Psyllid ID: psy3498

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80-
Protein Sequence
MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVPS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccEEEEEEccccEEEEEcccccccEEEcccccccHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccEEcccccccccEEEEEEEccccEEEEEEEEcccEEEEcccccccccEEHHHHHHHHccc
Coil and Loop (DISEMBL)
mgrrkskrkpppkrkniepldiqfncpfcnhekscEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYndwvdasvps
Flexible Loop (DISEMBL)
mgrrkskrkpppkrkniepldiqfncpFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVPS
Low Complexity Region (SEG)
MGrrkskrkpppkrkNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVPS
Disordered region (IsUnstruct)
*******************LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVD*****
Disordered Region (DISOPRED)
**********************QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP*
Disordered Region (DISEMBL)
*************RKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVPS
Disordered Region (DISPRO)
****************IEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP*
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVPS
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	81	2.2.26 [Sep-21-2011]
Q8MQI6	82	Transcription elongation	yes	N/A	0.950	0.939	0.909	5e-36
Q9U501	82	Transcription elongation	N/A	N/A	0.950	0.939	0.831	1e-32
Q9XVZ8	84	Transcription elongation	yes	N/A	0.950	0.916	0.714	9e-28
P60003	83	Transcription elongation	yes	N/A	0.716	0.698	0.672	1e-19
P60002	83	Transcription elongation	yes	N/A	0.716	0.698	0.672	1e-19
A4IFR3	83	Transcription elongation	yes	N/A	0.716	0.698	0.672	1e-19
Q8LHP0	89	Transcription elongation	yes	N/A	0.925	0.842	0.486	7e-17
Q8LEF3	120	Transcription elongation	yes	N/A	0.925	0.625	0.5	2e-16
P36053	145	Transcription elongation	yes	N/A	0.938	0.524	0.480	2e-16
O13868	107	Transcription elongation	yes	N/A	0.938	0.710	0.480	9e-15

>sp|Q8MQI6|ELOF1_DROME Transcription elongation factor 1 homolog OS=Drosophila melanogaster GN=CG40228 PE=1 SV=1

 Score =  149 bits (376), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 70/77 (90%), Positives = 72/77 (93%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRRKSKRKPPPKRKNIEPLD QFNCPFCNHEKSCEVKMDK RN+A+I CRVCLEDFQT 
Sbjct: 1  MGRRKSKRKPPPKRKNIEPLDQQFNCPFCNHEKSCEVKMDKSRNTAKITCRVCLEDFQTG 60

Query: 61 INFLSEAIDVYNDWVDA 77
          INFLSE IDVYNDWVDA
Sbjct: 61 INFLSEPIDVYNDWVDA 77

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.
Drosophila melanogaster (taxid: 7227)

>sp|Q9U501|ELOF1_MANSE Transcription elongation factor 1 homolog OS=Manduca sexta PE=3 SV=1

 Score =  138 bits (347), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 64/77 (83%), Positives = 67/77 (87%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRRKSKRKPPPKRK IEPLD QFNCPFCNHEKSCEVKMD+ +N+A I C VCLEDF TT
Sbjct: 1  MGRRKSKRKPPPKRKAIEPLDQQFNCPFCNHEKSCEVKMDRAKNTAMIQCTVCLEDFHTT 60

Query: 61 INFLSEAIDVYNDWVDA 77
           N LSE IDVYNDWVDA
Sbjct: 61 TNVLSEPIDVYNDWVDA 77

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Manduca sexta (taxid: 7130)

>sp|Q9XVZ8|ELOF1_CAEEL Transcription elongation factor 1 homolog OS=Caenorhabditis elegans GN=Y54G11A.11 PE=3 SV=1

 Score =  122 bits (305), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 55/77 (71%), Positives = 63/77 (81%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MG+RKSKRK P K K + PLD QFNCPFCNHE+ CEVKMD+ +N   I+CRVC EDFQT 
Sbjct: 1  MGKRKSKRKAPTKAKAVMPLDTQFNCPFCNHERVCEVKMDREKNVGYISCRVCSEDFQTN 60

Query: 61 INFLSEAIDVYNDWVDA 77
          IN+LSE IDVY+DWVDA
Sbjct: 61 INYLSEPIDVYSDWVDA 77

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Caenorhabditis elegans (taxid: 6239)

>sp|P60003|ELOF1_MOUSE Transcription elongation factor 1 homolog OS=Mus musculus GN=Elof1 PE=1 SV=1

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDA 77
          L+ QF CPFCNHEKSC+VKMD+ RN+  I+C VCLE+FQT I +LSE +DVY+DW+DA
Sbjct: 20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDA 77

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Mus musculus (taxid: 10090)

>sp|P60002|ELOF1_HUMAN Transcription elongation factor 1 homolog OS=Homo sapiens GN=ELOF1 PE=2 SV=1

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDA 77
          L+ QF CPFCNHEKSC+VKMD+ RN+  I+C VCLE+FQT I +LSE +DVY+DW+DA
Sbjct: 20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDA 77

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Homo sapiens (taxid: 9606)

>sp|A4IFR3|ELOF1_BOVIN Transcription elongation factor 1 homolog OS=Bos taurus GN=ELOF1 PE=2 SV=1

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDA 77
          L+ QF CPFCNHEKSC+VKMD+ RN+  I+C VCLE+FQT I +LSE +DVY+DW+DA
Sbjct: 20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDA 77

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Bos taurus (taxid: 9913)

>sp|Q8LHP0|ELOF1_ORYSJ Transcription elongation factor 1 homolog OS=Oryza sativa subsp. japonica GN=Os07g0631100 PE=3 SV=1

 Score = 85.9 bits (211), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 37/76 (48%), Positives = 54/76 (71%), Gaps = 1/76 (1%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MG+RKS  KPPPK++ ++ LD  F+CPFCNH  S E ++D        +CR+C E+F TT
Sbjct: 1  MGKRKSAAKPPPKKR-MDKLDTVFSCPFCNHGSSVECRIDMKNLIGEASCRICQENFSTT 59

Query: 61 INFLSEAIDVYNDWVD 76
          +N L+E ID+Y++W+D
Sbjct: 60 VNALTEPIDIYSEWID 75

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8LEF3|ELOF1_ARATH Transcription elongation factor 1 homolog OS=Arabidopsis thaliana GN=At5g46030 PE=2 SV=1

 Score = 84.3 bits (207), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/76 (50%), Positives = 51/76 (67%), Gaps = 1/76 (1%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MG+RKS+ KP P  K ++ LD  F+CPFCNH  S E  +D      + ACR+C E F TT
Sbjct: 1  MGKRKSRAKPAPT-KRMDKLDTIFSCPFCNHGSSVECIIDMKHLIGKAACRICEESFSTT 59

Query: 61 INFLSEAIDVYNDWVD 76
          I  L+EAID+Y++W+D
Sbjct: 60 ITALTEAIDIYSEWID 75

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Arabidopsis thaliana (taxid: 3702)

>sp|P36053|ELF1_YEAST Transcription elongation factor 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ELF1 PE=1 SV=1

 Score = 84.0 bits (206), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 37/77 (48%), Positives = 52/77 (67%), Gaps = 1/77 (1%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MG+RK   + P KR  ++ LD +FNC FCNHEKS    +DK  +   ++C++C + FQT 
Sbjct: 1  MGKRKKSTRKPTKRL-VQKLDTKFNCLFCNHEKSVSCTLDKKNSIGTLSCKICGQSFQTR 59

Query: 61 INFLSEAIDVYNDWVDA 77
          IN LS+ +DVY+DW DA
Sbjct: 60 INSLSQPVDVYSDWFDA 76

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|O13868|ELOF1_SCHPO Transcription elongation factor 1 homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC1B3.02c PE=1 SV=1

 Score = 78.6 bits (192), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 37/77 (48%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MG+RK+K K  PKR+   PLD  F C FCNHEKS    +DK      + C++C +  Q  
Sbjct: 1  MGKRKAKAKVKPKRR-APPLDTTFTCLFCNHEKSVSCSLDKQSGVGNLHCKICGQSHQCL 59

Query: 61 INFLSEAIDVYNDWVDA 77
          I  LS  IDVY+DW+DA
Sbjct: 60 ITALSAPIDVYSDWIDA 76

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

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

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	81
195483087	82	GE19761 [Drosophila yakuba] gi|194185993	0.950	0.939	0.935	2e-35
170038837	82	conserved hypothetical protein [Culex qu	0.950	0.939	0.909	4e-35
194764452	82	GF19993 [Drosophila ananassae] gi|194876	0.950	0.939	0.922	4e-35
289739519	82	transcription elongation factor 1-like p	0.950	0.939	0.896	9e-35
157138064	82	hypothetical protein AaeL_AAEL003749 [Ae	0.950	0.939	0.896	9e-35
161076122	82	CG40228, isoform C [Drosophila melanogas	0.950	0.939	0.909	2e-34
195446429	82	GK19168 [Drosophila willistoni] gi|19416	0.950	0.939	0.909	5e-34
91090556	82	PREDICTED: similar to CG40228 CG40228-PC	0.950	0.939	0.870	8e-34
242011866	82	conserved hypothetical protein [Pediculu	0.950	0.939	0.857	9e-34
31209067	82	AGAP003707-PA [Anopheles gambiae str. PE	0.950	0.939	0.870	2e-33

>gi|195483087|ref|XP_002086852.1| GE19761 [Drosophila yakuba] gi|194185993|gb|EDW99604.1| GE19761 [Drosophila yakuba]

 Score =  152 bits (385), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 72/77 (93%), Positives = 73/77 (94%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRRKSKRKPPPKRKNIEPLD QFNCPFCNHEKSCEVKMDKGRN+ARI CRVCLEDFQT 
Sbjct: 1  MGRRKSKRKPPPKRKNIEPLDQQFNCPFCNHEKSCEVKMDKGRNTARITCRVCLEDFQTG 60

Query: 61 INFLSEAIDVYNDWVDA 77
          INFLSE IDVYNDWVDA
Sbjct: 61 INFLSEPIDVYNDWVDA 77

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170038837|ref|XP_001847254.1| conserved hypothetical protein [Culex quinquefasciatus] gi|167862445|gb|EDS25828.1| conserved hypothetical protein [Culex quinquefasciatus]

 Score =  152 bits (383), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 70/77 (90%), Positives = 73/77 (94%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRRKSKRKPPPKRKNIEPLD QFNCPFCNHEKSCEVKMDK RNSARI CRVC+ED+QTT
Sbjct: 1  MGRRKSKRKPPPKRKNIEPLDQQFNCPFCNHEKSCEVKMDKSRNSARITCRVCMEDYQTT 60

Query: 61 INFLSEAIDVYNDWVDA 77
          INFLSE +DVYNDWVDA
Sbjct: 61 INFLSEPVDVYNDWVDA 77

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194764452|ref|XP_001964343.1| GF19993 [Drosophila ananassae] gi|194876816|ref|XP_001973846.1| GG16332 [Drosophila erecta] gi|195038885|ref|XP_001990829.1| GH18042 [Drosophila grimshawi] gi|195107686|ref|XP_001998439.1| GI23965 [Drosophila mojavensis] gi|195151761|ref|XP_002016807.1| GL21968 [Drosophila persimilis] gi|195403266|ref|XP_002060214.1| GJ22512 [Drosophila virilis] gi|198461808|ref|XP_002135770.1| GA17880 [Drosophila pseudoobscura pseudoobscura] gi|190614615|gb|EDV30139.1| GF19993 [Drosophila ananassae] gi|190655629|gb|EDV52872.1| GG16332 [Drosophila erecta] gi|193895025|gb|EDV93891.1| GH18042 [Drosophila grimshawi] gi|193915033|gb|EDW13900.1| GI23965 [Drosophila mojavensis] gi|194111864|gb|EDW33907.1| GL21968 [Drosophila persimilis] gi|194141797|gb|EDW58211.1| GJ22512 [Drosophila virilis] gi|198142734|gb|EDY71453.1| GA17880 [Drosophila pseudoobscura pseudoobscura]

 Score =  151 bits (382), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 71/77 (92%), Positives = 73/77 (94%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRRKSKRKPPPKRKNIEPLD QFNCPFCNHEKSCEVKMDKGRN+A+I CRVCLEDFQT 
Sbjct: 1  MGRRKSKRKPPPKRKNIEPLDQQFNCPFCNHEKSCEVKMDKGRNTAKITCRVCLEDFQTG 60

Query: 61 INFLSEAIDVYNDWVDA 77
          INFLSE IDVYNDWVDA
Sbjct: 61 INFLSEPIDVYNDWVDA 77

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|289739519|gb|ADD18507.1| transcription elongation factor 1-like protein [Glossina morsitans morsitans]

 Score =  150 bits (379), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 69/77 (89%), Positives = 74/77 (96%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRRKSKRKPPPKRKNI+PLD QFNCPFCNHEKSCEVKMDK RN+ARI+CRVCLED+QTT
Sbjct: 1  MGRRKSKRKPPPKRKNIQPLDQQFNCPFCNHEKSCEVKMDKSRNTARISCRVCLEDYQTT 60

Query: 61 INFLSEAIDVYNDWVDA 77
          INFLSE +DVYNDWVDA
Sbjct: 61 INFLSEPLDVYNDWVDA 77

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157138064|ref|XP_001657220.1| hypothetical protein AaeL_AAEL003749 [Aedes aegypti] gi|108880704|gb|EAT44929.1| AAEL003749-PA [Aedes aegypti]

 Score =  150 bits (379), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 69/77 (89%), Positives = 73/77 (94%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRRKSKRKPPPKRKNIEPLD QFNCPFCNHEKSCEVKMDK RNSARI CRVC+ED+QT+
Sbjct: 1  MGRRKSKRKPPPKRKNIEPLDQQFNCPFCNHEKSCEVKMDKSRNSARITCRVCMEDYQTS 60

Query: 61 INFLSEAIDVYNDWVDA 77
          INFLSE +DVYNDWVDA
Sbjct: 61 INFLSEPVDVYNDWVDA 77

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|161076122|ref|NP_001104426.1| CG40228, isoform C [Drosophila melanogaster] gi|442634478|ref|NP_001263166.1| CG40228, isoform D [Drosophila melanogaster] gi|195359298|ref|XP_002045341.1| GM19294 [Drosophila sechellia] gi|195556994|ref|XP_002077227.1| GD25376 [Drosophila simulans] gi|25453309|sp|Q8MQI6.1|ELOF1_DROME RecName: Full=Transcription elongation factor 1 homolog gi|21744283|gb|AAM76200.1| RE67573p [Drosophila melanogaster] gi|158529745|gb|EDP28091.1| CG40228, isoform C [Drosophila melanogaster] gi|194129331|gb|EDW51374.1| GM19294 [Drosophila sechellia] gi|194202320|gb|EDX15896.1| GD25376 [Drosophila simulans] gi|220959684|gb|ACL92385.1| CG40228-PC [synthetic construct] gi|440216244|gb|ELP57411.1| CG40228, isoform D [Drosophila melanogaster]

 Score =  149 bits (376), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 70/77 (90%), Positives = 72/77 (93%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRRKSKRKPPPKRKNIEPLD QFNCPFCNHEKSCEVKMDK RN+A+I CRVCLEDFQT 
Sbjct: 1  MGRRKSKRKPPPKRKNIEPLDQQFNCPFCNHEKSCEVKMDKSRNTAKITCRVCLEDFQTG 60

Query: 61 INFLSEAIDVYNDWVDA 77
          INFLSE IDVYNDWVDA
Sbjct: 61 INFLSEPIDVYNDWVDA 77

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195446429|ref|XP_002070776.1| GK19168 [Drosophila willistoni] gi|194166861|gb|EDW81762.1| GK19168 [Drosophila willistoni]

 Score =  148 bits (373), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 70/77 (90%), Positives = 72/77 (93%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRRKSKRKPPPKRKNIEPLD QFNCPFCNHEKSCEVKMDK RN+A+I CRVCLEDFQT 
Sbjct: 1  MGRRKSKRKPPPKRKNIEPLDQQFNCPFCNHEKSCEVKMDKRRNTAKITCRVCLEDFQTG 60

Query: 61 INFLSEAIDVYNDWVDA 77
          INFLSE IDVYNDWVDA
Sbjct: 61 INFLSEPIDVYNDWVDA 77

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91090556|ref|XP_971424.1| PREDICTED: similar to CG40228 CG40228-PC [Tribolium castaneum] gi|270014357|gb|EFA10805.1| hypothetical protein TcasGA2_TC030554 [Tribolium castaneum]

 Score =  147 bits (371), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 67/77 (87%), Positives = 72/77 (93%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRRKSKRKP PKRK +EPLD QFNCPFCNHEKSC+VKMDKGRN+ARI CRVCLEDFQTT
Sbjct: 1  MGRRKSKRKPAPKRKAVEPLDQQFNCPFCNHEKSCDVKMDKGRNTARITCRVCLEDFQTT 60

Query: 61 INFLSEAIDVYNDWVDA 77
          INFLSE +DVYNDW+DA
Sbjct: 61 INFLSEPVDVYNDWIDA 77

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242011866|ref|XP_002426665.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212510829|gb|EEB13927.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  147 bits (371), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 66/77 (85%), Positives = 72/77 (93%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRRKSKRKPPPKRKNIEPLD+QF CPFCNHEKSCEVKMDK RN+ARI+CRVC ED+QT 
Sbjct: 1  MGRRKSKRKPPPKRKNIEPLDVQFTCPFCNHEKSCEVKMDKSRNTARISCRVCSEDYQTV 60

Query: 61 INFLSEAIDVYNDWVDA 77
          INFLSE +DVYNDW+DA
Sbjct: 61 INFLSEPVDVYNDWIDA 77

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|31209067|ref|XP_313500.1| AGAP003707-PA [Anopheles gambiae str. PEST] gi|30177009|gb|EAA44682.1| AGAP003707-PA [Anopheles gambiae str. PEST]

 Score =  145 bits (367), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 67/77 (87%), Positives = 73/77 (94%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRRKSKRKPPPKRKNIEPLD QFNCPFCNHEKSCEVKMDK +NSA+I CRVCLE++QT+
Sbjct: 1  MGRRKSKRKPPPKRKNIEPLDQQFNCPFCNHEKSCEVKMDKPKNSAKILCRVCLEEYQTS 60

Query: 61 INFLSEAIDVYNDWVDA 77
          INFLSE +DVYNDWVDA
Sbjct: 61 INFLSEPVDVYNDWVDA 77

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	81
FB|FBgn0063670	82	CG40228 [Drosophila melanogast	0.765	0.756	0.887	1.7e-27
WB|WBGene00013219	84	Y54G11A.11.2 [Caenorhabditis e	0.753	0.726	0.721	4.3e-22
UNIPROTKB|Q9XVZ8	84	Y54G11A.11 "Transcription elon	0.753	0.726	0.721	4.3e-22
UNIPROTKB|A4IFR3	83	ELOF1 "Transcription elongatio	0.716	0.698	0.672	3.5e-20
UNIPROTKB|P60002	83	ELOF1 "Transcription elongatio	0.716	0.698	0.672	3.5e-20
MGI|MGI:1913376	83	Elof1 "elongation factor 1 hom	0.716	0.698	0.672	3.5e-20
ZFIN|ZDB-GENE-040426-1385	83	elof1 "elongation factor 1 hom	0.716	0.698	0.672	3.5e-20
FB|FBgn0036531	82	CG6244 [Drosophila melanogaste	0.765	0.756	0.645	4.4e-20
UNIPROTKB|G4MN17	123	MGG_06916 "Transcription elong	0.753	0.495	0.524	6.9e-15
ASPGD|ASPL0000078186	122	AN11131 [Emericella nidulans (	0.740	0.491	0.566	1.4e-14

