73)
T ss_dssp             CBCCSSSSCS-CEEEEETTEEEETTTCCEEECCS
T ss_pred             CccCCCCCCc-eeEEEEEEEEECCCCCCEEeCCe
Confidence            4589999975 44322  2 99999999875443

>d1ptqa_ g.49.1.1 (A:) Protein kinase C-delta (PKCdelta) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)
domain: Protein kinase C-delta (PKCdelta)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.71  E-value=0.44  Score=24.73  Aligned_cols=30  Identities=23%  Similarity=0.613  Sum_probs=23.5

Q ss_pred             CCcccCccCCCccccc-CCcEEeCCCCCeee
Q 040426            7 RDFLFCKFCGTMLRME-SNHVVCSSCKFKKN   36 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~-~~~~~C~~C~~~~~   36 (120)
                      ..+.+|..|+.+|.-- ...+.|+.|++.-.
T Consensus         9 ~~~~~C~~C~~~i~g~~~qg~~C~~C~~~~H   39 (50)
T d1ptqa_           9 MSPTFCDHCGSLLWGLVKQGLKCEDCGMNVH   39 (50)
T ss_dssp             SSCCBCTTTCCBCCSSSSCEEEETTTCCEEC
T ss_pred             CCCcCCcccCCcccCcccCcEECCCCCCeeC
Confidence            4578999999998643 33499999999764

>d1tbna_ g.49.1.1 (A:) Protein kinase c-gamma {Rat (Rattus rattus) [TaxId: 10117]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)
domain: Protein kinase c-gamma
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=84.15  E-value=0.48  Score=26.06  Aligned_cols=31  Identities=26%  Similarity=0.622  Sum_probs=24.0

Q ss_pred             CCcccCccCCCccccc-CCcEEeCCCCCeeec
Q 040426            7 RDFLFCKFCGTMLRME-SNHVVCSSCKFKKNV   37 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~-~~~~~C~~C~~~~~~   37 (120)
                      ..+.+|..|+.+|..- ...|.|+.|++....
T Consensus        17 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~   48 (66)
T d1tbna_          17 SSPTFCDHCGSLLYGLVHQGMKCSCCEMNVHR   48 (66)
T ss_dssp             SSCCBCSSSCCBCCTTSSSCEEETTTCCEECT
T ss_pred             CCCcCCcCCCCcccCcccCccccCcccCeECh
Confidence            4567999999998643 334999999998653

>d2fiya1 e.59.1.1 (A:19-308) FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId: 287]}

class: Multi-domain proteins (alpha and beta)
fold: FdhE-like
superfamily: FdhE-like
family: FdhE-like
domain: FdhE homolog PA4809
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=84.04  E-value=0.6  Score=33.29  Aligned_cols=37  Identities=24%  Similarity=0.635  Sum_probs=24.7

Q ss_pred             ccccccccCCCceEEEEeeccc-C-CCCceEEEEcCCCCceec
Q 040426           78 VKRACEKCQNPEMYYSTRQTRS-A-DEGQTTYYICPRCGHRCQ  118 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RS-A-DE~~T~fY~C~~C~~~w~  118 (120)
                      ....||-||..-.. -  .+|. + .+| .+|..|.-|++.|+
T Consensus       163 ~~~~CPvCGs~P~~-s--~l~~~~~~~G-~R~l~C~~C~teW~  201 (290)
T d2fiya1         163 SRTLCPACGSPPMA-G--MIRQGGKETG-LRYLSCSLCACEWH  201 (290)
T ss_dssp             TCSSCTTTCCCEEE-E--EEEC----CC-EEEEEETTTCCEEE
T ss_pred             cCCcCCCCCCcchh-h--eeeccCCCCC-ceEEECCCCCCccc
Confidence            34569999997332 1  2333 2 345 59999999999996

>d1x6ha1 g.37.1.1 (A:44-80) Transcriptional repressor CTCF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Transcriptional repressor CTCF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.57  E-value=0.25  Score=24.08  Aligned_cols=11  Identities=27%  Similarity=1.226  Sum_probs=9.6

Q ss_pred             EEcCCCCceec
Q 040426          108 YICPRCGHRCQ  118 (120)
Q Consensus       108 Y~C~~C~~~w~  118 (120)
                      |+|.+||++|+
T Consensus         5 fvcskcgktft   15 (37)
T d1x6ha1           5 FVCSKCGKTFT   15 (37)
T ss_dssp             EECSSSCCEES
T ss_pred             eeecccccchh
Confidence            88999999885

>d1pvma3 g.41.13.1 (A:143-178) Hypothetical protein Ta0289 C-terminal domain {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Hypothetical protein Ta0289 C-terminal domain
family: Hypothetical protein Ta0289 C-terminal domain
domain: Hypothetical protein Ta0289 C-terminal domain
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=83.45  E-value=1.2  Score=21.21  Aligned_cols=29  Identities=24%  Similarity=0.732  Sum_probs=20.8

Q ss_pred             ccccccCCCce--EEEEeecccCCCCceEEEEcCC--CCc
Q 040426           80 RACEKCQNPEM--YYSTRQTRSADEGQTTYYICPR--CGH  115 (120)
Q Consensus        80 ~~CpkCg~~ea--~y~~~Q~RSADE~~T~fY~C~~--C~~  115 (120)
                      ..|||||-.-.  +|-       ..|....|+|.+  |.+
T Consensus         2 hlcpkcgvgvl~pvy~-------~kgeikvfrcsnpacdy   34 (36)
T d1pvma3           2 HLCPKCGVGVLEPVYN-------EKGEIKVFRCSNPACDY   34 (36)
T ss_dssp             CBCTTTSSSBEEEEEC-------TTSCEEEEEESCTTCCC
T ss_pred             ccCCccCceEEEEeec-------CCCcEEEEEcCCCcccc
Confidence            57999998754  453       247788899974  765

>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=83.38  E-value=0.16  Score=28.00  Aligned_cols=31  Identities=26%  Similarity=0.650  Sum_probs=23.4

Q ss_pred             ccccccccCCCceEEEEeecccCCCCceEEEEcCCCCcee
Q 040426           78 VKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRC  117 (120)
Q Consensus        78 ~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~w  117 (120)
                      .+++||.|++...+|-..|        | --.|..||..-
T Consensus         6 ~~VkC~~C~n~~ivFsha~--------t-~V~C~~Cg~~L   36 (58)
T d1qxfa_           6 VKVKCPDCEHEQVIFDHPS--------T-IVKCIICGRTV   36 (58)
T ss_dssp             EEEECTTTCCEEEEESSCS--------S-CEECSSSCCEE
T ss_pred             EEeECCCCCCeEEEEecCc--------e-EEEccccCCEE
Confidence            5788999999999996533        2 36788888753

>d1k3xa3 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: Endonuclease VIII
species: Escherichia coli [TaxId: 562]

Probab=82.79  E-value=1.2  Score=22.28  Aligned_cols=31  Identities=26%  Similarity=0.685  Sum_probs=21.5

Q ss_pred             cccccccccCCCceEEEEeecccCCCCceEEEEcCCCCc
Q 040426           77 KVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH  115 (120)
Q Consensus        77 ~~~~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~  115 (120)
                      ....+|+.||..-..-.+        +.-.-|-|+.|.|
T Consensus        10 R~g~pC~~C~~~I~~~~~--------~gR~t~~Cp~CQ~   40 (40)
T d1k3xa3          10 RDGEPCERCGSIIEKTTL--------SSRPFYWCPGCQH   40 (40)
T ss_dssp             CTTSBCTTTCCBCEEEEE--------TTEEEEECTTTCC
T ss_pred             CCCCccCcCCCEEEEEEE--------CCCCCEEChhhCC
Confidence            346789999987554443        3445588999975

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=82.62  E-value=0.46  Score=27.01  Aligned_cols=27  Identities=26%  Similarity=0.592  Sum_probs=23.0

Q ss_pred             cCccCCCcccccCCcEEeCCCCCeeec
Q 040426           11 FCKFCGTMLRMESNHVVCSSCKFKKNV   37 (120)
Q Consensus        11 FCp~CgnlL~~~~~~~~C~~C~~~~~~   37 (120)
                      -||.|..-|.++.+.+.|..|......
T Consensus         4 ~CP~C~~eL~~~~~~~~C~~C~~~~~~   30 (71)
T d2jnea1           4 HCPQCQHVLDQDNGHARCRSCGEFIEM   30 (71)
T ss_dssp             BCSSSCSBEEEETTEEEETTTCCEEEE
T ss_pred             cCCCccCcccccCCCEehhhhhhhhee
Confidence            599999999998777999999876543

>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=82.37  E-value=0.76  Score=22.64  Aligned_cols=30  Identities=27%  Similarity=0.661  Sum_probs=22.6