FB|FBgn0063670 CG40228 [Drosophila melanogaster (taxid:7227)]

 Score = 308 (113.5 bits), Expect = 1.7e-27, P = 1.7e-27
 Identities = 55/62 (88%), Positives = 57/62 (91%)

Query:    16 NIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWV 75
             NIEPLD QFNCPFCNHEKSCEVKMDK RN+A+I CRVCLEDFQT INFLSE IDVYNDWV
Sbjct:    16 NIEPLDQQFNCPFCNHEKSCEVKMDKSRNTAKITCRVCLEDFQTGINFLSEPIDVYNDWV 75

Query:    76 DA 77
             DA
Sbjct:    76 DA 77

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

WB|WBGene00013219 Y54G11A.11.2 [Caenorhabditis elegans (taxid:6239)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 44/61 (72%), Positives = 51/61 (83%)

Query:    17 IEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVD 76
             + PLD QFNCPFCNHE+ CEVKMD+ +N   I+CRVC EDFQT IN+LSE IDVY+DWVD
Sbjct:    17 VMPLDTQFNCPFCNHERVCEVKMDREKNVGYISCRVCSEDFQTNINYLSEPIDVYSDWVD 76

Query:    77 A 77
             A
Sbjct:    77 A 77

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q9XVZ8 Y54G11A.11 "Transcription elongation factor 1 homolog" [Caenorhabditis elegans (taxid:6239)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 44/61 (72%), Positives = 51/61 (83%)

Query:    17 IEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVD 76
             + PLD QFNCPFCNHE+ CEVKMD+ +N   I+CRVC EDFQT IN+LSE IDVY+DWVD
Sbjct:    17 VMPLDTQFNCPFCNHERVCEVKMDREKNVGYISCRVCSEDFQTNINYLSEPIDVYSDWVD 76

Query:    77 A 77
             A
Sbjct:    77 A 77

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|A4IFR3 ELOF1 "Transcription elongation factor 1 homolog" [Bos taurus (taxid:9913)]

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query:    20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDA 77
             L+ QF CPFCNHEKSC+VKMD+ RN+  I+C VCLE+FQT I +LSE +DVY+DW+DA
Sbjct:    20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDA 77

GO:0005634 "nucleus" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

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

UNIPROTKB|P60002 ELOF1 "Transcription elongation factor 1 homolog" [Homo sapiens (taxid:9606)]

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query:    20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDA 77
             L+ QF CPFCNHEKSC+VKMD+ RN+  I+C VCLE+FQT I +LSE +DVY+DW+DA
Sbjct:    20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDA 77

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

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

MGI|MGI:1913376 Elof1 "elongation factor 1 homolog (ELF1, S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query:    20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDA 77
             L+ QF CPFCNHEKSC+VKMD+ RN+  I+C VCLE+FQT I +LSE +DVY+DW+DA
Sbjct:    20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDA 77

GO:0003674 "molecular_function" evidence=ND

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

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0006414 "translational elongation" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

ZFIN|ZDB-GENE-040426-1385 elof1 "elongation factor 1 homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query:    20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDA 77
             LD QF CPFCNHEKSC+VKM++ RN+  I+C VCLE+FQT I +LSE +DVY+DW+DA
Sbjct:    20 LDTQFTCPFCNHEKSCDVKMERSRNTGIISCTVCLEEFQTPITYLSEPVDVYSDWIDA 77

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

FB|FBgn0036531 CG6244 [Drosophila melanogaster (taxid:7227)]

 Score = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 40/62 (64%), Positives = 50/62 (80%)

Query:    16 NIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWV 75
             NI+PL I F+CPFCNH++SCE K+DK +   RI C VC E FQT IN+L+EAIDV+NDW+
Sbjct:    16 NIQPLPILFDCPFCNHKQSCEAKLDKAKKIGRITCTVCQEFFQTHINYLTEAIDVFNDWI 75

Query:    76 DA 77
             DA
Sbjct:    76 DA 77

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|G4MN17 MGG_06916 "Transcription elongation factor" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 189 (71.6 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 32/61 (52%), Positives = 43/61 (70%)

Query:    18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDA 77
             +PL  QF C FCNHEKS +VK+DK      + C++C + FQ  IN+LS A+DVY +WVDA
Sbjct:    17 DPLPTQFTCLFCNHEKSVDVKLDKKMGVGNLECKICGQRFQCGINYLSAAVDVYGEWVDA 76

Query:    78 S 78
             +
Sbjct:    77 A 77

GO:0005634 "nucleus" evidence=ISS

GO:0006325 "chromatin organization" evidence=ISS

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

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

GO:0008270 "zinc ion binding" evidence=ISS

ASPGD|ASPL0000078186 AN11131 [Emericella nidulans (taxid:162425)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 34/60 (56%), Positives = 42/60 (70%)

Query:    18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDA 77
             EPL   F C FCNHE S  VK+DK      ++C+VC + FQT IN+LS A+DVY+DWVDA
Sbjct:    18 EPLPSTFACLFCNHENSIVVKLDKKLGLGHLSCKVCGQRFQTGINYLSAAVDVYSDWVDA 77

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

GO:0000993 "RNA polymerase II core binding" evidence=IEA

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

GO:0034401 "regulation of transcription by chromatin organization" 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)
Q8LHP0	ELOF1_ORYSJ	No assigned EC number	0.4868	0.9259	0.8426	yes	N/A
P60002	ELOF1_HUMAN	No assigned EC number	0.6724	0.7160	0.6987	yes	N/A
P60003	ELOF1_MOUSE	No assigned EC number	0.6724	0.7160	0.6987	yes	N/A
A4IFR3	ELOF1_BOVIN	No assigned EC number	0.6724	0.7160	0.6987	yes	N/A
O13868	ELOF1_SCHPO	No assigned EC number	0.4805	0.9382	0.7102	yes	N/A
Q8MQI6	ELOF1_DROME	No assigned EC number	0.9090	0.9506	0.9390	yes	N/A
Q9U501	ELOF1_MANSE	No assigned EC number	0.8311	0.9506	0.9390	N/A	N/A
Q8LEF3	ELOF1_ARATH	No assigned EC number	0.5	0.9259	0.625	yes	N/A
Q54KR5	ELOF1_DICDI	No assigned EC number	0.4675	0.9259	0.9375	yes	N/A
Q9XVZ8	ELOF1_CAEEL	No assigned EC number	0.7142	0.9506	0.9166	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	81
pfam05129	74	pfam05129, Elf1, Transcription elongation factor E	3e-32
COG4888	104	COG4888, COG4888, Uncharacterized Zn ribbon-contai	1e-20
PRK14892	99	PRK14892, PRK14892, putative transcription elongat	2e-06

>gnl|CDD|218451 pfam05129, Elf1, Transcription elongation factor Elf1 like

 Score =  106 bits (266), Expect = 3e-32
 Identities = 40/71 (56%), Positives = 50/71 (70%)

Query: 7  KRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSE 66
          K++ PPK+K    L   F+CPFCNH+KS  VK+DK    A++ CRVC   FQT IN LSE
Sbjct: 1  KKRKPPKKKKKYKLPTVFDCPFCNHKKSVSVKIDKKTGIAKLHCRVCGLSFQTEINALSE 60

Query: 67 AIDVYNDWVDA 77
           IDVY+DW+DA
Sbjct: 61 PIDVYSDWIDA 71

This family of short proteins contains a putative zinc binding domain with four conserved cysteines. ELF1 has been identified as a transcription elongation factor in Saccharomyces cerevisiae. Length = 74

>gnl|CDD|227225 COG4888, COG4888, Uncharacterized Zn ribbon-containing protein [General function prediction only]

 Score = 77.9 bits (192), Expect = 1e-20
 Identities = 31/77 (40%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRR+ KR+   KR+  + L   F CP C HEK     + K  N     C  C   F+  
Sbjct: 1  MGRRRRKRRKIIKRR-PQVLPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECE 59

Query: 61 INFLSEAIDVYNDWVDA 77
          +  LSE +DVY+ WVDA
Sbjct: 60 VPELSEPVDVYSAWVDA 76

Length = 104

>gnl|CDD|184886 PRK14892, PRK14892, putative transcription elongation factor Elf1; Provisional

 Score = 41.2 bits (97), Expect = 2e-06
 Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT 60
          MGRR+ KRK   + K   P    F CP C  + S  VK+ K  N A I C  C    +  
Sbjct: 1  MGRRRKKRKKIIRPKPKLP--KIFECPRCG-KVSISVKIKK--NIAIITCGNCGLYTEFE 55

Query: 61 INFLSEAIDVYNDWVDA 77
          +  + + +DVYN ++D 
Sbjct: 56 VPSVYDEVDVYNKFIDL 72

Length = 99

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	81
PF05129	81	Elf1: Transcription elongation factor Elf1 like; I	100.0
KOG3214|consensus	109		100.0
COG4888	104	Uncharacterized Zn ribbon-containing protein [Gene	100.0
PRK14892	99	putative transcription elongation factor Elf1; Pro	100.0
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	97.35
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	97.02
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	96.95
PRK09710	64	lar restriction alleviation and modification prote	96.51
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	96.41
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	96.36
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	96.35
TIGR00244	147	transcriptional regulator NrdR. Members of this al	96.13
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	96.05
COG1327	156	Predicted transcriptional regulator, consists of a	96.04
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	95.94
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	95.42
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	95.19
TIGR00280	91	L37a ribosomal protein L37a. This model finds euka	95.13
PRK03976	90	rpl37ae 50S ribosomal protein L37Ae; Reviewed	95.11
PF14255	52	Cys_rich_CPXG: Cysteine-rich CPXCG	95.1
PTZ00255	90	60S ribosomal protein L37a; Provisional	94.98
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	94.7
PF01780	90	Ribosomal_L37ae: Ribosomal L37ae protein family; I	94.68
PF14353	128	CpXC: CpXC protein	94.35
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	94.3
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	93.77
PHA00626	59	hypothetical protein	93.69
smart00778	37	Prim_Zn_Ribbon Zinc-binding domain of primase-heli	93.59
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	93.28
PRK09678	72	DNA-binding transcriptional regulator; Provisional	93.26
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	92.75
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	92.6
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	92.15
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	91.78
PRK12286	57	rpmF 50S ribosomal protein L32; Reviewed	91.74
PRK00432	50	30S ribosomal protein S27ae; Validated	91.47
PF04606	47	Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I	91.45
PF13453	41	zf-TFIIB: Transcription factor zinc-finger	91.17
PF06044	254	DRP: Dam-replacing family; InterPro: IPR010324 Dam	90.75
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	90.64
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	90.61
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	90.3
TIGR03829	89	YokU_near_AblA uncharacterized protein, YokU famil	90.07
COG3677	129	Transposase and inactivated derivatives [DNA repli	89.62
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	89.53
PRK03988	138	translation initiation factor IF-2 subunit beta; V	89.32
TIGR00311	133	aIF-2beta translation initiation factor aIF-2, bet	89.29
COG3478	68	Predicted nucleic-acid-binding protein containing	89.23
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	89.11
PRK13130	56	H/ACA RNA-protein complex component Nop10p; Review	88.77
PF14205	55	Cys_rich_KTR: Cysteine-rich KTR	88.76
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	88.69
PF09986	214	DUF2225: Uncharacterized protein conserved in bact	88.53
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	88.19
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	87.86
smart00531	147	TFIIE Transcription initiation factor IIE.	87.84
smart00661	52	RPOL9 RNA polymerase subunit 9.	87.53
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	87.4
PF01873	125	eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro:	87.35
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	87.05
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	86.95
PF08273	40	Prim_Zn_Ribbon: Zinc-binding domain of primase-hel	86.66
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	86.6
PF05605	54	zf-Di19: Drought induced 19 protein (Di19), zinc-b	86.48
TIGR03831	46	YgiT_finger YgiT-type zinc finger domain. This dom	86.46
smart00653	110	eIF2B_5 domain present in translation initiation f	86.33
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	86.13
PF05180	66	zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc	86.13
TIGR01385	299	TFSII transcription elongation factor S-II. This m	85.98
COG1326	201	Uncharacterized archaeal Zn-finger protein [Genera	85.72
PF13248	26	zf-ribbon_3: zinc-ribbon domain	85.62
PF09526	71	DUF2387: Probable metal-binding protein (DUF2387);	85.54
TIGR02443	59	conserved hypothetical metal-binding protein. Memb	85.38
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	85.24
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	84.83
PRK12336	201	translation initiation factor IF-2 subunit beta; P	84.8
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	84.54
TIGR01031	55	rpmF_bact ribosomal protein L32. This protein desc	83.42
KOG0478|consensus	804		83.37
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	82.79
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	82.69
PHA02540	337	61 DNA primase; Provisional	82.62
PF13465	26	zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A	82.58
PF03367	161	zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004	82.56
PRK05978	148	hypothetical protein; Provisional	82.34
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	82.32
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	81.77
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	81.76
COG0675	364	Transposase and inactivated derivatives [DNA repli	81.68
TIGR01562	305	FdhE formate dehydrogenase accessory protein FdhE.	81.14
KOG0402|consensus	92		80.39
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	80.36

>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=100.00  E-value=1.2e-43  Score=225.86  Aligned_cols=79  Identities=56%  Similarity=0.978  Sum_probs=45.8

Q ss_pred             CCCCcCCC-CCCCCCCCCCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCC
Q psy3498           2 GRRKSKRK-PPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP   80 (81)
Q Consensus         2 GkRK~~~k-~~~kkk~~~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~   80 (81)
                      ||||++++ +++++ ++++|||.|+||||||++||+|+||++.++|+|+|++||++|+++|++|+||||||++|||+|+|
T Consensus         1 GkRK~~~k~~~~kk-~~~~l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L~epiDVY~~wiD~~~~   79 (81)
T PF05129_consen    1 GKRKKKRKKPPKKK-KKPKLPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPLSEPIDVYSEWIDACEE   79 (81)
T ss_dssp             --------------------SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS--TTHHHHHHHHHHH-
T ss_pred             CCCcccCCCCCccC-cCCCCCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCccCcccchhHHHHHHHHh
Confidence            89998888 44444 48999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             C
Q psy3498          81 S   81 (81)
Q Consensus        81 ~   81 (81)
                      .
T Consensus        80 ~   80 (81)
T PF05129_consen   80 G   80 (81)
T ss_dssp             -
T ss_pred             c
Confidence            3

; PDB: 1WII_A.

>KOG3214|consensus

Probab=100.00  E-value=1.4e-42  Score=230.24  Aligned_cols=80  Identities=61%  Similarity=1.090  Sum_probs=76.9

Q ss_pred             CCCCCcCCCCCCCCCCCCCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCC
Q psy3498           1 MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP   80 (81)
Q Consensus         1 MGkRK~~~k~~~kkk~~~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~   80 (81)
                      |||||+|++.++|.+++++|+|.|+||||||+++|+|+||++.++|.++|++|+++||+.||+|++||||||+|||+|++
T Consensus         1 MgkRk~K~k~~~k~r~~~~ldt~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFqt~it~LsepIDVYSdWiDaCe~   80 (109)
T KOG3214|consen    1 MGKRKSKRKEPPKERRVEPLDTQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQTTITALSEPIDVYSDWIDACEA   80 (109)
T ss_pred             CCcccccccCCchhhhccchheeeccCccccccceeeeehhhcCcceeeeeehhhhhccchHhhccchHHHHHHHHHHHH
Confidence            99999999988885569999999999999999999999999999999999999999999999999999999999999975

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

Probab=100.00  E-value=6.8e-39  Score=212.11  Aligned_cols=79  Identities=39%  Similarity=0.681  Sum_probs=75.9

Q ss_pred             CCCCCcCCCCCCCCCCCCCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCC
Q psy3498           1 MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP   80 (81)
Q Consensus         1 MGkRK~~~k~~~kkk~~~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~   80 (81)
                      |||||++++.++|++ .++|||.|+||||||+++++|.++++.++|.++|++||++|++.||.|++||||||+|||+|+|
T Consensus         1 MG~rr~krr~~ik~~-~~~L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~vDvYs~wvDay~e   79 (104)
T COG4888           1 MGRRRRKRRKIIKRR-PQVLPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEPVDVYSAWVDAYLE   79 (104)
T ss_pred             CCcccccccccCccc-CccCCceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccchhHHHHHHHHHHh
Confidence            999999988888887 6889999999999999999999999999999999999999999999999999999999999986

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=100.00  E-value=9.9e-35  Score=191.28  Aligned_cols=75  Identities=36%  Similarity=0.562  Sum_probs=68.7

Q ss_pred             CCCCCcCCCCCCCCCCCCCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCC
Q psy3498           1 MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP   80 (81)
Q Consensus         1 MGkRK~~~k~~~kkk~~~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~   80 (81)
                      |||||++++++ +|+ +.++|+.|+|||||+ .+|.|+|++  +++++.|.+||+.|.+.|++|++||||||+|||+|+|
T Consensus         1 MGkRk~~~k~~-~k~-k~klpt~f~CP~Cge-~~v~v~~~k--~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wiD~~~e   75 (99)
T PRK14892          1 MGRRRKKRKKI-IRP-KPKLPKIFECPRCGK-VSISVKIKK--NIAIITCGNCGLYTEFEVPSVYDEVDVYNKFIDLYLE   75 (99)
T ss_pred             CCCccccCCCC-ccc-ccCCCcEeECCCCCC-eEeeeecCC--CcceEECCCCCCccCEECCccccchhhHHHHHHHHHh
Confidence            99999998744 444 589999999999995 899999987  8999999999999999999999999999999999986

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=97.35  E-value=0.00026  Score=41.17  Aligned_cols=46  Identities=26%  Similarity=0.456  Sum_probs=29.3

Q ss_pred             cCCCCCCCCceEEE--eecCCceEEEEcccccceeEeccCCCCchhhhhh
Q psy3498          25 NCPFCNHEKSCEVK--MDKGRNSARIACRVCLEDFQTTINFLSEAIDVYN   72 (81)
Q Consensus        25 ~CPfC~~~~sV~v~--i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs   72 (81)
                      .|||||.+ .+.+.  .+-....+...|..||.+... .....++|+.++
T Consensus         3 PCPfCGg~-~~~~~~~~~~~~~~~~~~C~~Cga~~~~-~~~~~~Ai~~WN   50 (53)
T TIGR03655         3 PCPFCGGA-DVYLRRGFDPLDLSHYFECSTCGASGPV-EEDEAEAIEAWN   50 (53)
T ss_pred             CCCCCCCc-ceeeEeccCCCCCEEEEECCCCCCCccc-ccCHHHHHHHHh
Confidence            59999984 44343  344456666799999998664 334445555443

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.

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=97.02  E-value=0.0013  Score=38.43  Aligned_cols=32  Identities=25%  Similarity=0.608  Sum_probs=22.1

Q ss_pred             eecCCCCCCCCceEEEeecCCce---EEEEcccccc
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNS---ARIACRVCLE   55 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~---g~l~C~~C~~   55 (81)
                      .-.|||||. ..+.+.-+.....   ..+.|..||.
T Consensus         3 LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga   37 (61)
T PF14354_consen    3 LKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA   37 (61)
T ss_pred             CcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence            446999987 5555555433222   7899999998

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=96.95  E-value=0.0011  Score=39.51  Aligned_cols=33  Identities=24%  Similarity=0.703  Sum_probs=25.7

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      .|.||.||.    ++.+.....-..+.|..||+.|+-
T Consensus         2 ~~~CP~CG~----~iev~~~~~GeiV~Cp~CGaeleV   34 (54)
T TIGR01206         2 QFECPDCGA----EIELENPELGELVICDECGAELEV   34 (54)
T ss_pred             ccCCCCCCC----EEecCCCccCCEEeCCCCCCEEEE
Confidence            589999998    455554444458899999999985

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.

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=96.51  E-value=0.0046  Score=38.21  Aligned_cols=50  Identities=28%  Similarity=0.380  Sum_probs=34.0

Q ss_pred             CCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhh
Q psy3498          20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYND   73 (81)
Q Consensus        20 l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~   73 (81)
                      .+++=.|||||- ++|.++-  ..+...+.|..|++.-...-.. -++||+|+.
T Consensus         3 ~d~lKPCPFCG~-~~~~v~~--~~g~~~v~C~~CgA~~~~~~te-~~Aie~WN~   52 (64)
T PRK09710          3 YDNVKPCPFCGC-PSVTVKA--ISGYYRAKCNGCESRTGYGGSE-KEALERWNK   52 (64)
T ss_pred             cccccCCCCCCC-ceeEEEe--cCceEEEEcCCCCcCcccccCH-HHHHHHHHh
Confidence            466778999997 5666665  4677889999999864322111 157777654

>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=96.41  E-value=0.0036  Score=34.86  Aligned_cols=31  Identities=19%  Similarity=0.616  Sum_probs=22.4

Q ss_pred             ecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      |.||.|++..   +..|  ...|.+.|..||+--+.
T Consensus         1 m~Cp~Cg~~~---~~~D--~~~g~~vC~~CG~Vl~e   31 (43)
T PF08271_consen    1 MKCPNCGSKE---IVFD--PERGELVCPNCGLVLEE   31 (43)
T ss_dssp             ESBTTTSSSE---EEEE--TTTTEEEETTT-BBEE-
T ss_pred             CCCcCCcCCc---eEEc--CCCCeEECCCCCCEeec
Confidence            6899999943   4555  45588899999987664

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.

>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=96.36  E-value=0.0075  Score=33.30  Aligned_cols=35  Identities=17%  Similarity=0.493  Sum_probs=24.6

Q ss_pred             ecCCCCCCCCceEEEeecC----CceEEEEcccccceeE
Q psy3498          24 FNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQ   58 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~   58 (81)
                      |+||.|||.+++-..+.-.    .+.-...|..||..|.
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            6899999999888866442    3567888999998763

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 ....

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=96.35  E-value=0.0016  Score=35.03  Aligned_cols=32  Identities=19%  Similarity=0.609  Sum_probs=22.8

Q ss_pred             eecCCCCCCCCceEEEeecC---CceEEEEcccccceeE
Q psy3498          23 QFNCPFCNHEKSCEVKMDKG---RNSARIACRVCLEDFQ   58 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~---~~~g~l~C~~C~~~~~   58 (81)
                      .+.||.|+..    ..++..   ...+.+.|.+||..|.
T Consensus         2 ~~~CP~C~~~----~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         2 RIQCPNCKTS----FRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             EEECCCCCCE----EEeCHHHcCCCCCEEECCCCCCEEE
Confidence            4789999983    444432   2334899999999875

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.

>TIGR00244 transcriptional regulator NrdR

Probab=96.13  E-value=0.0052  Score=43.27  Aligned_cols=36  Identities=31%  Similarity=0.647  Sum_probs=24.5

Q ss_pred             cCCCCCCCCceEEEe-ecCCceE---EEEcccccceeEec
Q psy3498          25 NCPFCNHEKSCEVKM-DKGRNSA---RIACRVCLEDFQTT   60 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i-~k~~~~g---~l~C~~C~~~~~~~   60 (81)
                      .||||||+++-.+.= .-+++.+   .=.|..||.+|+|-
T Consensus         2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTy   41 (147)
T TIGR00244         2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTF   41 (147)
T ss_pred             CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcccee
Confidence            599999987744332 1134433   35799999999873

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.

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

Probab=96.05  E-value=0.017  Score=32.48  Aligned_cols=34  Identities=21%  Similarity=0.492  Sum_probs=25.1

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEecc
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTI   61 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i   61 (81)
                      ..|.||.||.    .+.++...  ..+.|..||..+....
T Consensus         2 ~~y~C~~CG~----~~~~~~~~--~~~~Cp~CG~~~~~~~   35 (46)
T PRK00398          2 AEYKCARCGR----EVELDEYG--TGVRCPYCGYRILFKE   35 (46)
T ss_pred             CEEECCCCCC----EEEECCCC--CceECCCCCCeEEEcc
Confidence            4799999998    55555433  3789999998876543

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

Probab=96.04  E-value=0.0039  Score=44.35  Aligned_cols=34  Identities=38%  Similarity=0.829  Sum_probs=23.5

Q ss_pred             cCCCCCCCCceEEEeecC--CceE---EEEcccccceeEe
Q psy3498          25 NCPFCNHEKSCEVKMDKG--RNSA---RIACRVCLEDFQT   59 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~--~~~g---~l~C~~C~~~~~~   59 (81)
                      .||||||+.|=.+. .+.  .|-+   .-.|..||.+|+|
T Consensus         2 ~CPfC~~~~tkViD-SR~~edg~aIRRRReC~~C~~RFTT   40 (156)
T COG1327           2 KCPFCGHEDTKVID-SRPAEEGNAIRRRRECLECGERFTT   40 (156)
T ss_pred             CCCCCCCCCCeeee-cccccccchhhhhhcccccccccch
Confidence            59999998884432 222  2222   4579999999987

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=95.94  E-value=0.009  Score=32.58  Aligned_cols=32  Identities=19%  Similarity=0.615  Sum_probs=23.6

Q ss_pred             eecCCCCCCCCceEEEeecC---CceEEEEcccccceeE
Q psy3498          23 QFNCPFCNHEKSCEVKMDKG---RNSARIACRVCLEDFQ   58 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~---~~~g~l~C~~C~~~~~   58 (81)
                      ..+||.|+.    .-+|+.+   .+.+.+.|..|+..|.
T Consensus         2 ~i~CP~C~~----~f~v~~~~l~~~~~~vrC~~C~~~f~   36 (37)
T PF13719_consen    2 IITCPNCQT----RFRVPDDKLPAGGRKVRCPKCGHVFR   36 (37)
T ss_pred             EEECCCCCc----eEEcCHHHcccCCcEEECCCCCcEee
Confidence            358999998    3344332   4567999999999875

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=95.42  E-value=0.039  Score=30.60  Aligned_cols=34  Identities=15%  Similarity=0.427  Sum_probs=26.2

Q ss_pred             ecCCCCCCCCceEEEeecC----CceEEEEccccccee
Q psy3498          24 FNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDF   57 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~   57 (81)
                      |.||.|||.+++-..+.-.    .+.-...|..||-.+
T Consensus         1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w   38 (40)
T smart00440        1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW   38 (40)
T ss_pred             CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence            6899999999987776432    346688999999765

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

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=95.19  E-value=0.0093  Score=32.48  Aligned_cols=34  Identities=18%  Similarity=0.457  Sum_probs=23.2

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF   57 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~   57 (81)
                      .++||.|+..-.|.-..-. ...+.+.|..||..|
T Consensus         2 ~i~Cp~C~~~y~i~d~~ip-~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    2 IITCPNCQAKYEIDDEKIP-PKGRKVRCSKCGHVF   35 (36)
T ss_pred             EEECCCCCCEEeCCHHHCC-CCCcEEECCCCCCEe
Confidence            4689999985443333211 455689999999876

>TIGR00280 L37a ribosomal protein L37a

Probab=95.13  E-value=0.031  Score=36.62  Aligned_cols=33  Identities=30%  Similarity=0.763  Sum_probs=25.8

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEec
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT   60 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~   60 (81)
                      ..+.||||+.. +  ++   ...+|+-.|+.|+..|.--
T Consensus        34 a~y~CpfCgk~-~--vk---R~a~GIW~C~~C~~~~AGG   66 (91)
T TIGR00280        34 AKYVCPFCGKK-T--VK---RGSTGIWTCRKCGAKFAGG   66 (91)
T ss_pred             cCccCCCCCCC-c--eE---EEeeEEEEcCCCCCEEeCC
Confidence            67899999973 2  22   2688999999999998643

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

>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed

Probab=95.11  E-value=0.031  Score=36.49  Aligned_cols=40  Identities=23%  Similarity=0.443  Sum_probs=28.2

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCch
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEA   67 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~ep   67 (81)
                      ..+.||||+..   .++   ...+|+-.|+.|+..|.--.-.++.|
T Consensus        35 a~y~CpfCgk~---~vk---R~a~GIW~C~~C~~~~AGGAy~~~T~   74 (90)
T PRK03976         35 AKHVCPVCGRP---KVK---RVGTGIWECRKCGAKFAGGAYTPETP   74 (90)
T ss_pred             cCccCCCCCCC---ceE---EEEEEEEEcCCCCCEEeCCccccccc
Confidence            67899999863   222   26889999999999986533333333

>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG

Probab=95.10  E-value=0.028  Score=33.22  Aligned_cols=46  Identities=22%  Similarity=0.521  Sum_probs=30.1

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccc--eeEeccCCCCchhhh
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLE--DFQTTINFLSEAIDV   70 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~--~~~~~i~~L~epIDV   70 (81)
                      +||+||+...+.+..........--|.+|-.  .+...+.....-|.|
T Consensus         2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~v~~d~~~~~v~v   49 (52)
T PF14255_consen    2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQVTVDEDEPSVSV   49 (52)
T ss_pred             CCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEEEEEECCCCCEEEE
Confidence            7999999766666555555566788999986  444445444333333

>PTZ00255 60S ribosomal protein L37a; Provisional

Probab=94.98  E-value=0.035  Score=36.25  Aligned_cols=33  Identities=24%  Similarity=0.642  Sum_probs=25.7

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEec
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT   60 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~   60 (81)
                      ..+.||||+.. +  ++   ...+|+-.|+.|+..|.--
T Consensus        35 a~y~CpfCgk~-~--vk---R~a~GIW~C~~C~~~~AGG   67 (90)
T PTZ00255         35 AKYFCPFCGKH-A--VK---RQAVGIWRCKGCKKTVAGG   67 (90)
T ss_pred             CCccCCCCCCC-c--ee---eeeeEEEEcCCCCCEEeCC
Confidence            67999999973 2  22   2577999999999998643

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=94.70  E-value=0.049  Score=38.30  Aligned_cols=35  Identities=29%  Similarity=0.658  Sum_probs=22.6

Q ss_pred             cCCCCCCCCceEEEeec-CCc--e-EEEEcccccceeEe
Q psy3498          25 NCPFCNHEKSCEVKMDK-GRN--S-ARIACRVCLEDFQT   59 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k-~~~--~-g~l~C~~C~~~~~~   59 (81)
                      .||+||++.+-.+.=.- ..|  + -.-.|..||-+|++
T Consensus         2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~   40 (154)
T PRK00464          2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT   40 (154)
T ss_pred             cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence            69999997743332221 111  2 24789999999976

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

Probab=94.68  E-value=0.03  Score=36.60  Aligned_cols=41  Identities=24%  Similarity=0.535  Sum_probs=27.5

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchh
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAI   68 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epI   68 (81)
                      ..+.||||+...   ++.   ..+|+-.|+.|+..|.--.-.++.|.
T Consensus        34 ~ky~Cp~Cgk~~---vkR---~a~GIW~C~~C~~~~AGGAy~~~T~~   74 (90)
T PF01780_consen   34 AKYTCPFCGKTS---VKR---VATGIWKCKKCGKKFAGGAYTPSTPA   74 (90)
T ss_dssp             S-BEESSSSSSE---EEE---EETTEEEETTTTEEEE-BSSSSS-HH
T ss_pred             CCCcCCCCCCce---eEE---eeeEEeecCCCCCEEeCCCccccchH
Confidence            578999999842   332   56788999999999876444444443

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 ....

>PF14353 CpXC: CpXC protein

Probab=94.35  E-value=0.049  Score=35.98  Aligned_cols=40  Identities=25%  Similarity=0.513  Sum_probs=27.2

Q ss_pred             ecCCCCCCCCceEEEeec-------------CCceEEEEcccccceeEeccCC
Q psy3498          24 FNCPFCNHEKSCEVKMDK-------------GRNSARIACRVCLEDFQTTINF   63 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k-------------~~~~g~l~C~~C~~~~~~~i~~   63 (81)
                      -+||.|+|+..+++--.-             ........|..||..+....+-
T Consensus         2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~   54 (128)
T PF14353_consen    2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPL   54 (128)
T ss_pred             cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCE
Confidence            379999997666553211             1245689999999988754443

>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=94.30  E-value=0.087  Score=32.27  Aligned_cols=48  Identities=19%  Similarity=0.458  Sum_probs=31.4

Q ss_pred             ecCCCCCCCCceEEEe-----------ecC-CceEEEEcccccc--eeEeccCCCCchhhhh
Q psy3498          24 FNCPFCNHEKSCEVKM-----------DKG-RNSARIACRVCLE--DFQTTINFLSEAIDVY   71 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i-----------~k~-~~~g~l~C~~C~~--~~~~~i~~L~epIDVY   71 (81)
                      +.||-||++..-.=.+           |-. +..-.++|..||-  -|....+.|.+-+|.+
T Consensus         1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~Y~~~~~~~~~i~D~~   62 (64)
T PF09855_consen    1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEFYKAKTSNGSNILDFF   62 (64)
T ss_pred             CCCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEEEeecCcccchhhhhh
Confidence            4799999964322121           211 1234789999994  4667888888887764

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

Probab=93.77  E-value=0.072  Score=28.67  Aligned_cols=30  Identities=17%  Similarity=0.410  Sum_probs=22.6

Q ss_pred             ecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      -.|+-|||+.-+.      ...+...|..||.+|++
T Consensus         4 ~~C~~C~~~~i~~------~~~~~~~C~~Cg~~~~~   33 (33)
T PF08792_consen    4 KKCSKCGGNGIVN------KEDDYEVCIFCGSSFPY   33 (33)
T ss_pred             eEcCCCCCCeEEE------ecCCeEEcccCCcEeeC
Confidence            4699999965332      34478999999999874

>PHA00626 hypothetical protein

Probab=93.69  E-value=0.073  Score=32.41  Aligned_cols=34  Identities=24%  Similarity=0.408  Sum_probs=24.8

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      .||.||+.+-+-+.+-++ ....-.|..||-.|+-
T Consensus         2 ~CP~CGS~~Ivrcg~cr~-~snrYkCkdCGY~ft~   35 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMRG-WSDDYVCCDCGYNDSK   35 (59)
T ss_pred             CCCCCCCceeeeeceecc-cCcceEcCCCCCeech
Confidence            599999976665555443 2467789999998863

>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase

Probab=93.59  E-value=0.054  Score=29.98  Aligned_cols=29  Identities=24%  Similarity=0.567  Sum_probs=24.9

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLE   55 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~   55 (81)
                      .||.|+-.....  ++.+.+.|...|..|+.
T Consensus         5 pCP~CGG~DrFr--~~d~~g~G~~~C~~Cg~   33 (37)
T smart00778        5 PCPNCGGSDRFR--FDDKDGRGTWFCSVCGA   33 (37)
T ss_pred             CCCCCCCccccc--cccCCCCcCEEeCCCCC
Confidence            599999988877  66678889999999985

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

>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=93.28  E-value=0.07  Score=29.98  Aligned_cols=31  Identities=26%  Similarity=0.741  Sum_probs=21.3

Q ss_pred             CCceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498          20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE   55 (81)
Q Consensus        20 l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~   55 (81)
                      -+.-|.||+||+.+  ...+   ...+.-.|..|+.
T Consensus        15 W~~g~~CP~Cg~~~--~~~~---~~~~~~~C~~C~~   45 (46)
T PF12760_consen   15 WPDGFVCPHCGSTK--HYRL---KTRGRYRCKACRK   45 (46)
T ss_pred             CCCCCCCCCCCCee--eEEe---CCCCeEECCCCCC
Confidence            45669999999952  2222   2267889999974

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

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=93.26  E-value=0.11  Score=32.58  Aligned_cols=43  Identities=21%  Similarity=0.519  Sum_probs=25.4

Q ss_pred             ecCCCCCCCCceEEEeec-CC--ceEEEEcc--cccceeEecc---CCCCch
Q psy3498          24 FNCPFCNHEKSCEVKMDK-GR--NSARIACR--VCLEDFQTTI---NFLSEA   67 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k-~~--~~g~l~C~--~C~~~~~~~i---~~L~ep   67 (81)
                      |.||+||+.. ...+=.. ..  ..-.-.|.  .||.+|.+..   +.|+.|
T Consensus         2 m~CP~Cg~~a-~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~es~s~tis~p   52 (72)
T PRK09678          2 FHCPLCQHAA-HARTSRYITDTTKERYHQCQNVNCSATFITYESVQRYIVKP   52 (72)
T ss_pred             ccCCCCCCcc-EEEEChhcChhhheeeeecCCCCCCCEEEEEEEEEEEEcCC
Confidence            7899999954 2222111 12  22456788  7999997632   245544

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

Probab=92.75  E-value=0.24  Score=26.77  Aligned_cols=28  Identities=36%  Similarity=0.621  Sum_probs=20.5

Q ss_pred             CCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      ||.||+  ....+-++...+   .|+.|+-.++
T Consensus         4 Cp~C~n--lL~p~~~~~~~~---~C~~C~Y~~~   31 (35)
T PF02150_consen    4 CPECGN--LLYPKEDKEKRV---ACRTCGYEEP   31 (35)
T ss_dssp             ETTTTS--BEEEEEETTTTE---EESSSS-EEE
T ss_pred             CCCCCc--cceEcCCCccCc---CCCCCCCccC
Confidence            899996  566666665555   9999997665

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 ....