Q ss_pred             ccccccCCCceEEEEeecccCCCCceEEEEcCCCCce
Q 040426           80 RACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR  116 (120)
Q Consensus        80 ~~CpkCg~~ea~y~~~Q~RSADE~~T~fY~C~~C~~~  116 (120)
                      +.|+.||.+.-...-       |+-+.|-.|..||-+
T Consensus         1 V~C~~C~spDT~l~k-------e~R~~~l~C~aCGa~   30 (36)
T d1k81a_           1 VICRECGKPDTKIIK-------EGRVHLLKCMACGAI   30 (36)
T ss_dssp             CCCSSSCSCEEEEEE-------ETTEEEEEEETTTEE
T ss_pred             CCCCCCCCCCCEEEE-------cCCEEEEEeccCCCC
Confidence            369999999765532       356788899999865

>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=82.16  E-value=0.19  Score=24.84  Aligned_cols=12  Identities=17%  Similarity=0.495  Sum_probs=9.8

Q ss_pred             cccccccCCCce
Q 040426           79 KRACEKCQNPEM   90 (120)
Q Consensus        79 ~~~CpkCg~~ea   90 (120)
                      .-.||+||.++|
T Consensus         2 ~G~CP~C~~~~a   13 (35)
T d1rqga3           2 IGTCPYCGAEDQ   13 (35)
T ss_dssp             CSBCSSSCCSCC
T ss_pred             eEECCCCCCCcc
Confidence            457999999887

>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=81.58  E-value=0.35  Score=27.72  Aligned_cols=31  Identities=19%  Similarity=0.450  Sum_probs=21.8

Q ss_pred             CcccCccCCCcccccCC--c-EEeCCCCCeeeccc
Q 040426            8 DFLFCKFCGTMLRMESN--H-VVCSSCKFKKNVQD   39 (120)
Q Consensus         8 ~~~FCp~CgnlL~~~~~--~-~~C~~C~~~~~~~~   39 (120)
                      ....||.||.. .++..  . |.|+.|++..--..
T Consensus        26 ~ky~Cp~Cgk~-~vkR~a~GIW~C~kC~~~~AGgA   59 (73)
T d1jj2y_          26 KKHKCPVCGFK-KLKRAGTGIWMCGHCGYKIAGGC   59 (73)
T ss_dssp             SCBCCSSSCCS-CEEEEETTEEEETTTCCEEECCS
T ss_pred             CCccCCCCCCC-ceEEEEEEEEECCCCCCEEeCcc
Confidence            35689999964 33322  2 99999999875443

>d1faqa_ g.49.1.1 (A:) RAF-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)
domain: RAF-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.46  E-value=0.44  Score=25.04  Aligned_cols=28  Identities=29%  Similarity=0.732  Sum_probs=22.8

Q ss_pred             CCcccCccCCCcccccCCcEEeCCCCCeeec
Q 040426            7 RDFLFCKFCGTMLRMESNHVVCSSCKFKKNV   37 (120)
Q Consensus         7 ~~~~FCp~CgnlL~~~~~~~~C~~C~~~~~~   37 (120)
                      ..+.+|..|+.+|.   .++.|+.|++....
T Consensus        12 ~~~~~C~~C~~~i~---~g~~C~~C~~~~H~   39 (52)
T d1faqa_          12 LKLAFCDICQKFLL---NGFRCQTCGYKFHE   39 (52)
T ss_dssp             SSCEECTTSSSEEC---SEEECTTTTCCBCS
T ss_pred             CCCcCCccCCCccc---cCCCcCCCCChhhh
Confidence            45789999999985   35999999998653

>d1vk6a4 g.41.14.1 (A:97-125) NADH pyrophosphatase intervening domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: NADH pyrophosphatase intervening domain
family: NADH pyrophosphatase intervening domain
domain: NADH pyrophosphatase intervening domain
species: Escherichia coli [TaxId: 562]

Probab=80.64  E-value=0.57  Score=21.76  Aligned_cols=23  Identities=26%  Similarity=0.918  Sum_probs=18.9

Q ss_pred             cCccCCCcccccCCc--EEeCCCCC
Q 040426           11 FCKFCGTMLRMESNH--VVCSSCKF   33 (120)
Q Consensus        11 FCp~CgnlL~~~~~~--~~C~~C~~   33 (120)
                      ||.-||.-+.++...  .-|..|.-
T Consensus         1 fCGYCGh~Mh~s~tEwa~LC~hC~e   25 (29)
T d1vk6a4           1 YCGYCGHEMYPSKTEWAMLCSHCRE   25 (29)
T ss_dssp             BCTTTCCBEEECSSSSCEEESSSSC
T ss_pred             CccccCCccccchhHHHHHHHHHHh
Confidence            899999999998776  77777754