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

Probab=92.60  E-value=0.11  Score=33.90  Aligned_cols=31  Identities=32%  Similarity=0.710  Sum_probs=24.5

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      ....||+|+..   .|+   -...|+-.|+.||..|.
T Consensus        34 ~~~~Cp~C~~~---~Vk---R~a~GIW~C~kCg~~fA   64 (89)
T COG1997          34 AKHVCPFCGRT---TVK---RIATGIWKCRKCGAKFA   64 (89)
T ss_pred             cCCcCCCCCCc---cee---eeccCeEEcCCCCCeec
Confidence            56899999984   332   25779999999999885

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=92.15  E-value=0.053  Score=26.95  Aligned_cols=21  Identities=29%  Similarity=0.615  Sum_probs=13.3

Q ss_pred             CCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498          26 CPFCNHEKSCEVKMDKGRNSARIACRVCLED   56 (81)
Q Consensus        26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~   56 (81)
                      ||.||++..-..          .-|..||..
T Consensus         2 Cp~CG~~~~~~~----------~fC~~CG~~   22 (23)
T PF13240_consen    2 CPNCGAEIEDDA----------KFCPNCGTP   22 (23)
T ss_pred             CcccCCCCCCcC----------cchhhhCCc
Confidence            899998644322          238888763

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=91.78  E-value=0.11  Score=27.68  Aligned_cols=31  Identities=23%  Similarity=0.516  Sum_probs=21.5

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED   56 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~   56 (81)
                      .|.|+.||+.-.+...+  .. -..+.|-.||..
T Consensus         5 ~y~C~~Cg~~fe~~~~~--~~-~~~~~CP~Cg~~   35 (41)
T smart00834        5 EYRCEDCGHTFEVLQKI--SD-DPLATCPECGGD   35 (41)
T ss_pred             EEEcCCCCCEEEEEEec--CC-CCCCCCCCCCCc
Confidence            68999999953333333  22 467889999984

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

>PRK12286 rpmF 50S ribosomal protein L32; Reviewed

Probab=91.74  E-value=0.21  Score=29.84  Aligned_cols=26  Identities=19%  Similarity=0.405  Sum_probs=21.1

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE   55 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~   55 (81)
                      .++....||.||+-           ...+-.|..||.
T Consensus        23 ~~~~l~~C~~CG~~-----------~~~H~vC~~CG~   48 (57)
T PRK12286         23 KAPGLVECPNCGEP-----------KLPHRVCPSCGY   48 (57)
T ss_pred             cCCcceECCCCCCc-----------cCCeEECCCCCc
Confidence            46889999999982           346889999995

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=91.47  E-value=0.12  Score=29.99  Aligned_cols=26  Identities=23%  Similarity=0.423  Sum_probs=18.1

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF   57 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~   57 (81)
                      -||.||++ -..   .   ..+...|+.||..+
T Consensus        22 fCP~Cg~~-~m~---~---~~~r~~C~~Cgyt~   47 (50)
T PRK00432         22 FCPRCGSG-FMA---E---HLDRWHCGKCGYTE   47 (50)
T ss_pred             cCcCCCcc-hhe---c---cCCcEECCCcCCEE
Confidence            79999984 111   1   12688999999765

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

Probab=91.45  E-value=0.31  Score=27.57  Aligned_cols=36  Identities=17%  Similarity=0.436  Sum_probs=22.3

Q ss_pred             cCCCCCCCCceEEEeecCC--ceEEEEccc--ccceeEec
Q psy3498          25 NCPFCNHEKSCEVKMDKGR--NSARIACRV--CLEDFQTT   60 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~--~~g~l~C~~--C~~~~~~~   60 (81)
                      .||+||+...+.-.-....  ......|.+  ||.+|.+.
T Consensus         1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~~   40 (47)
T PF04606_consen    1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVAN   40 (47)
T ss_pred             CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEEE
Confidence            4999999543332222222  234667888  99999764

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

>PF13453 zf-TFIIB: Transcription factor zinc-finger

Probab=91.17  E-value=0.38  Score=26.29  Aligned_cols=27  Identities=22%  Similarity=0.529  Sum_probs=21.0

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLE   55 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~   55 (81)
                      +||.|++ ......+   ..+..-.|..||=
T Consensus         1 ~CP~C~~-~l~~~~~---~~~~id~C~~C~G   27 (41)
T PF13453_consen    1 KCPRCGT-ELEPVRL---GDVEIDVCPSCGG   27 (41)
T ss_pred             CcCCCCc-ccceEEE---CCEEEEECCCCCe
Confidence            5999999 5666666   5577888999984

>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=90.75  E-value=0.24  Score=37.69  Aligned_cols=36  Identities=25%  Similarity=0.634  Sum_probs=15.1

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEcccccceeEec
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT   60 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~   60 (81)
                      -.-||.||+...-  .+....-+|-..|..|++.||.+
T Consensus        31 n~yCP~Cg~~~L~--~f~NN~PVaDF~C~~C~eeyELK   66 (254)
T PF06044_consen   31 NMYCPNCGSKPLS--KFENNRPVADFYCPNCNEEYELK   66 (254)
T ss_dssp             H---TTT--SS-E--E--------EEE-TTT--EEEEE
T ss_pred             CCcCCCCCChhHh--hccCCCccceeECCCCchHHhhh
Confidence            4679999996443  33445678999999999999864

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

>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=90.64  E-value=0.14  Score=28.41  Aligned_cols=30  Identities=20%  Similarity=0.571  Sum_probs=23.5

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE   55 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~   55 (81)
                      .|.|+-|||.-.+...+..   ...+.|-.||.
T Consensus         5 ey~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~   34 (42)
T PF09723_consen    5 EYRCEECGHEFEVLQSISE---DDPVPCPECGS   34 (42)
T ss_pred             EEEeCCCCCEEEEEEEcCC---CCCCcCCCCCC
Confidence            5999999997655555543   67889999998

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.

>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=90.61  E-value=0.29  Score=36.55  Aligned_cols=35  Identities=20%  Similarity=0.490  Sum_probs=19.1

Q ss_pred             ecCCCCCCCCceEEEeecCC-ceEEEEcccccceeE
Q psy3498          24 FNCPFCNHEKSCEVKMDKGR-NSARIACRVCLEDFQ   58 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k~~-~~g~l~C~~C~~~~~   58 (81)
                      =.||.||..-++++...... |.=.+.|..||..+.
T Consensus       173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~  208 (290)
T PF04216_consen  173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWR  208 (290)
T ss_dssp             SS-TTT---EEEEEEE------EEEEEETTT--EEE
T ss_pred             CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeee
Confidence            47999999777776665543 667999999998764

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.

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

Probab=90.30  E-value=0.16  Score=30.94  Aligned_cols=34  Identities=18%  Similarity=0.414  Sum_probs=20.4

Q ss_pred             CceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498          21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE   55 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~   55 (81)
                      -..|.||.||.+.-..|.-=++.+ ..-.|..||.
T Consensus        23 ~~~F~CPnCG~~~I~RC~~CRk~~-~~Y~CP~CGF   56 (59)
T PRK14890         23 AVKFLCPNCGEVIIYRCEKCRKQS-NPYTCPKCGF   56 (59)
T ss_pred             cCEeeCCCCCCeeEeechhHHhcC-CceECCCCCC
Confidence            378999999983233333323332 3457877775

>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family

Probab=90.07  E-value=0.36  Score=31.45  Aligned_cols=35  Identities=26%  Similarity=0.639  Sum_probs=23.9

Q ss_pred             cCCCCCCCC----ceEEEeecCC--------ceEEEEcccccceeEe
Q psy3498          25 NCPFCNHEK----SCEVKMDKGR--------NSARIACRVCLEDFQT   59 (81)
Q Consensus        25 ~CPfC~~~~----sV~v~i~k~~--------~~g~l~C~~C~~~~~~   59 (81)
                      .|+.|++..    .+++..+..+        .+-.+.|..||+.|.+
T Consensus         1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~   47 (89)
T TIGR03829         1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQD   47 (89)
T ss_pred             CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeec
Confidence            499997633    4455555533        3446799999999975

Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.

>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=89.62  E-value=0.32  Score=33.06  Aligned_cols=36  Identities=25%  Similarity=0.523  Sum_probs=26.4

Q ss_pred             ecCCCCCCCCceEEEeecCCceEEEEcccccceeEec
Q psy3498          24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT   60 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~   60 (81)
                      =.||+|++.+ |...=....+...-.|..|+-+|+-.
T Consensus        31 ~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~~~   66 (129)
T COG3677          31 VNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFTVE   66 (129)
T ss_pred             CcCCCCCccc-eeeECCccccccccccCCcCcceeee
Confidence            4799999988 33332233457888999999999753

>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=89.53  E-value=0.51  Score=35.22  Aligned_cols=49  Identities=14%  Similarity=0.298  Sum_probs=26.7

Q ss_pred             eecCCCCCCCCceEEEee---cCCceEEEEcccccceeEeccCCCCchhhhh
Q psy3498          23 QFNCPFCNHEKSCEVKMD---KGRNSARIACRVCLEDFQTTINFLSEAIDVY   71 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~---k~~~~g~l~C~~C~~~~~~~i~~L~epIDVY   71 (81)
                      ...||+||+++.......   -..+.-.-.|..|+...-+--...+..+|.+
T Consensus       211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd~~~~~~~~~~  262 (290)
T PF04216_consen  211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVDREKDPELDPV  262 (290)
T ss_dssp             TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEETTT-TT--HH
T ss_pred             CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHhhhhCcccchh
Confidence            457999999998877765   3456778899999987665335566666655

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.

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

Probab=89.32  E-value=0.59  Score=32.29  Aligned_cols=34  Identities=18%  Similarity=0.343  Sum_probs=26.6

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      ..=.||.|+...+.-++   +..+-.+.|..||+...
T Consensus       101 ~yVlC~~C~spdT~l~k---~~r~~~l~C~ACGa~~~  134 (138)
T PRK03988        101 EYVICPECGSPDTKLIK---EGRIWVLKCEACGAETP  134 (138)
T ss_pred             hcEECCCCCCCCcEEEE---cCCeEEEEcccCCCCCc
Confidence            44579999998876554   46688999999998644

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

Probab=89.29  E-value=0.54  Score=32.32  Aligned_cols=35  Identities=17%  Similarity=0.331  Sum_probs=26.7

Q ss_pred             CceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      ...=.||.|+...+.-++   +..+-.+.|..||+...
T Consensus        95 ~~yVlC~~C~sPdT~l~k---~~r~~~l~C~ACGa~~~  129 (133)
T TIGR00311        95 RKYVICRECNRPDTRIIK---EGRVSLLKCEACGAKAP  129 (133)
T ss_pred             hheEECCCCCCCCcEEEE---eCCeEEEecccCCCCCc
Confidence            345579999999886554   45667899999998654

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

Probab=89.23  E-value=0.52  Score=29.41  Aligned_cols=43  Identities=21%  Similarity=0.458  Sum_probs=27.2

Q ss_pred             CceecCCCCCCCCceEEEeecC------------CceEEEEcccccce--eEeccCC
Q psy3498          21 DIQFNCPFCNHEKSCEVKMDKG------------RNSARIACRVCLED--FQTTINF   63 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~k~------------~~~g~l~C~~C~~~--~~~~i~~   63 (81)
                      ...|.||-||..+-.+=.|.-.            +..-.+.|.+||-+  |+..+..
T Consensus         2 ~~~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEfY~a~~st   58 (68)
T COG3478           2 KNAFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEFYSAKIST   58 (68)
T ss_pred             CccccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCchhheeccccc
Confidence            3468899999876655444332            23357899999942  4444443

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=89.11  E-value=1.1  Score=28.46  Aligned_cols=40  Identities=18%  Similarity=0.419  Sum_probs=29.2

Q ss_pred             CCCc-eecCCCCCCCCceEEEeecC----CceEEEEcccccceeE
Q psy3498          19 PLDI-QFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQ   58 (81)
Q Consensus        19 ~l~~-~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~   58 (81)
                      .+|+ ...||.|||..++-..+.-.    .+.-.-.|-.||..+.
T Consensus        57 ~~~~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~  101 (104)
T TIGR01384        57 TLPTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWR  101 (104)
T ss_pred             CCCcccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeE
Confidence            4443 79999999999888776442    2455778999997654

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.

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

Probab=88.77  E-value=0.36  Score=28.94  Aligned_cols=40  Identities=20%  Similarity=0.370  Sum_probs=32.1

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhh
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDW   74 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~W   74 (81)
                      .-.|+.||.   .+.         ...|.+||.......++-..|.|-|++.
T Consensus         5 mr~C~~Cgv---YTL---------k~~CP~CG~~t~~~~P~rfSp~D~y~~y   44 (56)
T PRK13130          5 IRKCPKCGV---YTL---------KEICPVCGGKTKNPHPPRFSPEDKYGKY   44 (56)
T ss_pred             ceECCCCCC---EEc---------cccCcCCCCCCCCCCCCCCCCCCccHHH
Confidence            346888886   222         3479999999999999999999999975

>PF14205 Cys_rich_KTR: Cysteine-rich KTR

Probab=88.76  E-value=0.48  Score=28.53  Aligned_cols=36  Identities=17%  Similarity=0.487  Sum_probs=26.8

Q ss_pred             ecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      --||.||...-+.+.-|-...-.-+.|..|.++.-.
T Consensus         5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI   40 (55)
T PF14205_consen    5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLI   40 (55)
T ss_pred             EECCCCCCccceeeecCceeccccccCCCCCceEEE
Confidence            359999987667666665556678899999987643

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

Probab=88.69  E-value=0.7  Score=28.81  Aligned_cols=29  Identities=24%  Similarity=0.665  Sum_probs=22.8

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      .||-|+|   .++.+++.  .-.+.|.+||..--
T Consensus        21 kCpdC~N---~q~vFsha--st~V~C~~CG~~l~   49 (67)
T COG2051          21 KCPDCGN---EQVVFSHA--STVVTCLICGTTLA   49 (67)
T ss_pred             ECCCCCC---EEEEeccC--ceEEEecccccEEE
Confidence            7999999   46677664  47899999998654

>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function

Probab=88.53  E-value=0.79  Score=33.23  Aligned_cols=46  Identities=20%  Similarity=0.263  Sum_probs=27.6

Q ss_pred             CceecCCCCCCCCceEEEeecCC--------------c-----eEEEEcccccceeEe-ccCCCCc
Q psy3498          21 DIQFNCPFCNHEKSCEVKMDKGR--------------N-----SARIACRVCLEDFQT-TINFLSE   66 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~k~~--------------~-----~g~l~C~~C~~~~~~-~i~~L~e   66 (81)
                      ++..+||+|+++-...-......              +     --...|..||-.+.. ..+.|+.
T Consensus         3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~l~~   68 (214)
T PF09986_consen    3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEKLSP   68 (214)
T ss_pred             CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccccccCCH
Confidence            57789999998644332221111              0     137899999976643 3555543

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

Probab=88.19  E-value=0.67  Score=25.07  Aligned_cols=28  Identities=29%  Similarity=0.739  Sum_probs=17.0

Q ss_pred             CCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498          26 CPFCNHEKSCEVKMDKGRNSARIACRVCLE   55 (81)
Q Consensus        26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~   55 (81)
                      ||.||+.  ++..|-..+..-.+.|..||.
T Consensus         3 C~~CG~~--l~~~ip~gd~r~R~vC~~Cg~   30 (34)
T PF14803_consen    3 CPQCGGP--LERRIPEGDDRERLVCPACGF   30 (34)
T ss_dssp             -TTT--B---EEE--TT-SS-EEEETTTTE
T ss_pred             cccccCh--hhhhcCCCCCccceECCCCCC
Confidence            9999984  777777667888999999996

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=87.86  E-value=0.57  Score=26.54  Aligned_cols=28  Identities=21%  Similarity=0.538  Sum_probs=20.6

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF   57 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~   57 (81)
                      .|.|..||++    ++++   ..+.+.|..||-+-
T Consensus         2 ~Y~C~~Cg~~----~~~~---~~~~irC~~CG~rI   29 (44)
T smart00659        2 IYICGECGRE----NEIK---SKDVVRCRECGYRI   29 (44)
T ss_pred             EEECCCCCCE----eecC---CCCceECCCCCceE
Confidence            4889999994    3343   34779999999754

present in RNA polymerase I, II and III

>smart00531 TFIIE Transcription initiation factor IIE

Probab=87.84  E-value=0.18  Score=34.46  Aligned_cols=42  Identities=17%  Similarity=0.366  Sum_probs=26.3

Q ss_pred             CceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccC
Q psy3498          21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTIN   62 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~   62 (81)
                      ...|.||+|+..=+..--+......|...|..||..-...-|
T Consensus        97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn  138 (147)
T smart00531       97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDN  138 (147)
T ss_pred             CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCc
Confidence            468999999974332211111123577999999987654333

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=87.53  E-value=0.61  Score=25.98  Aligned_cols=29  Identities=31%  Similarity=0.677  Sum_probs=16.5

Q ss_pred             CCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      ||.||+  .+..+  .........|..||..+.
T Consensus         3 Cp~Cg~--~l~~~--~~~~~~~~vC~~Cg~~~~   31 (52)
T smart00661        3 CPKCGN--MLIPK--EGKEKRRFVCRKCGYEEP   31 (52)
T ss_pred             CCCCCC--ccccc--cCCCCCEEECCcCCCeEE
Confidence            888887  22222  111123778999996543

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

Probab=87.40  E-value=0.37  Score=24.46  Aligned_cols=11  Identities=36%  Similarity=1.059  Sum_probs=9.6

Q ss_pred             CCceecCCCCC
Q psy3498          20 LDIQFNCPFCN   30 (81)
Q Consensus        20 l~~~F~CPfC~   30 (81)
                      ....|.||.||
T Consensus        13 ~~v~f~CPnCG   23 (24)
T PF07754_consen   13 QAVPFPCPNCG   23 (24)
T ss_pred             cCceEeCCCCC
Confidence            46899999998

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

>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=87.35  E-value=0.76  Score=31.19  Aligned_cols=32  Identities=19%  Similarity=0.388  Sum_probs=24.8

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED   56 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~   56 (81)
                      +.-.||.|+...+.-++-   ...-.+.|..||++
T Consensus        92 ~yVlC~~C~spdT~l~k~---~r~~~l~C~aCGa~  123 (125)
T PF01873_consen   92 EYVLCPECGSPDTELIKE---GRLIFLKCKACGAS  123 (125)
T ss_dssp             HHSSCTSTSSSSEEEEEE---TTCCEEEETTTSCE
T ss_pred             HEEEcCCCCCCccEEEEc---CCEEEEEecccCCc
Confidence            445799999988754443   66789999999985

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 ....

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=87.05  E-value=0.35  Score=27.23  Aligned_cols=30  Identities=23%  Similarity=0.547  Sum_probs=21.6

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE   55 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~   55 (81)
                      .|.|+.||+.-.+...++.   ...+.|-.||.
T Consensus         5 ey~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~   34 (52)
T TIGR02605         5 EYRCTACGHRFEVLQKMSD---DPLATCPECGG   34 (52)
T ss_pred             EEEeCCCCCEeEEEEecCC---CCCCCCCCCCC
Confidence            5899999996555444432   45678999997

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

>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=86.95  E-value=0.29  Score=25.03  Aligned_cols=24  Identities=33%  Similarity=0.701  Sum_probs=14.5

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      +||.|+++-          ..+...|..||-.|+
T Consensus         2 ~CP~C~~~V----------~~~~~~Cp~CG~~F~   25 (26)
T PF10571_consen    2 TCPECGAEV----------PESAKFCPHCGYDFE   25 (26)
T ss_pred             cCCCCcCCc----------hhhcCcCCCCCCCCc
Confidence            477777742          234446777776664

Several members are annotated as putative helicases.

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

Probab=86.66  E-value=0.46  Score=26.62  Aligned_cols=29  Identities=28%  Similarity=0.631  Sum_probs=18.0

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEccccc
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCL   54 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~   54 (81)
                      .||.|+-..-..+--|+ .+.|.-.|+.|+
T Consensus         5 pCP~CGG~DrFri~~d~-~~~G~~~C~~C~   33 (40)
T PF08273_consen    5 PCPICGGKDRFRIFDDK-DGRGTWICRQCG   33 (40)
T ss_dssp             --TTTT-TTTEEEETT-----S-EEETTTT
T ss_pred             CCCCCcCccccccCcCc-ccCCCEECCCCC
Confidence            69999998888776665 566999999994

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

>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=86.60  E-value=0.36  Score=28.50  Aligned_cols=35  Identities=23%  Similarity=0.546  Sum_probs=25.1

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccC
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTIN   62 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~   62 (81)
                      |.=.||.||+...-      ........|..||..+.-.+|
T Consensus        27 TSq~C~~CG~~~~~------~~~~r~~~C~~Cg~~~~rD~n   61 (69)
T PF07282_consen   27 TSQTCPRCGHRNKK------RRSGRVFTCPNCGFEMDRDVN   61 (69)
T ss_pred             CccCccCccccccc------ccccceEEcCCCCCEECcHHH
Confidence            66679999993221      345678999999998765544

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

>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins

Probab=86.48  E-value=0.29  Score=28.08  Aligned_cols=34  Identities=24%  Similarity=0.677  Sum_probs=19.9

Q ss_pred             eecCCCCCCCCceEEEeec------CCceEEEEccccccee
Q psy3498          23 QFNCPFCNHEKSCEVKMDK------GRNSARIACRVCLEDF   57 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k------~~~~g~l~C~~C~~~~   57 (81)
                      .|.||||+.+-++. .+-.      ......+.|.+|...+
T Consensus         2 ~f~CP~C~~~~~~~-~L~~H~~~~H~~~~~~v~CPiC~~~~   41 (54)
T PF05605_consen    2 SFTCPYCGKGFSES-SLVEHCEDEHRSESKNVVCPICSSRV   41 (54)
T ss_pred             CcCCCCCCCccCHH-HHHHHHHhHCcCCCCCccCCCchhhh
Confidence            59999999832211 1100      1223368999998643

Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.

>TIGR03831 YgiT_finger YgiT-type zinc finger domain

Probab=86.46  E-value=1.2  Score=23.85  Aligned_cols=12  Identities=25%  Similarity=0.786  Sum_probs=9.1

Q ss_pred             EEEcccccceeE
Q psy3498          47 RIACRVCLEDFQ   58 (81)
Q Consensus        47 ~l~C~~C~~~~~   58 (81)
                      -..|..||+.|-
T Consensus        32 ~~~C~~CGE~~~   43 (46)
T TIGR03831        32 ALVCPQCGEEYL   43 (46)
T ss_pred             ccccccCCCEee
Confidence            346999999774

This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.

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

Probab=86.33  E-value=1.2  Score=29.58  Aligned_cols=32  Identities=19%  Similarity=0.366  Sum_probs=24.3

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED   56 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~   56 (81)
                      ..=.||.|+...+.-++   ++..-.+.|..||+.
T Consensus        79 ~yVlC~~C~spdT~l~k---~~r~~~l~C~aCGa~  110 (110)
T smart00653       79 EYVLCPECGSPDTELIK---ENRLFFLKCEACGAR  110 (110)
T ss_pred             hcEECCCCCCCCcEEEE---eCCeEEEEccccCCC
Confidence            44579999998764433   467889999999973

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

Probab=86.13  E-value=0.32  Score=29.81  Aligned_cols=34  Identities=18%  Similarity=0.390  Sum_probs=20.5

Q ss_pred             CceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498          21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE   55 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~   55 (81)
                      -..|.||.||.+.-..+..-++ .-..-.|.+||.
T Consensus        25 ~v~F~CPnCGe~~I~Rc~~CRk-~g~~Y~Cp~CGF   58 (61)
T COG2888          25 AVKFPCPNCGEVEIYRCAKCRK-LGNPYRCPKCGF   58 (61)
T ss_pred             eeEeeCCCCCceeeehhhhHHH-cCCceECCCcCc
Confidence            3789999999732222222222 234567888885

>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.13  E-value=0.95  Score=27.95  Aligned_cols=35  Identities=17%  Similarity=0.448  Sum_probs=23.1

Q ss_pred             eecCCCCCCCCceEEEeecC---CceEEEEcccccceeEe
Q psy3498          23 QFNCPFCNHEKSCEVKMDKG---RNSARIACRVCLEDFQT   59 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~---~~~g~l~C~~C~~~~~~   59 (81)
                      .|+|..|++..+  =.|.+.   .|+-.+.|..|+..+-.
T Consensus         4 ~FTC~~C~~Rs~--~~~sk~aY~~GvViv~C~gC~~~HlI   41 (66)
T PF05180_consen    4 TFTCNKCGTRSA--KMFSKQAYHKGVVIVQCPGCKNRHLI   41 (66)
T ss_dssp             EEEETTTTEEEE--EEEEHHHHHTSEEEEE-TTS--EEES
T ss_pred             EEEcCCCCCccc--eeeCHHHHhCCeEEEECCCCcceeee
Confidence            699999998322  233332   68999999999997753

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. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.

>TIGR01385 TFSII transcription elongation factor S-II

Probab=85.98  E-value=1.4  Score=33.84  Aligned_cols=40  Identities=15%  Similarity=0.406  Sum_probs=29.8

Q ss_pred             CCceecCCCCCCCCceEEEeecC----CceEEEEcccccceeEe
Q psy3498          20 LDIQFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQT   59 (81)
Q Consensus        20 l~~~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~~   59 (81)
                      ....|.||.|+|.+++--.+.-.    .+.-...|..||..+.+
T Consensus       255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~f  298 (299)
T TIGR01385       255 VTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKF  298 (299)
T ss_pred             CcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeeee
Confidence            44679999999998887666332    24667899999987653

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.

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

Probab=85.72  E-value=0.38  Score=35.50  Aligned_cols=36  Identities=17%  Similarity=0.427  Sum_probs=24.6

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      ...||.|+.+...+--|.....-..+.|..||.-+.
T Consensus         6 y~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~~   41 (201)
T COG1326           6 YIECPSCGSEEVSHEVIKERGREPLVRCEECGTVHP   41 (201)
T ss_pred             EEECCCCCcchhhHHHHHhcCCceEEEccCCCcEee
Confidence            568999995444333333334447999999999883

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=85.62  E-value=0.37  Score=24.20  Aligned_cols=22  Identities=27%  Similarity=0.588  Sum_probs=15.0

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLED   56 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~   56 (81)
                      .||.||++.          ..+...|..||+.
T Consensus         4 ~Cp~Cg~~~----------~~~~~fC~~CG~~   25 (26)
T PF13248_consen    4 FCPNCGAEI----------DPDAKFCPNCGAK   25 (26)
T ss_pred             CCcccCCcC----------CcccccChhhCCC
Confidence            599999842          2245578888864

>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=85.54  E-value=2.1  Score=26.53  Aligned_cols=36  Identities=14%  Similarity=0.234  Sum_probs=28.0

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccceeEeccC
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTIN   62 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~   62 (81)
                      .||.|+.-.++..-.  .+++-.+.|-.||-+.+.+..
T Consensus        10 ~CP~C~~~D~i~~~~--e~~ve~vECV~CGy~e~~~~~   45 (71)
T PF09526_consen   10 VCPKCQAMDTIMMWR--ENGVEYVECVECGYTERQPDQ   45 (71)
T ss_pred             cCCCCcCccEEEEEE--eCCceEEEecCCCCeeccCCc
Confidence            699999988665554  557999999999987765443

Members are found in various proteobacteria.

>TIGR02443 conserved hypothetical metal-binding protein

Probab=85.38  E-value=1.5  Score=26.71  Aligned_cols=33  Identities=24%  Similarity=0.443  Sum_probs=26.8

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      .||-|+.-.++..-  +.+++-.+.|-.||-+-+.
T Consensus        11 ~CP~C~~~Dtl~~~--~e~~~e~vECv~Cg~~~~~   43 (59)
T TIGR02443        11 VCPACSAQDTLAMW--KENNIELVECVECGYQEQQ   43 (59)
T ss_pred             cCCCCcCccEEEEE--EeCCceEEEeccCCCcccc
Confidence            69999998887544  5678899999999976643

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.

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

Probab=85.24  E-value=1  Score=30.38  Aligned_cols=23  Identities=30%  Similarity=0.834  Sum_probs=18.0

Q ss_pred             CCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      ||.||++          -.+-.+.|..|+...+
T Consensus         1 CPvCg~~----------l~vt~l~C~~C~t~i~   23 (113)
T PF09862_consen    1 CPVCGGE----------LVVTRLKCPSCGTEIE   23 (113)
T ss_pred             CCCCCCc----------eEEEEEEcCCCCCEEE
Confidence            9999983          3456889999998653

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

Probab=84.83  E-value=1  Score=30.03  Aligned_cols=29  Identities=24%  Similarity=0.602  Sum_probs=18.7

Q ss_pred             CCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      ||-||.    -....++...+.+.|+.||-.++
T Consensus         5 Cp~Cgs----ll~p~~~~~~~~l~C~kCgye~~   33 (113)
T COG1594           5 CPKCGS----LLYPKKDDEGGKLVCRKCGYEEE   33 (113)
T ss_pred             cCCccC----eeEEeEcCCCcEEECCCCCcchh
Confidence            888886    22223333445899999997654

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

Probab=84.80  E-value=1.1  Score=32.34  Aligned_cols=35  Identities=20%  Similarity=0.302  Sum_probs=26.8

Q ss_pred             CceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      ...=.||.|+...+--+   ++...-.+.|..||+...
T Consensus        96 ~~yV~C~~C~~pdT~l~---k~~~~~~l~C~aCGa~~~  130 (201)
T PRK12336         96 DEYVICSECGLPDTRLV---KEDRVLMLRCDACGAHRP  130 (201)
T ss_pred             HheEECCCCCCCCcEEE---EcCCeEEEEcccCCCCcc
Confidence            34557999999877544   345778899999999764

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=84.54  E-value=0.83  Score=34.62  Aligned_cols=31  Identities=23%  Similarity=0.536  Sum_probs=22.6

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      .-.||.||. .  .+..|.  ..|.+.|..||.-.+
T Consensus        11 ~~~Cp~Cg~-~--~iv~d~--~~Ge~vC~~CG~Vl~   41 (310)
T PRK00423         11 KLVCPECGS-D--KLIYDY--ERGEIVCADCGLVIE   41 (310)
T ss_pred             CCcCcCCCC-C--CeeEEC--CCCeEeecccCCccc
Confidence            346999997 3  344443  569999999998654

>TIGR01031 rpmF_bact ribosomal protein L32

Probab=83.42  E-value=1.8  Score=25.56  Aligned_cols=26  Identities=19%  Similarity=0.390  Sum_probs=19.7

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccc
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLE   55 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~   55 (81)
                      +.+..-.||.||.           -...+-.|..||.
T Consensus        22 ~~p~l~~C~~cG~-----------~~~~H~vc~~cG~   47 (55)
T TIGR01031        22 TAPTLVVCPNCGE-----------FKLPHRVCPSCGY   47 (55)
T ss_pred             cCCcceECCCCCC-----------cccCeeECCccCe
Confidence            4578888999997           2346778888883

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.

>KOG0478|consensus

Probab=83.37  E-value=0.54  Score=40.56  Aligned_cols=36  Identities=31%  Similarity=0.649  Sum_probs=27.2

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      ..|.|..|||+  +.+.+++..-.--..|..|+.++++
T Consensus       263 afFrC~vC~~~--~~ve~drg~i~eP~~C~~C~~~~~~  298 (804)
T KOG0478|consen  263 AFFRCSVCGHE--IAVESDRGRIKEPMLCKECGTTNSF  298 (804)
T ss_pred             HhhhhhhcCce--EEEEeecCccCCCcccccccCcccc
Confidence            68999999996  5666666444456789999987765

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

Probab=82.79  E-value=0.82  Score=34.92  Aligned_cols=40  Identities=23%  Similarity=0.507  Sum_probs=28.6

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhh
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWV   75 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~Wi   75 (81)
                      .||.||..     .+..+..-|.+.|..||+--+      +.+||-..+|-
T Consensus         3 ~CpeCg~~-----~~~~d~~~ge~VC~~CG~Vi~------~~~id~gpewr   42 (285)
T COG1405           3 SCPECGST-----NIITDYERGEIVCADCGLVLE------DSLIDPGPEWR   42 (285)
T ss_pred             CCCCCCCc-----cceeeccCCeEEeccCCEEec------cccccCCCCcc
Confidence            69999984     333344479999999998543      24677777775

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=82.69  E-value=1.2  Score=34.55  Aligned_cols=37  Identities=16%  Similarity=0.531  Sum_probs=25.7

Q ss_pred             CceecCCCCCCCCceEE-EeecCCceEEEEccccccee
Q psy3498          21 DIQFNCPFCNHEKSCEV-KMDKGRNSARIACRVCLEDF   57 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v-~i~k~~~~g~l~C~~C~~~~   57 (81)
                      +..=.||.||..-..++ .+.-..|.-.+.|..|+...
T Consensus       185 ~~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW  222 (309)
T PRK03564        185 EQRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEW  222 (309)
T ss_pred             cCCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcc
Confidence            45678999999775554 33334566788888888754

>PHA02540 61 DNA primase; Provisional

Probab=82.62  E-value=1.6  Score=34.11  Aligned_cols=41  Identities=20%  Similarity=0.406  Sum_probs=28.7

Q ss_pred             ceecCCCCCCCC------ceEEEeecCCceEEEEcccccce-----eEeccCCC
Q psy3498          22 IQFNCPFCNHEK------SCEVKMDKGRNSARIACRVCLED-----FQTTINFL   64 (81)
Q Consensus        22 ~~F~CPfC~~~~------sV~v~i~k~~~~g~l~C~~C~~~-----~~~~i~~L   64 (81)
                      =.|.|||||..+      |..|.-++.  .+.-+|-.||++     |-+.+..|
T Consensus        26 ~~~~CPf~~ds~~~~~kpsF~V~p~k~--~~~yhCFgCGa~Gd~i~Flme~e~l   77 (337)
T PHA02540         26 YNFRCPICGDSQKDKNKARGWIYEKKD--GGVFKCHNCGYHRPFGNFLKDYEPD   77 (337)
T ss_pred             EEecCCCCCCccccCcCCcEEEeccCC--ceEEEecCCCCCCCHHHHHHHhcCC
Confidence            478999999743      566665553  568899999985     44455554

>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A

Probab=82.58  E-value=0.56  Score=23.33  Aligned_cols=11  Identities=27%  Similarity=1.301  Sum_probs=8.8

Q ss_pred             CceecCCCCCC
Q psy3498          21 DIQFNCPFCNH   31 (81)
Q Consensus        21 ~~~F~CPfC~~   31 (81)
                      ++.|.||.|+.
T Consensus        12 ~k~~~C~~C~k   22 (26)
T PF13465_consen   12 EKPYKCPYCGK   22 (26)
T ss_dssp             SSSEEESSSSE
T ss_pred             CCCCCCCCCcC
Confidence            46799999984

...

>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=82.56  E-value=1.9  Score=30.25  Aligned_cols=34  Identities=15%  Similarity=0.353  Sum_probs=18.8

Q ss_pred             cCCCCCCCCceEEEeec-----CCceEEEEcccccceeE
Q psy3498          25 NCPFCNHEKSCEVKMDK-----GRNSARIACRVCLEDFQ   58 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k-----~~~~g~l~C~~C~~~~~   58 (81)
                      .||.|+++......+..     +-.+-...|..||-++.
T Consensus         3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~   41 (161)
T PF03367_consen    3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNN   41 (161)
T ss_dssp             E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEE
T ss_pred             cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEee
Confidence            59999986544333322     23566789999998763

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.

>PRK05978 hypothetical protein; Provisional

Probab=82.34  E-value=0.61  Score=32.72  Aligned_cols=31  Identities=29%  Similarity=0.488  Sum_probs=22.0

Q ss_pred             ecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      =.||.||..+...     .-..-.-+|..||+.|+.
T Consensus        34 grCP~CG~G~LF~-----g~Lkv~~~C~~CG~~~~~   64 (148)
T PRK05978         34 GRCPACGEGKLFR-----AFLKPVDHCAACGEDFTH   64 (148)
T ss_pred             CcCCCCCCCcccc-----cccccCCCccccCCcccc
Confidence            4699999865432     333345689999999874

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

Probab=82.32  E-value=1.3  Score=36.22  Aligned_cols=34  Identities=38%  Similarity=0.780  Sum_probs=26.4

Q ss_pred             ecCCCCCCCCceE---EEeecC--CceEEEEccccccee
Q psy3498          24 FNCPFCNHEKSCE---VKMDKG--RNSARIACRVCLEDF   57 (81)
Q Consensus        24 F~CPfC~~~~sV~---v~i~k~--~~~g~l~C~~C~~~~   57 (81)
                      ..||+|||.+.+.   ++.+..  ...+...|..||...
T Consensus       201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i  239 (557)
T PF05876_consen  201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEI  239 (557)
T ss_pred             ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCC
Confidence            4799999998876   555443  467899999999754

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 [].

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

Probab=81.77  E-value=1.3  Score=30.76  Aligned_cols=27  Identities=22%  Similarity=0.529  Sum_probs=20.4

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF   57 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~   57 (81)
                      .-+||-||..      +.+  ..|.+.|-+||..+
T Consensus        28 ~~hCp~Cg~P------LF~--KdG~v~CPvC~~~~   54 (131)
T COG1645          28 AKHCPKCGTP------LFR--KDGEVFCPVCGYRE   54 (131)
T ss_pred             HhhCcccCCc------cee--eCCeEECCCCCceE
Confidence            4589999983      333  56999999999544

>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=81.76  E-value=2  Score=23.40  Aligned_cols=30  Identities=27%  Similarity=0.617  Sum_probs=18.1

Q ss_pred             ecCCCCCCCCceEEEeec-CCceEEEEccccc
Q psy3498          24 FNCPFCNHEKSCEVKMDK-GRNSARIACRVCL   54 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k-~~~~g~l~C~~C~   54 (81)
                      -.||+|+...+| ++--+ ..+.-.-.|..|.
T Consensus         6 v~CP~C~s~~~v-~k~G~~~~G~qryrC~~C~   36 (36)
T PF03811_consen    6 VHCPRCQSTEGV-KKNGKSPSGHQRYRCKDCR   36 (36)
T ss_pred             eeCCCCCCCCcc-eeCCCCCCCCEeEecCcCC
Confidence            479999986543 22222 2345567777773

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

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

Probab=81.68  E-value=0.91  Score=32.44  Aligned_cols=34  Identities=24%  Similarity=0.479  Sum_probs=25.4

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCC
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINF   63 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~   63 (81)
                      +-.|.=.||.||+           .......|..||..+.-.+|+
T Consensus       305 ~~~tS~~C~~cg~-----------~~~r~~~C~~cg~~~~rD~na  338 (364)
T COG0675         305 PYYTSKTCPCCGH-----------LSGRLFKCPRCGFVHDRDVNA  338 (364)
T ss_pred             CCCCcccccccCC-----------ccceeEECCCCCCeehhhHHH
Confidence            3456667999999           335788999999987665554

>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE

Probab=81.14  E-value=0.98  Score=34.90  Aligned_cols=35  Identities=14%  Similarity=0.475  Sum_probs=24.4

Q ss_pred             eecCCCCCCCCceEEEeec--CCceEEEEccccccee
Q psy3498          23 QFNCPFCNHEKSCEVKMDK--GRNSARIACRVCLEDF   57 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k--~~~~g~l~C~~C~~~~   57 (81)
                      .=.||.||..-..++....  ++|.-.++|..|+..+
T Consensus       184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW  220 (305)
T TIGR01562       184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEW  220 (305)
T ss_pred             CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcc
Confidence            4489999997766654442  4666678888887654

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).

>KOG0402|consensus

Probab=80.39  E-value=0.72  Score=30.20  Aligned_cols=30  Identities=20%  Similarity=0.654  Sum_probs=23.2

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF   57 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~   57 (81)
                      ..++|+|||.. +    + +...+|+-.|+.|...+
T Consensus        35 aky~CsfCGK~-~----v-KR~AvGiW~C~~C~kv~   64 (92)
T KOG0402|consen   35 AKYTCSFCGKK-T----V-KRKAVGIWKCGSCKKVV   64 (92)
T ss_pred             hhhhhhhcchh-h----h-hhhceeEEecCCcccee
Confidence            56899999983 2    2 23678999999998765

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=80.36  E-value=2.6  Score=25.55  Aligned_cols=28  Identities=25%  Similarity=0.667  Sum_probs=21.5

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF   57 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~   57 (81)
                      .||-|++   .++.+++..  -.+.|.+||..-
T Consensus        13 kCp~C~n---~q~vFsha~--t~V~C~~Cg~~L   40 (59)
T PRK00415         13 KCPDCGN---EQVVFSHAS--TVVRCLVCGKTL   40 (59)
T ss_pred             ECCCCCC---eEEEEecCC--cEEECcccCCCc
Confidence            6999999   466676543  688999999754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	81
1wii_A	85	Solution Structure Of Rsgi Ruh-025, A Duf701 Domain		3e-21

>pdb|1WII|A Chain A, Solution Structure Of Rsgi Ruh-025, A Duf701 Domain From Mouse Cdna Length = 85

Iteration: 1
 Score = 96.7 bits (239), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)
Query: 20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDA 77
          L+ QF CPFCNHEKSC+VKMD+ RN+  I+C VCLE+FQT I +LSE +DVY+DW+DA
Sbjct: 20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDA 77

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	81
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	3e-32

>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4 Length = 85

 Score =  106 bits (265), Expect = 3e-32
 Identities = 47/75 (62%), Positives = 58/75 (77%)

Query: 3  RRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTIN 62
             S RKPPPK+K    L+ QF CPFCNHEKSC+VKMD+ RN+  I+C VCLE+FQT I 
Sbjct: 3  SGSSGRKPPPKKKMTGTLETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPIT 62

Query: 63 FLSEAIDVYNDWVDA 77
          +LSE +DVY+DW+DA
Sbjct: 63 YLSEPVDVYSDWIDA 77

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	81
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	100.0
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	96.14
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	96.08
3j21_i	83	50S ribosomal protein L37AE; archaea, archaeal, KI	95.55
3iz5_m	92	60S ribosomal protein L43 (L37AE); eukaryotic ribo	95.37
4a17_Y	103	RPL37A, 60S ribosomal protein L32; eukaryotic ribo	95.19
3izc_m	92	60S ribosomal protein RPL43 (L37AE); eukaryotic ri	95.19
3jyw_9	72	60S ribosomal protein L43; eukaryotic ribosome, RA	95.15
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	95.14
1ffk_W	73	Ribosomal protein L37AE; ribosome assembly, RNA-RN	94.82
1k81_A	36	EIF-2-beta, probable translation initiation factor	94.1
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	93.86
3cc2_Z	116	50S ribosomal protein L37AE, 50S ribosomal protein	93.82
1tfi_A	50	Transcriptional elongation factor SII; transcripti	93.09
3ga8_A	78	HTH-type transcriptional regulator MQSA (YGIT/B30;	92.7
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	92.03
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	91.9
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	90.68
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	90.18
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	89.8
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	89.71
2e9h_A	157	EIF-5, eukaryotic translation initiation factor 5;	89.34
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	88.88
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	88.65
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	88.45
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	88.44
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	88.01
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	87.77
4esj_A	257	Type-2 restriction enzyme DPNI; restriction endonu	87.56
2apo_B	60	Ribosome biogenesis protein NOP10; protein-protein	87.04
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	86.84
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	86.8
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	85.56
1nui_A	255	DNA primase/helicase; zinc-biding domain, toprim f	85.07
2aus_D	60	NOP10, ribosome biogenesis protein NOP10; isomeras	84.75
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	83.93
2g2k_A	170	EIF-5, eukaryotic translation initiation factor 5;	83.45
3po3_S	178	Transcription elongation factor S-II; RNA polymera	82.07
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	82.07
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	81.94
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	80.4
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	80.14

>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4

Probab=100.00  E-value=2.5e-45  Score=235.21  Aligned_cols=80  Identities=59%  Similarity=1.134  Sum_probs=72.0

Q ss_pred             CCCCcCCCCCCCCCCCCCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCCC
Q psy3498           2 GRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVPS   81 (81)
Q Consensus         2 GkRK~~~k~~~kkk~~~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~~   81 (81)
                      ||||+++++++|++.+++|||.|+||||||++||+|+||++.++|.|+|++||++||++||+|+|||||||+|||+|+|.
T Consensus         2 ~rRKs~~k~~~k~k~~~~L~t~F~CPfCnh~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epiDVYs~WiDac~~~   81 (85)
T 1wii_A            2 SSGSSGRKPPPKKKMTGTLETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDACESG   81 (85)
T ss_dssp             CCCCCCCCCCCCCCCCCCCSSCCCCTTTCCSSCEEEEEETTTTEEEEEESSSCCEEEEECCSSCCTTHHHHHHHHHHHHC
T ss_pred             CCccccCCCCCCcccCCCCCCeEcCCCCCCCCeEEEEEEccCCEEEEEcccCCCeEEeccCccCcchhhHHHHHHHHHHH
Confidence            44556667766665358999999999999999999999999999999999999999999999999999999999999873

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

Probab=96.14  E-value=0.0028  Score=39.60  Aligned_cols=44  Identities=14%  Similarity=0.232  Sum_probs=30.5

Q ss_pred             CceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhh
Q psy3498          21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDV   70 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDV   70 (81)
                      ...|.|||||.+ .   ..  ....|...|..||..|.--+-.++.|.-+
T Consensus        25 ~~~y~Cp~CG~~-~---v~--r~atGiW~C~~Cg~~~aggay~~~t~~~~   68 (83)
T 1vq8_Z           25 NEDHACPNCGED-R---VD--RQGTGIWQCSYCDYKFTGGSYKPETPGGK   68 (83)
T ss_dssp             HSCEECSSSCCE-E---EE--EEETTEEEETTTCCEEECCSSSSSCHHHH
T ss_pred             cccCcCCCCCCc-c---ee--ccCCCeEECCCCCCEecCCEecccchHHH
Confidence            468999999972 1   11  23568999999999987654444555443

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

Probab=96.08  E-value=0.0033  Score=34.94  Aligned_cols=33  Identities=27%  Similarity=0.509  Sum_probs=24.7

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      ..+.||.|+.+   .+..|.  ..|.+.|..||+.|..
T Consensus         4 ~~~~CP~C~~~---~l~~d~--~~gelvC~~CG~v~~e   36 (50)
T 1pft_A            4 KQKVCPACESA---ELIYDP--ERGEIVCAKCGYVIEE   36 (50)
T ss_dssp             SCCSCTTTSCC---CEEEET--TTTEEEESSSCCBCCC
T ss_pred             ccEeCcCCCCc---ceEEcC--CCCeEECcccCCcccc
Confidence            45789999984   344555  3478999999998864

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

Probab=95.55  E-value=0.007  Score=38.08  Aligned_cols=40  Identities=20%  Similarity=0.481  Sum_probs=28.6

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCch
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEA   67 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~ep   67 (81)
                      ..+.||||+...   ++  + ..+|+-.|+.|+..|.--.-.++.|
T Consensus        34 ~ky~CpfCGk~~---vk--R-~a~GIW~C~kCg~~~AGGAy~~~T~   73 (83)
T 3j21_i           34 QKHTCPVCGRKA---VK--R-ISTGIWQCQKCGATFAGGAYLPVTP   73 (83)
T ss_dssp             SCBCCSSSCSSC---EE--E-EETTEEEETTTCCEEECCSSSSSCH
T ss_pred             cccCCCCCCCce---eE--e-cCcCeEEcCCCCCEEeCCccccCcc
Confidence            478999999852   22  2 4678999999999987544444444

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

Probab=95.19  E-value=0.014  Score=38.07  Aligned_cols=40  Identities=18%  Similarity=0.475  Sum_probs=28.2

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCch
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEA   67 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~ep   67 (81)
                      ..+.|||||..   .  +.+ ..+|+-.|+.|+..|.--.-.++.|
T Consensus        35 aky~CpfCgk~---~--vKR-~a~GIW~C~kCg~~~AGGAy~~~T~   74 (103)
T 4a17_Y           35 AKYGCPFCGKV---A--VKR-AAVGIWKCKPCKKIIAGGAWELTTP   74 (103)
T ss_dssp             SCEECTTTCCE---E--EEE-EETTEEEETTTTEEEECCSSCSSCH
T ss_pred             cCCCCCCCCCc---e--eee-cCcceEEcCCCCCEEeCCcccCCCc
Confidence            67899999973   3  333 4678999999999987543333333

>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=95.15  E-value=0.0063  Score=37.39  Aligned_cols=40  Identities=18%  Similarity=0.532  Sum_probs=28.6

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCch
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEA   67 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~ep   67 (81)
                      ..+.||||+...     +.+ ..+|+-.|+.|+..|.--.-.++.|
T Consensus        25 ~ky~C~fCgk~~-----vkR-~a~GIW~C~~C~~~~AGGAy~~~T~   64 (72)
T 3jyw_9           25 ARYDCSFCGKKT-----VKR-GAAGIWTCSCCKKTVAGGAYTVSTA   64 (72)
T ss_dssp             SCBCCSSCCSSC-----BSB-CSSSCBCCSSSCCCCCCSSSSSCCH
T ss_pred             cCccCCCCCCce-----eEe-cCCCeEECCCCCCEEeCCccccCCc
Confidence            678999999853     433 5689999999999886543333333

>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=95.14  E-value=0.0077  Score=34.99  Aligned_cols=46  Identities=20%  Similarity=0.317  Sum_probs=31.5

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhh
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWV   75 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~Wi   75 (81)
                      +|...-.||.|+.++   +..|  ...|.+.|..||+.++.      ..||.=.+|-
T Consensus         7 ~ll~~~~Cp~C~~~~---lv~D--~~~ge~vC~~CGlVl~e------~~iD~gpEWR   52 (58)
T 1dl6_A            7 DALPRVTCPNHPDAI---LVED--YRAGDMICPECGLVVGD------RVIDVGSEWR   52 (58)
T ss_dssp             CCCSCCSBTTBSSSC---CEEC--SSSCCEECTTTCCEECC------SCCCCCCSCC
T ss_pred             hccccccCcCCCCCc---eeEe--CCCCeEEeCCCCCEEec------cccccCCccc
Confidence            355566899999865   3334  35588999999998864      3455555553

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

Probab=94.82  E-value=0.032  Score=34.22  Aligned_cols=35  Identities=17%  Similarity=0.506  Sum_probs=26.1

Q ss_pred             CCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEec
Q psy3498          20 LDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT   60 (81)
Q Consensus        20 l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~   60 (81)
                      ....+.||||+.. .  ++  + ..+|+-.|+.|+..|.--
T Consensus        24 q~~ky~C~fCgk~-~--vk--R-~a~GIW~C~~C~~~~AGG   58 (73)
T 1ffk_W           24 HKKKYKCPVCGFP-K--LK--R-ASTSIWVCGHCGYKIAGG   58 (73)
T ss_pred             cccCccCCCCCCc-e--eE--E-EEeEEEECCCCCcEEECC
Confidence            4578999999973 2  22  2 457999999999988643

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

Probab=94.10  E-value=0.052  Score=28.79  Aligned_cols=31  Identities=16%  Similarity=0.275  Sum_probs=24.3

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      .||.|+...+.-++   ++..-.+.|..||....
T Consensus         2 lC~~C~~peT~l~~---~~~~~~l~C~aCG~~~~   32 (36)
T 1k81_A            2 ICRECGKPDTKIIK---EGRVHLLKCMACGAIRP   32 (36)
T ss_dssp             CCSSSCSCEEEEEE---ETTEEEEEEETTTEEEE
T ss_pred             CCcCCCCCCcEEEE---eCCcEEEEhhcCCCccc
Confidence            49999998765444   46788999999998665

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

Probab=93.86  E-value=0.12  Score=29.29  Aligned_cols=40  Identities=18%  Similarity=0.463  Sum_probs=29.2

Q ss_pred             CCC-ceecCCCCCCCCceEEEeec----CCceEEEEcccccceeE
Q psy3498          19 PLD-IQFNCPFCNHEKSCEVKMDK----GRNSARIACRVCLEDFQ   58 (81)
Q Consensus        19 ~l~-~~F~CPfC~~~~sV~v~i~k----~~~~g~l~C~~C~~~~~   58 (81)
                      .+| +.+.||.|||...+--.+.-    ..+.....|..||-.+.
T Consensus        10 ~~~~~~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~   54 (57)
T 1qyp_A           10 TLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWR   54 (57)
T ss_dssp             SSCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEE
T ss_pred             cCCceEeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCEec
Confidence            344 35899999998777666543    13567889999998765

>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=93.82  E-value=0.05  Score=36.10  Aligned_cols=45  Identities=16%  Similarity=0.276  Sum_probs=30.8

Q ss_pred             CceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhh
Q psy3498          21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVY   71 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVY   71 (81)
                      ...+.|||||..   .++-   ..+|+-.|+.|+..|.--+-.++.|.-+.
T Consensus        58 ~akytCPfCGk~---~vKR---~avGIW~C~~Cgk~fAGGAy~~~T~~~~t  102 (116)
T 3cc2_Z           58 NEDHACPNCGED---RVDR---QGTGIWQCSYCDYKFTGGSYKPETPGGKT  102 (116)
T ss_dssp             HSCEECSSSCCE---EEEE---EETTEEEETTTCCEEECCSSSSSCHHHHH
T ss_pred             ccCCcCCCCCCc---eeEe---cCceeEECCCCCCEEECCCcccccchhhh
Confidence            467899999972   3332   34689999999999976544455554433

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

Probab=93.09  E-value=0.22  Score=28.05  Aligned_cols=37  Identities=14%  Similarity=0.409  Sum_probs=28.7

Q ss_pred             ceecCCCCCCCCceEEEeecC----CceEEEEcccccceeE
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQ   58 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~   58 (81)
                      +.+.||.|||.+.+--.+.-.    .+.-...|..||-.+.
T Consensus         8 ~~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~w~   48 (50)
T 1tfi_A            8 DLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK   48 (50)
T ss_dssp             CCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEE
T ss_pred             CccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCeEE
Confidence            468999999999887776542    3556788999998764

>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=92.70  E-value=0.12  Score=30.81  Aligned_cols=52  Identities=13%  Similarity=0.370  Sum_probs=31.2

Q ss_pred             cCCCCCCCCc----eEEEeecCC------ceEEEEcccccceeEe--ccCCCCchhhhhhhhhh
Q psy3498          25 NCPFCNHEKS----CEVKMDKGR------NSARIACRVCLEDFQT--TINFLSEAIDVYNDWVD   76 (81)
Q Consensus        25 ~CPfC~~~~s----V~v~i~k~~------~~g~l~C~~C~~~~~~--~i~~L~epIDVYs~WiD   76 (81)
                      .||+|+....    ..+.++.+.      ++--..|..||+.|-+  ....+++.++-+.+=+|
T Consensus         4 ~Cp~Cg~~~l~~~~~~~~~~~~G~~~~I~~Vp~~~C~~CGE~~~~~e~~~~~~~~~~~f~~~vd   67 (78)
T 3ga8_A            4 KCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRASVN   67 (78)
T ss_dssp             BCTTTSSSBEEEEEEEEEEEETTEEEEEEEEEEEEETTTCCEECCHHHHHHHHHHHHHHHHHHH
T ss_pred             ECCCCCCCeeEeEEEEEEEEECCEEEEEcCceeEECCCCCCEEECHHHHHHHHHHHHHHHHHHh
Confidence            6999998633    334454443      3345689999998754  23344455555554444

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

Probab=92.03  E-value=0.12  Score=31.05  Aligned_cols=35  Identities=20%  Similarity=0.463  Sum_probs=26.7

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      .|-....||.|+..    ..++..  -|.+.|..||..|..
T Consensus         4 ~LL~iL~CP~ck~~----L~~~~~--~~~LiC~~cg~~YPI   38 (70)
T 2js4_A            4 RLLDILVCPVCKGR----LEFQRA--QAELVCNADRLAFPV   38 (70)
T ss_dssp             CCCCCCBCTTTCCB----EEEETT--TTEEEETTTTEEEEE
T ss_pred             HHhhheECCCCCCc----CEEeCC--CCEEEcCCCCceecC
Confidence            46678899999982    334333  478999999999975

>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=91.90  E-value=0.26  Score=31.97  Aligned_cols=32  Identities=28%  Similarity=0.409  Sum_probs=25.4

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      =||.||+  .+...-++......+.|+.||..+.
T Consensus         6 FCp~Cgn--lL~~~~~~~~~~~~~~C~~C~y~~~   37 (122)
T 1twf_I            6 FCRDCNN--MLYPREDKENNRLLFECRTCSYVEE   37 (122)
T ss_dssp             BCSSSCC--BCEEEEETTTTEEEEECSSSSCEEE
T ss_pred             cccccCc--cCcccccCcCCCCEEECCcCCCeee
Confidence            3999996  5666666667789999999997665

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

Probab=90.68  E-value=0.14  Score=30.59  Aligned_cols=35  Identities=11%  Similarity=0.177  Sum_probs=26.1

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      .|-....||.|...  +.  ++.  .-+.+.|..||..|..
T Consensus         4 ~LL~iL~CP~ck~~--L~--~~~--~~~~LiC~~cg~~YPI   38 (68)
T 2jr6_A            4 KFLDILVCPVTKGR--LE--YHQ--DKQELWSRQAKLAYPI   38 (68)
T ss_dssp             SSSCCCBCSSSCCB--CE--EET--TTTEEEETTTTEEEEE
T ss_pred             HHhhheECCCCCCc--Ce--EeC--CCCEEEcCCCCcEecC
Confidence            46678899999973  33  333  2378999999999975

>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=90.18  E-value=0.14  Score=30.57  Aligned_cols=35  Identities=20%  Similarity=0.400  Sum_probs=26.1

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      .|-....||.|...  +.  ++.  ..+.+.|..||..|..
T Consensus         4 ~LL~iL~CP~ck~~--L~--~~~--~~~~LiC~~cg~~YPI   38 (68)
T 2hf1_A            4 KFLEILVCPLCKGP--LV--FDK--SKDELICKGDRLAFPI   38 (68)
T ss_dssp             CCEEECBCTTTCCB--CE--EET--TTTEEEETTTTEEEEE
T ss_pred             HHhhheECCCCCCc--Ce--EeC--CCCEEEcCCCCcEecC
Confidence            46678899999973  33  333  2478999999999975

>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=89.80  E-value=0.14  Score=30.77  Aligned_cols=35  Identities=14%  Similarity=0.312  Sum_probs=26.1

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      .|-....||.|+..  +  .++.  ..+.+.|..||..|..
T Consensus         4 ~LLeiL~CP~ck~~--L--~~~~--~~~~LiC~~cg~~YPI   38 (69)
T 2pk7_A            4 KLLDILACPICKGP--L--KLSA--DKTELISKGAGLAYPI   38 (69)
T ss_dssp             CGGGTCCCTTTCCC--C--EECT--TSSEEEETTTTEEEEE
T ss_pred             HHHhheeCCCCCCc--C--eEeC--CCCEEEcCCCCcEecC
Confidence            45677899999973  2  2333  3478999999999975

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

Probab=89.71  E-value=0.28  Score=27.57  Aligned_cols=28  Identities=25%  Similarity=0.343  Sum_probs=18.8

Q ss_pred             ecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498          24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF   57 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~   57 (81)
                      =-||.||+. .+.. -    ......|+.||..+
T Consensus        20 k~CP~CG~~-~fm~-~----~~~R~~C~kCG~t~   47 (50)
T 3j20_Y           20 KFCPRCGPG-VFMA-D----HGDRWACGKCGYTE   47 (50)
T ss_dssp             EECSSSCSS-CEEE-E----CSSEEECSSSCCEE
T ss_pred             ccCCCCCCc-eEEe-c----CCCeEECCCCCCEE
Confidence            349999984 2222 1    12578999999865

>2e9h_A EIF-5, eukaryotic translation initiation factor 5; zinc binding, C4 type zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=89.34  E-value=0.61  Score=32.01  Aligned_cols=36  Identities=14%  Similarity=0.363  Sum_probs=28.4

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      .=.||.|+...+. ..++++...-.+.|..||+...-
T Consensus       103 YVlC~~C~sPdT~-L~~~~~~r~~~l~C~ACGa~~~V  138 (157)
T 2e9h_A          103 FVLCPECENPETD-LHVNPKKQTIGNSCKACGYRGML  138 (157)
T ss_dssp             TTSCTTTCCSCCE-EEEETTTTEEEEECSSSCCEEEC
T ss_pred             eEECCCCCCCccE-EEEecCCCEEEEEccCCCCCCcc
Confidence            3469999998885 44456678899999999997664

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=88.88  E-value=0.49  Score=29.63  Aligned_cols=34  Identities=18%  Similarity=0.470  Sum_probs=21.0

Q ss_pred             cCCCCCCCCceE----EEeecCC------ceEEEEcccccceeE
Q psy3498          25 NCPFCNHEKSCE----VKMDKGR------NSARIACRVCLEDFQ   58 (81)
Q Consensus        25 ~CPfC~~~~sV~----v~i~k~~------~~g~l~C~~C~~~~~   58 (81)
                      .||+|+.+..+.    ..++-+.      .+-...|..||+.+-
T Consensus         4 ~Cp~Cg~~~~~~~~~~~~~~~kg~~~~v~~v~~~~C~~CGE~~~   47 (133)
T 3o9x_A            4 KCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIM   47 (133)
T ss_dssp             BCTTTSSSBEEEEEEEEEEEETTEEEEEEEEEEEEESSSSCEEC
T ss_pred             CCCcCCCCceeeceEEEEEEECCEEEEECCCceeECCCCCCEee
Confidence            699999874432    2222232      223567999998764

>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=88.65  E-value=0.47  Score=35.36  Aligned_cols=38  Identities=16%  Similarity=0.453  Sum_probs=27.3

Q ss_pred             CceecCCCCCCCCceEEEee--cCCceEEEEcccccceeE
Q psy3498          21 DIQFNCPFCNHEKSCEVKMD--KGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~--k~~~~g~l~C~~C~~~~~   58 (81)
                      ...=.||.||..-++++...  ..++.-.++|..|+....
T Consensus       180 ~~~~~CPvCGs~P~~s~l~~~g~~~G~R~l~Cs~C~t~W~  219 (309)
T 2fiy_A          180 ESRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWH  219 (309)
T ss_dssp             TTCSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEE
T ss_pred             ccCCCCCCCCCcCceeEEeecCCCCCcEEEEeCCCCCEEe
Confidence            45568999999877775442  235666899999998764

>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=88.45  E-value=0.86  Score=29.44  Aligned_cols=41  Identities=17%  Similarity=0.365  Sum_probs=30.4

Q ss_pred             CCC-ceecCCCCCCCCceEEEeecC----CceEEEEcccccceeEe
Q psy3498          19 PLD-IQFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQT   59 (81)
Q Consensus        19 ~l~-~~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~~   59 (81)
                      .+| +.+.||.|||..++-..+.-.    .+.-...|..||-.+..
T Consensus        67 t~p~t~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~~w~~  112 (122)
T 1twf_I           67 TLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTS  112 (122)
T ss_dssp             TSCCCCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEEC
T ss_pred             cccccCCCCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCCEecc
Confidence            344 358999999998887776432    24567789999988765

>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=88.44  E-value=0.56  Score=34.95  Aligned_cols=37  Identities=14%  Similarity=0.385  Sum_probs=27.5

Q ss_pred             eecCCCCCCCCceEEE-eec------CCceEEEEcccccceeEe
Q psy3498          23 QFNCPFCNHEKSCEVK-MDK------GRNSARIACRVCLEDFQT   59 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~-i~k------~~~~g~l~C~~C~~~~~~   59 (81)
                      ...||+||+++.+..- ++.      ...+-.-.|..|+...-+
T Consensus       222 R~~C~~Cg~~~~l~y~~~e~~~~~~~~~~~r~e~C~~C~~YlK~  265 (309)
T 2fiy_A          222 RIKCSHCEESKHLAYLSLEHDGQPAEKAVLRAETCPSCQGYLKQ  265 (309)
T ss_dssp             TTSCSSSCCCSCCEEECCCC-CCCSTTCSEEEEEETTTTEEEEE
T ss_pred             CcCCcCCCCCCCeeEEEecCccccCCCcceEEEEcccccchHhh
Confidence            4589999998877665 443      256778899999986654

>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=88.01  E-value=0.34  Score=27.75  Aligned_cols=29  Identities=21%  Similarity=0.361  Sum_probs=20.7

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEccccccee
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDF   57 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~   57 (81)
                      ...||.||+.--+.      .......|+.||.++
T Consensus        18 ~~fCPkCG~~~~ma------~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A           18 HRFCPRCGPGVFLA------EHADRYSCGRCGYTE   46 (55)
T ss_dssp             SCCCTTTTTTCCCE------ECSSEEECTTTCCCE
T ss_pred             cccCcCCCCceeEe------ccCCEEECCCCCCEE
Confidence            67899999843333      112489999999875

>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=87.77  E-value=0.55  Score=34.70  Aligned_cols=38  Identities=16%  Similarity=0.401  Sum_probs=28.4

Q ss_pred             ceecCCCCCCCCceEEEeecC----CceEEEEcccccceeEe
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQT   59 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~~   59 (81)
                      +.|.||.|||...+--.+.-.    .+.-...|..||-.+.+
T Consensus       267 ~~~~C~~C~~~~~~~~q~Q~rsaDe~~t~f~~C~~Cg~~w~f  308 (309)
T 1pqv_S          267 DRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWKF  308 (309)
T ss_pred             ccccCCCCCCCeeEEEEeecccCCCCCcEEEEeCCCCCceec
Confidence            479999999988876665431    34557889999987753

>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=87.56  E-value=0.38  Score=35.60  Aligned_cols=35  Identities=29%  Similarity=0.632  Sum_probs=24.7

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      -+-||.||+...  -.+....-+|--.|.+|++.||-
T Consensus        34 n~yCPnCG~~~l--~~f~nN~PVaDF~C~~C~EeyEL   68 (257)
T 4esj_A           34 QSYCPNCGNNPL--NHFENNRPVADFYCNHCSEEFEL   68 (257)
T ss_dssp             HCCCTTTCCSSC--EEC----CCCEEECTTTCCEEEE
T ss_pred             CCcCCCCCChhh--hhccCCCcccccccCCcchhhee
Confidence            467999999532  24444568899999999999985

>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A

Probab=87.04  E-value=0.26  Score=29.07  Aligned_cols=40  Identities=18%  Similarity=0.301  Sum_probs=31.4

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhh
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDW   74 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~W   74 (81)
                      .=.||.|+.   .+  +       .-.|..||.......++-..|-|-|++.
T Consensus         6 mr~C~~Cgv---YT--L-------k~~CP~CG~~T~~~hParfSp~Dky~~y   45 (60)
T 2apo_B            6 MKKCPKCGL---YT--L-------KEICPKCGEKTVIPKPPKFSLEDRWGKY   45 (60)
T ss_dssp             CEECTTTCC---EE--S-------SSBCSSSCSBCBCCCCCCCCTTCTTHHH
T ss_pred             ceeCCCCCC---Ee--c-------cccCcCCCCcCCCCCCCCCCCCcchHHH
Confidence            446999975   12  2       1249999999999999999999999875

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

Probab=86.84  E-value=0.32  Score=31.16  Aligned_cols=31  Identities=32%  Similarity=0.438  Sum_probs=23.2

Q ss_pred             CCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          26 CPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        26 CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      ||.||+  .+..+.+...+.-.+.|+.|+-.+.
T Consensus         7 Cp~Cgn--~L~~~~~~~~~~~~~~C~~C~y~~~   37 (113)
T 3h0g_I            7 CIECNN--MLYPREDKVDRVLRLACRNCDYSEI   37 (113)
T ss_dssp             CSSSCC--CCEECCCTTTCCCCEECSSSCCEEC
T ss_pred             CcCCCC--EeeEcccCCCCeeEEECCCCCCeEE
Confidence            999997  4556665555677899999997653

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

Probab=86.80  E-value=0.49  Score=27.12  Aligned_cols=33  Identities=21%  Similarity=0.476  Sum_probs=25.5

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcc--cccceeEe
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACR--VCLEDFQT   59 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~--~C~~~~~~   59 (81)
                      .|-....||.|..+    ...+.    +.+.|.  .||..|..
T Consensus         6 ~lL~iL~CP~c~~~----L~~~~----~~L~C~~~~c~~~YPI   40 (56)
T 2kpi_A            6 GLLEILACPACHAP----LEERD----AELICTGQDCGLAYPV   40 (56)
T ss_dssp             SCTTSCCCSSSCSC----EEEET----TEEEECSSSCCCEEEE
T ss_pred             HHHhheeCCCCCCc----ceecC----CEEEcCCcCCCcEEee
Confidence            46678899999983    22332    889999  99999975

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

Probab=85.56  E-value=0.33  Score=28.94  Aligned_cols=35  Identities=9%  Similarity=0.068  Sum_probs=25.9

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      .|-....||.|..+    ...+.  ..|.+.|..||..|..
T Consensus         6 ~LLeiL~CP~ck~~----L~~~~--~~g~LvC~~c~~~YPI   40 (67)
T 2jny_A            6 QLLEVLACPKDKGP----LRYLE--SEQLLVNERLNLAYRI   40 (67)
T ss_dssp             GGTCCCBCTTTCCB----CEEET--TTTEEEETTTTEEEEE
T ss_pred             HHHHHhCCCCCCCc----CeEeC--CCCEEEcCCCCccccC
Confidence            46677899999983    23333  3478999999999975

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

Probab=85.07  E-value=0.38  Score=33.67  Aligned_cols=30  Identities=17%  Similarity=0.376  Sum_probs=21.9

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccce
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLED   56 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~   56 (81)
                      .-+.||.||......+-  . .+  ...|.+||..
T Consensus        13 ~~~~CP~Cg~~d~~~~~--~-dg--~~~C~~Cg~~   42 (255)
T 1nui_A           13 YHIPCDNCGSSDGNSLF--S-DG--HTFCYVCEKW   42 (255)
T ss_dssp             EEECCSSSCCSSCEEEE--T-TS--CEEETTTCCE
T ss_pred             cCCcCCCCCCCCCceEe--C-CC--CeecccCCCc
Confidence            46899999986654443  3 23  5899999975

>2aus_D NOP10, ribosome biogenesis protein NOP10; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_B 3lwo_B* 3lwq_B* 3lwp_B 3lwv_B 3hax_C* 2hvy_C* 3hay_C* 2ey4_E 3hjw_B* 2rfk_B* 3hjy_B 3mqk_B

Probab=84.75  E-value=0.47  Score=28.01  Aligned_cols=40  Identities=23%  Similarity=0.462  Sum_probs=30.8

Q ss_pred             eecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhh
Q psy3498          23 QFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDW   74 (81)
Q Consensus        23 ~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~W   74 (81)
                      .-.||.||.     -++       .-.|-+||+.....-++-..|-|-|++.
T Consensus         5 mr~C~~Cg~-----YTL-------k~~CP~CG~~t~~ahParfSP~Dky~~y   44 (60)
T 2aus_D            5 IRKCPKCGR-----YTL-------KETCPVCGEKTKVAHPPRFSPEDPYGEY   44 (60)
T ss_dssp             CEECTTTCC-----EES-------SSBCTTTCSBCEESSCCCCCSCCTTHHH
T ss_pred             ceECCCCCC-----EEc-------cccCcCCCCccCCCCCCCCCCCCchHHH
Confidence            346899975     112       1149999999999999999999999875

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

Probab=83.93  E-value=0.7  Score=29.49  Aligned_cols=40  Identities=18%  Similarity=0.321  Sum_probs=27.5

Q ss_pred             CCCC-ceecCCCCCCCCceEEEeecC----CceEEEEccccccee
Q psy3498          18 EPLD-IQFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDF   57 (81)
Q Consensus        18 ~~l~-~~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~   57 (81)
                      +.|| +.+.||.|||..++--.+.-.    .+.-...|..||-.+
T Consensus        66 ~tlp~~~~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~~w  110 (113)
T 3h0g_I           66 PTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFAF  110 (113)
T ss_dssp             SSSCBCCSCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCCCC
T ss_pred             ccCCCcccCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCCEE
Confidence            3455 459999999988776654421    244567899999765

>2g2k_A EIF-5, eukaryotic translation initiation factor 5; EIF125 fold; NMR {Homo sapiens}

Probab=83.45  E-value=1.3  Score=30.77  Aligned_cols=35  Identities=14%  Similarity=0.330  Sum_probs=26.4

Q ss_pred             ecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          24 FNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        24 F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      =.||.|+...+.-+ ++.+...-.+.|..||+...-
T Consensus        97 VlC~~C~sPdT~L~-k~~~~r~~~l~C~ACGa~~~V  131 (170)
T 2g2k_A           97 VLCPECENPETDLH-VNPKKQTIGNSCKACGYRGML  131 (170)
T ss_dssp             HSCTTTSSSCEEEE-EETTTTEEEEEETTTCCCCCS
T ss_pred             EECCCCCCCccEEE-EecCCCEEEEEccccCCcccc
Confidence            46999999877544 343567788999999986543

>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=82.07  E-value=0.4  Score=33.08  Aligned_cols=37  Identities=16%  Similarity=0.432  Sum_probs=26.1

Q ss_pred             ceecCCCCCCCCceEEEeecC----CceEEEEcccccceeE
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQ   58 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~   58 (81)
                      +.|.||.|||..++--.+.-.    .+.-...|..||-.+.
T Consensus       136 ~~~~Cp~C~~~~a~~~q~Q~rsaDE~mt~f~~C~~C~~~w~  176 (178)
T 3po3_S          136 DRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNRWK  176 (178)
T ss_dssp             SSSCCSSSCCSCEECCCCCCSCTTSCCCCCEEETTTCCEEC
T ss_pred             CCcCCCCCCCCceEEEEeecccCCCCCcEEEEcCCCCCeec
Confidence            479999999987764433321    2455778999998765

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

Probab=82.07  E-value=0.84  Score=34.02  Aligned_cols=49  Identities=18%  Similarity=0.467  Sum_probs=29.7

Q ss_pred             CCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhh
Q psy3498          18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWV   75 (81)
Q Consensus        18 ~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~Wi   75 (81)
                      +-|.-.-.||.|+... -.+..|.  .-|.+.|..||+--+.      ..||.=++|-
T Consensus        16 ~~l~~~~~Cp~C~~~~-~~lv~D~--~~G~~vC~~CGlVl~e------~~iD~g~EWR   64 (345)
T 4bbr_M           16 PNLNIVLTCPECKVYP-PKIVERF--SEGDVVCALCGLVLSD------KLVDTRSEWR   64 (345)
T ss_dssp             ------CCCSSCCCSS-CCEEEEG--GGTEEEETTTCBEEES------CCBCHHHHHT
T ss_pred             cccccCCcCCCCCCCC-CceeEEC--CCCcEEeCCCCCCccC------cccccCcccc
Confidence            4566666899999721 1233343  5599999999987653      4577777775

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

Probab=81.94  E-value=0.28  Score=36.36  Aligned_cols=38  Identities=18%  Similarity=0.436  Sum_probs=25.9

Q ss_pred             CCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        18 ~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      +-|...-.||.|+.... .+..  +...|.+.|..||.--+
T Consensus        16 ~~~~~~~~Cp~Cg~~~~-~iv~--D~~~G~~vC~~CG~Vl~   53 (345)
T 3k7a_M           16 PNLNIVLTCPECKVYPP-KIVE--RFSEGDVVCALCGLVLS   53 (345)
T ss_dssp             -CCCCCCCCSTTCCSCC-CCCC--CSSSCSCCCSSSCCCCC
T ss_pred             ccccCCCcCcCCCCCCC-ceEE--ECCCCCEecCCCCeEcc
Confidence            45666778999998531 1222  34568999999998654

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

Probab=80.40  E-value=2.5  Score=26.26  Aligned_cols=38  Identities=18%  Similarity=0.504  Sum_probs=28.5

Q ss_pred             CCCCCcee---cCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          17 IEPLDIQF---NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        17 ~~~l~~~F---~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      ++...+.|   .||-|++   +++.++...  -.+.|.+||...-.
T Consensus        23 v~~PnS~Fm~VkCp~C~n---~q~VFShA~--t~V~C~~Cg~~L~~   63 (81)
T 2xzm_6           23 IQAPNSYFMDVKCAQCQN---IQMIFSNAQ--STIICEKCSAILCK   63 (81)
T ss_dssp             SCCCSCCEEEEECSSSCC---EEEEETTCS--SCEECSSSCCEEEE
T ss_pred             eeCCCCcEEEeECCCCCC---eeEEEecCc--cEEEccCCCCEEee
Confidence            44556888   9999999   577776644  57899999986543

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

Probab=80.14  E-value=1.1  Score=32.01  Aligned_cols=49  Identities=18%  Similarity=0.470  Sum_probs=33.4

Q ss_pred             CCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhh
Q psy3498          18 EPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWV   75 (81)
Q Consensus        18 ~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~Wi   75 (81)
                      +-|...-.||.|+... ..+..|.  ..|.+.|..||+-.+      +..||-=.+|-
T Consensus        16 ~~ln~~~~CPECGs~~-t~IV~D~--erGE~VCsdCGLVLE------EriID~GPEWR   64 (197)
T 3k1f_M           16 PNLNIVLTCPECKVYP-PKIVERF--SEGDVVCALCGLVLS------DKLVDTRSEWR   64 (197)
T ss_dssp             SCCCCCCCCTTTCCSS-CCEEEEG--GGTEEEETTTCBBCC------CCCBCHHHHHH
T ss_pred             cccccCeECcCCCCcC-CeEEEeC--CCCEEEEcCCCCCcC------CceeECCCCCc
Confidence            4566666899999832 2233333  459999999998654      24577777775

---

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	81
d1wiia_	85	g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549	1e-37

>d1wiia_ g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Putative zinc binding domain
domain: Hypothetical UPF0222 protein MGC4549
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  118 bits (298), Expect = 1e-37
 Identities = 47/75 (62%), Positives = 58/75 (77%)

Query: 3  RRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTIN 62
             S RKPPPK+K    L+ QF CPFCNHEKSC+VKMD+ RN+  I+C VCLE+FQT I 
Sbjct: 3  SGSSGRKPPPKKKMTGTLETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPIT 62

Query: 63 FLSEAIDVYNDWVDA 77
          +LSE +DVY+DW+DA
Sbjct: 63 YLSEPVDVYSDWIDA 77

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	81
d1wiia_	85	Hypothetical UPF0222 protein MGC4549 {Mouse (Mus m	100.0
d1vqoz1	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	95.53
d1jj2y_	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	95.43
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	95.07
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	94.32
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	94.04
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	93.52
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	92.54
d1k81a_	36	Zinc-binding domain of translation initiation fact	90.46
d2epqa1	32	PATZ1 {Human (Homo sapiens) [TaxId: 9606]}	87.63
d1neea2	37	Zinc-binding domain of translation initiation fact	87.56
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	86.1
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	85.12
d2ct1a2	36	Transcriptional repressor CTCF {Human (Homo sapien	83.5
d6rxna_	45	Rubredoxin {Desulfovibrio desulfuricans, strain 27	82.73
d2pk7a1	59	Uncharacterized protein PFL1779 {Pseudomonas fluor	80.89
d2hf1a1	59	Hypothetical protein CV3345 {Chromobacterium viola	80.75
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	80.41

>d1wiia_ g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Putative zinc binding domain
domain: Hypothetical UPF0222 protein MGC4549
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=3.3e-45  Score=233.40  Aligned_cols=80  Identities=60%  Similarity=1.158  Sum_probs=73.5

Q ss_pred             CCCCc-CCCCCCCCCCCCCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCCCCchhhhhhhhhhhcCC
Q psy3498           2 GRRKS-KRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDASVP   80 (81)
Q Consensus         2 GkRK~-~~k~~~kkk~~~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~L~epIDVYs~WiD~c~~   80 (81)
                      |+||+ +|+++++++.+++|||.|+||||||++||+|+||++.++|.|+|++||++||++||+|+|||||||+|||+|||
T Consensus         1 g~~~~s~rk~~pkkk~~~kL~t~F~CPfCnh~~sV~vk~dkk~~~g~l~C~vCg~~~~~~i~~L~epiDVYs~WiDace~   80 (85)
T d1wiia_           1 GSSGSSGRKPPPKKKMTGTLETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDACES   80 (85)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCSSCCCCTTTCCSSCEEEEEETTTTEEEEEESSSCCEEEEECCSSCCTTHHHHHHHHHHHH
T ss_pred             CCCcccCCCCCCCccccCCCCceEcCCCCCCCCeEEEEEEecCCEEEEEEecCCCeEEecccccCccHhHHHHHHHHHHH
Confidence            77764 46666677667999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q psy3498          81 S   81 (81)
Q Consensus        81 ~   81 (81)
                      .
T Consensus        81 ~   81 (85)
T d1wiia_          81 G   81 (85)
T ss_dssp             C
T ss_pred             h
Confidence            4

>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=95.53  E-value=0.0032  Score=37.42  Aligned_cols=33  Identities=21%  Similarity=0.519  Sum_probs=25.7

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEec
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTT   60 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~   60 (81)
                      ..+.|||||.. .  |+   ...+|+-.|+.|+..|.--
T Consensus        26 ~ky~Cp~Cgk~-~--vk---R~a~GIW~C~kC~~~~AGG   58 (73)
T d1vqoz1          26 EDHACPNCGED-R--VD---RQGTGIWQCSYCDYKFTGG   58 (73)
T ss_dssp             SCBCCSSSSCS-C--EE---EEETTEEEETTTCCEEECC
T ss_pred             CCccCCCCCCc-e--eE---EEEEEEEECCCCCCEEeCC
Confidence            56899999984 2  22   2578999999999998753

>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=95.43  E-value=0.0037  Score=37.10  Aligned_cols=36  Identities=17%  Similarity=0.373  Sum_probs=26.6

Q ss_pred             ceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCC
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINF   63 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~   63 (81)
                      ..+.|||||.. .  ++   ...+|+-.|+.|+..|.--.-.
T Consensus        26 ~ky~Cp~Cgk~-~--vk---R~a~GIW~C~kC~~~~AGgAy~   61 (73)
T d1jj2y_          26 KKHKCPVCGFK-K--LK---RAGTGIWMCGHCGYKIAGGCYQ   61 (73)
T ss_dssp             SCBCCSSSCCS-C--EE---EEETTEEEETTTCCEEECCSSS
T ss_pred             CCccCCCCCCC-c--eE---EEEEEEEECCCCCCEEeCccce
Confidence            56899999973 2  22   2578899999999999754333

>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=95.07  E-value=0.0084  Score=32.73  Aligned_cols=33  Identities=24%  Similarity=0.508  Sum_probs=23.5

Q ss_pred             CceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          21 DIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      ++.-.||.||..+   +..|.  ..|.+.|..||+--+
T Consensus         3 ~~~~~Cp~Cgs~~---iv~D~--~~Ge~vC~~CG~Vie   35 (50)
T d1pfta_           3 NKQKVCPACESAE---LIYDP--ERGEIVCAKCGYVIE   35 (50)
T ss_dssp             SSCCSCTTTSCCC---EEEET--TTTEEEESSSCCBCC
T ss_pred             cccccCcCCCCCc---EEEEC--CCCeEecccCCcEec
Confidence            4455799999743   44554  447999999998544

>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=94.32  E-value=0.041  Score=32.05  Aligned_cols=42  Identities=17%  Similarity=0.353  Sum_probs=32.1

Q ss_pred             CCCC-ceecCCCCCCCCceEEEeecC----CceEEEEcccccceeEe
Q psy3498          18 EPLD-IQFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQT   59 (81)
Q Consensus        18 ~~l~-~~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~~   59 (81)
                      +.|| +...||.|||...+-..+.-.    .+.-...|-+||-.+..
T Consensus        17 Ptlp~t~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~C~h~Wr~   63 (72)
T d1twfi2          17 PTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTS   63 (72)
T ss_dssp             TTSCCCCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEEC
T ss_pred             CCCCccCCCCCCCCCCeEEEEEeecCccCCCceEEEEcCCCCCCccc
Confidence            3444 458999999988887776552    35678999999998875

>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=94.04  E-value=0.047  Score=30.43  Aligned_cols=37  Identities=16%  Similarity=0.469  Sum_probs=29.9

Q ss_pred             ceecCCCCCCCCceEEEeecC----CceEEEEcccccceeE
Q psy3498          22 IQFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQ   58 (81)
Q Consensus        22 ~~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~   58 (81)
                      +.+.||.|+|.+++-..+.-.    .+.-...|..||-.|.
T Consensus        14 ~~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~Cg~~wr   54 (57)
T d1qypa_          14 TKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWR   54 (57)
T ss_dssp             EECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEE
T ss_pred             ccCCCCCCCCCceEEEEeecccccCCCeEEEEeCCCCCcce
Confidence            568999999998888877552    3677899999998875

>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=93.52  E-value=0.074  Score=28.98  Aligned_cols=38  Identities=13%  Similarity=0.399  Sum_probs=28.2

Q ss_pred             CceecCCCCCCCCceEEEeecC----CceEEEEcccccceeE
Q psy3498          21 DIQFNCPFCNHEKSCEVKMDKG----RNSARIACRVCLEDFQ   58 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~k~----~~~g~l~C~~C~~~~~   58 (81)
                      -..|.||.|++.+.....+.-.    ...-.+.|..||..+-
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            3578999999988766665442    2455899999998764

>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=92.54  E-value=0.035  Score=31.04  Aligned_cols=35  Identities=14%  Similarity=0.185  Sum_probs=25.1

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      .+.....||.|+..+   +..|  ...|.+.|..||+--+
T Consensus         7 ~~~~~~~Cp~Cgs~~---ii~D--~~~Ge~vC~~CG~Vle   41 (58)
T d1dl6a_           7 DALPRVTCPNHPDAI---LVED--YRAGDMICPECGLVVG   41 (58)
T ss_dssp             CCCSCCSBTTBSSSC---CEEC--SSSCCEECTTTCCEEC
T ss_pred             ccccccCCCCCCCCC---EEEE--CCCCcEecccCCCEec
Confidence            345667899999743   3333  4558999999998654

>d1k81a_ g.59.1.1 (A:) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Small proteins
fold: Zinc-binding domain of translation initiation factor 2 beta
superfamily: Zinc-binding domain of translation initiation factor 2 beta
family: Zinc-binding domain of translation initiation factor 2 beta
domain: Zinc-binding domain of translation initiation factor 2 beta
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=90.46  E-value=0.14  Score=26.21  Aligned_cols=31  Identities=16%  Similarity=0.275  Sum_probs=24.6

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      .|+-|+..++.-+   +++.+-.+.|..||+..+
T Consensus         2 ~C~~C~spDT~l~---ke~R~~~l~C~aCGa~r~   32 (36)
T d1k81a_           2 ICRECGKPDTKII---KEGRVHLLKCMACGAIRP   32 (36)
T ss_dssp             CCSSSCSCEEEEE---EETTEEEEEEETTTEEEE
T ss_pred             CCCCCCCCCCEEE---EcCCEEEEEeccCCCCCc
Confidence            5999999776544   456789999999998765

>d2epqa1 g.37.1.1 (A:380-411) PATZ1 {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: PATZ1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.63  E-value=0.062  Score=26.82  Aligned_cols=11  Identities=27%  Similarity=1.078  Sum_probs=8.2

Q ss_pred             CceecCCCCCC
Q psy3498          21 DIQFNCPFCNH   31 (81)
Q Consensus        21 ~~~F~CPfC~~   31 (81)
                      ++.|+||.|+.
T Consensus         1 ekp~~cpic~q   11 (32)
T d2epqa1           1 EKPYSCPVCGL   11 (32)
T ss_dssp             CCSSEETTTTE
T ss_pred             CCCcccchHHH
Confidence            36788888874

>d1neea2 g.59.1.1 (A:99-135) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Small proteins
fold: Zinc-binding domain of translation initiation factor 2 beta
superfamily: Zinc-binding domain of translation initiation factor 2 beta
family: Zinc-binding domain of translation initiation factor 2 beta
domain: Zinc-binding domain of translation initiation factor 2 beta
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=87.56  E-value=0.081  Score=27.31  Aligned_cols=31  Identities=16%  Similarity=0.400  Sum_probs=24.6

Q ss_pred             cCCCCCCCCceEEEeecCCceEEEEcccccceeE
Q psy3498          25 NCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        25 ~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~   58 (81)
                      .|+-|+..++.-++   ++.+-.+.|..||+.-.
T Consensus         3 ~C~~C~spDT~l~k---e~R~~~l~C~aCGa~r~   33 (37)
T d1neea2           3 ICHECNRPDTRIIR---EGRISLLKCEACGAKAP   33 (37)
T ss_dssp             HHTCCSSCSSCCEE---ETTTTEEECSTTSCCCC
T ss_pred             ECCCCCCCCCEEEE---cCCEEEEEeccCCCCcc
Confidence            59999999886665   45677899999998643

>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=86.10  E-value=0.39  Score=33.77  Aligned_cols=38  Identities=16%  Similarity=0.453  Sum_probs=26.4

Q ss_pred             CceecCCCCCCCCceEEEee--cCCceEEEEcccccceeE
Q psy3498          21 DIQFNCPFCNHEKSCEVKMD--KGRNSARIACRVCLEDFQ   58 (81)
Q Consensus        21 ~~~F~CPfC~~~~sV~v~i~--k~~~~g~l~C~~C~~~~~   58 (81)
                      ...=.||.||..-..++...  ..+|.=.++|..|+....
T Consensus       162 ~~~~~CPvCGs~P~~s~l~~~~~~~G~R~l~C~~C~teW~  201 (290)
T d2fiya1         162 ESRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWH  201 (290)
T ss_dssp             TTCSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEE
T ss_pred             ccCCcCCCCCCcchhheeeccCCCCCceEEECCCCCCccc
Confidence            33345999999777666654  345666899999998764

>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=85.12  E-value=0.64  Score=25.88  Aligned_cols=54  Identities=13%  Similarity=0.306  Sum_probs=35.3

Q ss_pred             CCCCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEeccCC------CCchhhhhhhhhh
Q psy3498          17 IEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTINF------LSEAIDVYNDWVD   76 (81)
Q Consensus        17 ~~~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~~i~~------L~epIDVYs~WiD   76 (81)
                      ...-|..--||.|+..    +.  +..+.-.+.|..||..|-+.-..      -...=+-|.+|-+
T Consensus        12 l~~~~~~k~CP~C~~~----~~--~~~~~~~~~C~~C~~~fC~~C~~~w~~~H~~~tC~~~~~wk~   71 (73)
T d2ct7a1          12 LMRDPKFLWCAQCSFG----FI--YEREQLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKR   71 (73)
T ss_dssp             CCSCCCEECCSSSCCC----EE--CCCSCSCEECTTTCCEECSSSCSBCCTTTTTSCHHHHHHHHH
T ss_pred             HHHCCCCCCCCCCCCE----eE--ECCCCCEEEcCCCCCeECcccCcchhcCCCCCCHHHHHHHHH
Confidence            4556788899999982    23  33455678999999998653322      2234456777744

>d2ct1a2 g.37.1.1 (A:8-43) 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=83.50  E-value=0.18  Score=25.22  Aligned_cols=11  Identities=18%  Similarity=0.839  Sum_probs=9.4

Q ss_pred             CceecCCCCCC
Q psy3498          21 DIQFNCPFCNH   31 (81)
Q Consensus        21 ~~~F~CPfC~~   31 (81)
                      ++.|.|++||.
T Consensus         6 ekP~~C~~C~k   16 (36)
T d2ct1a2           6 EKPYECYICHA   16 (36)
T ss_dssp             CCSEECTTTCC
T ss_pred             CCCEeCCCCcc
Confidence            57899999986

>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=82.73  E-value=0.2  Score=26.60  Aligned_cols=18  Identities=28%  Similarity=0.717  Sum_probs=15.0

Q ss_pred             CCCCCceecCCCCCCCCc
Q psy3498          17 IEPLDIQFNCPFCNHEKS   34 (81)
Q Consensus        17 ~~~l~~~F~CPfC~~~~s   34 (81)
                      -..||.-|.||.|++.++
T Consensus        23 Fe~LP~dw~CP~C~a~K~   40 (45)
T d6rxna_          23 FDQLPDDWCCPVCGVSKD   40 (45)
T ss_dssp             GGGSCTTCBCTTTCCBGG
T ss_pred             HHHCCCCCCCcCCCCcHH
Confidence            356899999999999765

>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=80.89  E-value=0.32  Score=27.06  Aligned_cols=35  Identities=14%  Similarity=0.343  Sum_probs=25.6

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      +|-.+--||.|..+    ...+.  ..+.|.|..|+..|..
T Consensus         2 kLL~iL~CP~ck~~----L~~~~--~~~~Lvc~~~~laYPI   36 (59)
T d2pk7a1           2 KLLDILACPICKGP----LKLSA--DKTELISKGAGLAYPI   36 (59)
T ss_dssp             CGGGTCCCTTTCCC----CEECT--TSSEEEETTTTEEEEE
T ss_pred             chHhheECCCCCCc----ceEeC--CCCEEecCCcCccccc
Confidence            34456789999973    33444  3468999999999975

>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=80.75  E-value=0.41  Score=26.51  Aligned_cols=35  Identities=20%  Similarity=0.433  Sum_probs=25.4

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      +|-.+--||.|...    ..++.  ..+.|.|..|+..|..
T Consensus         3 ~LL~iL~CP~ck~~----L~~~~--~~~~Lvc~~~~l~YPI   37 (59)
T d2hf1a1           3 KFLEILVCPLCKGP----LVFDK--SKDELICKGDRLAFPI   37 (59)
T ss_dssp             CCEEECBCTTTCCB----CEEET--TTTEEEETTTTEEEEE
T ss_pred             hHhhhhcCCCCCCe----eeEeC--CCCEEecCCcCccccc
Confidence            35567789999973    33444  3457999999999975

>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=80.41  E-value=0.34  Score=26.81  Aligned_cols=35  Identities=9%  Similarity=0.068  Sum_probs=25.6

Q ss_pred             CCCceecCCCCCCCCceEEEeecCCceEEEEcccccceeEe
Q psy3498          19 PLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQT   59 (81)
Q Consensus        19 ~l~~~F~CPfC~~~~sV~v~i~k~~~~g~l~C~~C~~~~~~   59 (81)
                      .|-..--||.|+.+    ...+.  ..+.+.|..|+..|..
T Consensus         6 ~LL~iL~CP~ck~~----L~~~~--~~~~Lvc~~~~~~YPI   40 (59)
T d2jnya1           6 QLLEVLACPKDKGP----LRYLE--SEQLLVNERLNLAYRI   40 (59)
T ss_dssp             GGTCCCBCTTTCCB----CEEET--TTTEEEETTTTEEEEE
T ss_pred             HHHHHhcCCCCCCE----eEEeC--CCCEEEcCccCccccc
Confidence            35567789999973    33333  4468999999999975